Contacts of the helix formed by residues 74 - 121 (chain O) in PDB entry 5KHU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 74 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73O ILE* 3.8 29.6 - - - +
75O LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74O THR* 3.8 28.7 - - - +
76O SER* 3.8 24.2 - - - +
78O LEU* 4.4 19.3 - - - +
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Residues in contact with SER 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75O LEU* 3.8 25.4 - - - +
77O LYS* 3.8 29.4 - - - +
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Residues in contact with LYS 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76O SER* 3.8 29.4 - - - +
78O LEU* 3.8 26.0 - - - +
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Residues in contact with LEU 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75O LEU* 4.4 15.9 - - - +
77O LYS* 3.8 29.4 - - - +
79O TYR* 3.8 25.8 - - - +
81O LEU* 4.4 15.7 - - - +
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Residues in contact with TYR 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O LEU* 3.8 29.4 - - - +
80O LYS* 3.8 25.8 - - - +
----------------------------------------------------------
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Residues in contact with LYS 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79O TYR* 3.8 29.4 - - - +
81O LEU* 3.8 25.8 - - - +
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Residues in contact with LEU 81 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O LEU* 4.4 16.2 - - - +
80O LYS* 3.8 26.2 - - - +
82O ILE* 3.8 29.2 - - - +
----------------------------------------------------------
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Residues in contact with ILE 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81O LEU* 3.8 29.4 - - - +
83O GLU* 3.8 26.9 - - - +
85O SER* 4.4 16.6 - - - +
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Residues in contact with GLU 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82O ILE* 3.8 25.8 - - - +
84O GLU* 3.8 29.2 - - - +
86O CYS* 4.3 8.5 - - - +
87O PRO* 4.1 25.8 - - - -
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Residues in contact with GLU 84 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83O GLU* 3.8 28.9 - - - +
85O SER* 3.8 24.5 - - - +
----------------------------------------------------------
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Residues in contact with SER 85 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82O ILE* 4.4 15.9 - - - +
84O GLU* 3.8 29.4 - - - +
86O CYS* 3.9 25.1 - - - +
----------------------------------------------------------
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Residues in contact with CYS 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83O GLU* 4.3 9.6 - - - +
85O SER* 3.9 29.2 - - - +
87O PRO* 3.8 28.9 - - - -
----------------------------------------------------------
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Residues in contact with PRO 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83O GLU* 4.1 17.3 - - - -
86O CYS* 3.8 28.9 - - - -
88O GLN* 3.8 25.1 - - - -
90O ALA* 4.5 12.3 - - - -
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Residues in contact with GLN 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87O PRO* 3.8 25.1 - - - -
89O LEU* 3.8 29.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 89 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88O GLN* 3.8 28.9 - - - +
90O ALA* 3.8 26.0 - - - +
----------------------------------------------------------
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Residues in contact with ALA 90 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87O PRO* 4.5 17.9 - - - -
89O LEU* 3.8 28.0 - - - +
91O ASN* 3.8 29.8 - - - +
----------------------------------------------------------
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Residues in contact with ASN 91 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90O ALA* 3.8 29.4 - - - +
92O SER* 3.8 28.3 - - - +
94O GLN* 4.4 19.1 - - - +
----------------------------------------------------------
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Residues in contact with SER 92 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91O ASN* 3.8 26.0 - - - +
93O VAL* 3.8 29.2 - - - +
----------------------------------------------------------
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Residues in contact with VAL 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92O SER* 3.8 30.1 - - - +
94O GLN* 3.8 25.1 - - - +
96O ARG* 4.6 17.5 - - - +
----------------------------------------------------------
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Residues in contact with GLN 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91O ASN* 4.4 17.9 - - - +
93O VAL* 3.8 24.5 - - - +
95O ILE* 3.8 29.4 - - - +
----------------------------------------------------------
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Residues in contact with ILE 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94O GLN* 3.8 28.9 - - - +
96O ARG* 3.8 26.7 - - - +
----------------------------------------------------------
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Residues in contact with ARG 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93O VAL* 4.6 14.6 - - - +
95O ILE* 3.8 29.2 - - - +
97O ILE* 3.8 25.4 - - - +
----------------------------------------------------------
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Residues in contact with ILE 97 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96O ARG* 3.8 26.7 - - - +
98O LYS* 3.8 29.4 - - - +
----------------------------------------------------------
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Residues in contact with LYS 98 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97O ILE* 3.8 29.4 - - - +
99O LEU* 3.8 27.6 - - - +
----------------------------------------------------------
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Residues in contact with LEU 99 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98O LYS* 3.8 26.5 - - - +
100O MET* 3.8 28.7 - - - +
----------------------------------------------------------
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Residues in contact with MET 100 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O LEU* 3.8 26.5 - - - +
101O ALA* 3.8 29.4 - - - +
103O GLY* 4.0 18.6 - - - +
----------------------------------------------------------
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Residues in contact with ALA 101 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100O MET* 3.8 25.6 - - - +
102O GLU* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with GLU 102 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101O ALA* 3.8 24.5 - - - +
103O GLY* 3.8 29.8 - - - +
----------------------------------------------------------
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Residues in contact with GLY 103 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100O MET* 4.0 22.4 - - - +
102O GLU* 3.8 29.2 - - - +
104O GLU* 3.8 29.4 - - - +
----------------------------------------------------------
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Residues in contact with GLU 104 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O GLY* 3.8 29.2 - - - +
105O LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 105 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104O GLU* 3.8 29.2 - - - +
106O LYS* 3.8 25.8 - - - +
----------------------------------------------------------
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Residues in contact with LYS 106 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105O LEU* 3.8 28.9 - - - +
107O ASP* 3.8 25.6 - - - +
109O GLU* 4.1 20.4 - - - +
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Residues in contact with ASP 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106O LYS* 3.8 25.1 - - - +
108O MET* 3.8 28.9 - - - +
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Residues in contact with MET 108 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107O ASP* 3.8 29.8 - - - +
109O GLU* 3.8 24.7 - - - +
----------------------------------------------------------
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Residues in contact with GLU 109 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106O LYS* 4.1 17.7 - - - +
108O MET* 3.8 29.4 - - - +
110O GLN* 3.8 27.4 - - - +
----------------------------------------------------------
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Residues in contact with GLN 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109O GLU* 3.8 24.9 - - - +
111O PHE* 3.8 28.9 - - - +
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Residues in contact with PHE 111 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110O GLN* 3.8 28.9 - - - +
112O PHE* 3.8 25.6 - - - +
114O ASP* 4.3 17.9 - - - +
----------------------------------------------------------
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Residues in contact with PHE 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111O PHE* 3.8 25.1 - - - +
113O ASP* 3.8 29.4 - - - +
115O LEU* 4.2 17.3 - - - +
----------------------------------------------------------
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Residues in contact with ASP 113 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112O PHE* 3.8 30.1 - - - +
114O ASP* 3.8 24.2 - - - +
116O SER* 4.7 15.5 - - - +
----------------------------------------------------------
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Residues in contact with ASP 114 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111O PHE* 4.3 16.6 - - - +
113O ASP* 3.8 28.9 - - - +
115O LEU* 3.8 24.2 - - - +
----------------------------------------------------------
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Residues in contact with LEU 115 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112O PHE* 4.2 17.9 - - - +
114O ASP* 3.8 28.9 - - - +
116O SER* 3.8 28.0 - - - +
----------------------------------------------------------
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Residues in contact with SER 116 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113O ASP* 4.7 14.6 - - - +
115O LEU* 3.8 28.5 - - - +
117O ASP* 3.8 26.5 - - - +
----------------------------------------------------------
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Residues in contact with ASP 117 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116O SER* 3.8 29.4 - - - +
118O SER* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with SER 118 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117O ASP* 3.8 26.0 - - - +
119O PHE* 3.8 29.8 - - - +
----------------------------------------------------------
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Residues in contact with PHE 119 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118O SER* 3.8 29.6 - - - +
120O SER* 3.8 27.1 - - - +
----------------------------------------------------------
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Residues in contact with SER 120 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119O PHE* 3.8 28.9 - - - +
121O GLY* 3.8 25.1 - - - +
----------------------------------------------------------
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Residues in contact with GLY 121 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120O SER* 3.8 29.4 - - - +
122O THR* 3.8 26.5 - - - +
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il