Contacts of the helix formed by residues 86 - 103 (chain O) in PDB entry 5G04
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 CYS 86 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56O GLU* 3.4 49.8 - - - +
60O LEU* 4.6 12.8 - - - -
82O ILE* 2.8 25.5 + - - +
83O GLU* 3.2 8.9 + - - -
85O SER* 1.3 89.2 - - - +
87O PRO* 1.3 70.0 - - - +
88O GLN 3.3 0.8 + - - +
89O LEU* 3.8 28.1 + - + +
90O ALA 3.9 3.5 + - - -
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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
----------------------------------------------------------
56O GLU* 4.2 11.9 - - - +
83O GLU* 3.2 19.4 - - + +
84O GLU 5.2 1.1 - - - +
85O SER 4.5 2.7 - - - +
86O CYS* 1.3 82.4 - - + +
88O GLN* 1.3 62.8 + - + +
90O ALA* 4.0 12.0 - - - +
91O ASN* 4.0 12.8 - - - +
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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
----------------------------------------------------------
51O ALA* 4.6 1.2 - - - -
52O VAL* 3.4 43.3 + - + +
56O GLU* 4.9 1.8 - - - +
86O CYS* 3.3 0.8 - - - +
87O PRO* 1.3 81.2 - - + +
89O LEU* 1.3 68.7 + - + +
91O ASN* 3.2 19.4 + - + +
92O SER* 3.4 10.7 + - - -
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Residues in contact with LEU 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O LEU* 4.5 12.6 - - + +
43O GLU* 5.4 4.0 - - + -
44O MET* 4.2 23.1 - - + +
50O GLY 5.4 1.3 - - - +
51O ALA* 4.7 12.1 - - + -
52O VAL 4.7 12.3 - - - +
56O GLU* 4.5 15.0 - - + +
60O LEU* 4.0 28.3 - - + -
82O ILE* 4.4 12.1 - - + -
86O CYS* 3.8 16.4 + - + +
87O PRO 3.7 0.4 - - - -
88O GLN* 1.3 78.7 - - + +
90O ALA* 1.3 56.4 + - - +
92O SER* 3.1 13.9 + - - +
93O VAL* 2.8 36.8 + - + +
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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
----------------------------------------------------------
79O TYR* 4.1 4.9 - - + +
82O ILE* 3.9 18.4 - - + +
83O GLU* 3.1 43.5 - - + +
86O CYS 3.9 3.8 + - - -
87O PRO 4.0 6.1 - - - +
88O GLN 3.4 0.4 - - - -
89O LEU* 1.3 76.3 - - - +
91O ASN* 1.3 58.9 + - - +
93O VAL* 3.1 13.2 - - - +
94O GLN* 3.0 31.0 + - - +
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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
----------------------------------------------------------
83O GLU* 5.6 3.2 + - - -
87O PRO 4.0 12.4 + - - +
88O GLN* 3.2 11.3 + - + +
89O LEU 3.2 0.6 - - - -
90O ALA* 1.3 78.0 - - - +
92O SER* 1.3 57.3 + - - +
94O GLN* 3.4 6.6 + - - +
95O ILE* 2.9 44.5 + - + +
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Residues in contact with SER 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O GLU* 4.4 17.0 - - - +
46O ARG* 5.3 5.0 + - - -
88O GLN 3.4 6.3 + - - -
89O LEU* 3.1 20.2 + - - +
91O ASN* 1.3 79.3 - - - +
93O VAL* 1.3 60.9 + - - +
95O ILE* 3.8 7.1 - - - +
96O ARG* 3.2 24.1 + - - +
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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
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36O ALA 4.4 3.1 - - - +
39O VAL* 3.7 26.9 - - + -
40O LEU* 4.2 21.8 - - + +
43O GLU* 5.4 5.4 - - + -
75O LEU* 5.6 7.9 - - + -
78O LEU* 6.2 4.3 - - + -
79O TYR* 5.9 4.0 - - + -
82O ILE* 4.5 16.4 - - + -
89O LEU* 2.8 19.4 + - + +
90O ALA* 3.1 22.4 - - - +
92O SER* 1.3 72.2 + - - +
94O GLN* 1.3 69.1 + - + +
96O ARG* 3.2 6.0 + - - +
97O ILE* 3.0 36.7 + - + +
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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
----------------------------------------------------------
75O LEU* 5.8 8.5 - - + -
79O TYR* 6.3 2.2 - - + -
90O ALA 3.0 21.0 + - - +
91O ASN* 3.7 7.5 + - - +
93O VAL* 1.3 77.8 - - + +
95O ILE* 1.3 66.7 + - - +
97O ILE* 3.8 6.6 - - - +
98O LYS* 2.8 48.0 + - - +
162O PHE* 3.9 25.5 - - + -
166O GLU* 5.4 7.3 - - - +
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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
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91O ASN* 2.9 37.5 + - + +
92O SER* 3.8 6.5 - - - +
93O VAL 3.4 0.2 - - - -
94O GLN* 1.3 84.7 - - - +
96O ARG* 1.3 64.6 + - - +
98O LYS* 3.4 23.3 + - - +
99O LEU* 3.0 33.8 + - + +
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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
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39O VAL* 3.4 23.6 - - + -
42O ASN* 4.2 4.8 - - - +
43O GLU* 3.2 34.0 + - + +
92O SER 3.2 15.2 + - - +
93O VAL 3.7 3.6 - - - +
95O ILE* 1.3 79.5 - - - +
97O ILE* 1.3 63.6 + - - +
99O LEU* 3.4 21.9 - - - +
100O MET* 3.1 32.2 + - + +
110O GLN* 6.1 0.8 - - - +
111O PHE* 3.2 44.1 - - - +
114O ASP* 4.7 15.6 + - - +
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Residues in contact with ILE 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35O ILE* 5.8 2.2 - - + -
36O ALA* 3.7 31.4 - - + -
39O VAL* 3.7 27.1 - - + -
75O LEU* 4.0 25.6 - - + -
93O VAL* 3.0 19.0 + - + +
94O GLN* 4.0 4.3 - - - +
96O ARG* 1.3 74.0 - - - +
98O LYS* 1.3 54.6 + - - +
100O MET* 3.1 17.5 + - + +
101O ALA* 2.8 33.9 + - + +
158O LEU* 5.7 7.9 - - + -
161O TYR* 5.1 2.5 - - + -
162O PHE* 3.6 29.8 - - + -
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Residues in contact with LYS 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94O GLN* 2.8 33.8 + - - +
95O ILE* 3.8 32.8 - - + +
97O ILE* 1.3 71.3 - - - +
99O LEU* 1.4 65.0 + - + +
101O ALA* 3.8 0.9 - - - +
102O GLU* 2.9 57.7 + - - +
162O PHE* 3.6 27.6 - - + -
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Residues in contact with LEU 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95O ILE* 3.0 25.0 + - + +
96O ARG* 3.4 25.6 - - - +
98O LYS* 1.4 84.0 - - + +
100O MET* 1.3 66.1 + - + +
102O GLU* 3.6 3.9 + - - +
103O GLY* 2.9 26.7 + - - -
107O ASP* 5.2 11.7 - - + +
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Residues in contact with MET 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O ILE* 4.7 4.9 - - + -
39O VAL* 4.4 12.8 - - + -
96O ARG* 3.1 29.2 + - - +
97O ILE* 3.1 18.9 + - + +
99O LEU* 1.3 84.0 - - + +
101O ALA* 1.3 59.9 + - - +
103O GLY 3.4 16.5 + - - +
104O GLU 4.5 2.8 - - - +
107O ASP* 4.6 8.3 - - - -
108O MET* 4.1 29.7 + - + +
111O PHE* 3.4 40.2 - - + -
155O TYR* 4.1 7.6 - - - -
158O LEU* 3.9 26.2 - - + -
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Residues in contact with ALA 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97O ILE* 2.8 19.6 + - + +
98O LYS 3.8 1.1 - - - +
100O MET* 1.3 70.3 - - - +
102O GLU* 1.3 62.2 + - - +
155O TYR* 3.3 7.6 + - - -
158O LEU* 4.9 8.3 - - + +
159O GLN* 2.7 45.1 + - + +
162O PHE* 3.4 42.2 - - + -
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Residues in contact with GLU 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98O LYS* 2.9 45.9 + - - +
99O LEU* 4.2 3.3 - - - +
101O ALA* 1.3 77.0 - - - +
103O GLY* 1.3 60.3 + - - +
155O TYR* 4.4 1.6 + - - -
159O GLN* 4.8 3.4 + - - +
162O PHE* 4.5 15.3 - - + -
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Residues in contact with GLY 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99O LEU 2.9 18.9 + - - -
100O MET 3.4 6.4 + - - +
101O ALA 3.3 0.8 - - - -
102O GLU* 1.3 77.9 - - - +
104O GLU* 1.3 60.3 + - - +
107O ASP* 3.0 12.1 - - - -
155O TYR* 2.5 31.1 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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