Contacts of the helix formed by residues 93 - 108 (chain O) in PDB entry 2X86
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 ASN 93 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74O HIS* 4.9 0.2 + - - -
77O ALA* 3.4 13.0 - - + +
78O CYS* 2.8 46.9 + - - +
89O MET* 2.9 28.8 + - - +
92O ASN* 1.3 82.7 + - - +
94O TYR* 1.3 63.5 + - - +
97O SER* 2.8 33.2 + - - -
140O PHE* 4.0 7.9 - - - -
143O SER* 3.2 28.8 + - - +
144O LYS* 4.6 7.4 - - + +
147O PHE* 6.0 0.4 - - - -
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Residues in contact with TYR 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48K ALA 4.3 0.5 + - - -
49K ASP* 2.2 43.7 + - - -
50K TYR* 3.5 20.6 - + + -
89O MET 3.7 0.2 + - - -
90O MET* 3.2 36.5 + - + +
93O ASN* 1.3 76.4 - - - +
95O GLN* 1.3 71.6 + - - +
97O SER* 3.2 6.5 + - - -
98O LYS* 2.9 38.6 + - + +
143O SER 4.1 10.1 - - - +
146O LEU* 3.5 42.1 - - + +
147O PHE* 3.6 27.5 - + + -
150O TYR* 3.7 15.8 - - + +
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Residues in contact with GLN 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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50K TYR 4.1 10.0 - - - +
51K MET* 5.4 7.3 - - - +
55K ASP* 5.5 5.2 - - - +
90O MET 2.8 15.6 + - - +
91O ASP* 3.3 27.4 - - - +
94O TYR* 1.3 75.5 - - + +
96O TYR* 1.3 64.4 + - - +
98O LYS* 3.0 42.8 + - - +
99O GLU* 3.0 47.5 + - - +
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Residues in contact with TYR 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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5O THR* 5.4 0.9 - - + -
30O VAL* 4.1 0.2 - - - +
53O LYS* 2.7 42.0 + - + -
54O GLU* 5.5 1.6 - - - -
56O PHE* 3.5 18.6 - + - -
57O LEU* 3.6 35.7 + - + -
74O HIS* 3.9 17.0 - + - +
91O ASP 2.9 12.6 + - - +
92O ASN* 3.1 26.2 - - - +
94O TYR 3.3 0.2 - - - -
95O GLN* 1.3 74.5 - - - +
97O SER* 1.3 64.1 + - - +
99O GLU* 3.0 16.9 + - - +
100O LEU* 3.0 32.2 + - + +
400O NAP 3.4 36.3 + + - -
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Residues in contact with SER 97 (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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74O HIS* 2.8 32.5 + - - -
76O GLY 5.2 0.2 + - - -
93O ASN* 2.8 22.0 + - - -
94O TYR 3.5 3.4 - - - -
95O GLN 3.2 0.2 - - - -
96O TYR* 1.3 79.3 - - - +
98O LYS* 1.3 63.4 + - - +
100O LEU* 3.3 3.5 + - - +
101O LEU* 2.9 24.6 + - - +
111O PHE* 4.1 1.0 - - - -
113O TYR* 5.9 0.3 - - - -
144O LYS* 5.6 3.3 + - - -
147O PHE* 3.6 33.1 - - - -
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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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49K ASP* 2.9 30.4 + - - +
50K TYR 4.2 2.4 + - - -
51K MET* 4.9 6.5 - - - +
94O TYR* 2.9 30.1 + - + +
95O GLN* 3.0 44.2 + - - +
97O SER* 1.3 76.2 - - - +
99O GLU* 1.3 65.0 + - - +
101O LEU* 3.2 3.6 + - - +
102O HIS* 3.0 37.7 + - + +
147O PHE* 3.5 11.9 - - + -
150O TYR* 3.6 45.0 - - + +
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Residues in contact with GLU 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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57O LEU* 4.0 14.6 - - + -
60O ILE* 3.9 8.0 - - + +
61O MET* 3.4 43.9 - - + +
95O GLN* 3.0 38.5 + - - +
96O TYR* 3.2 10.1 - - - +
98O LYS* 1.3 80.2 - - - +
100O LEU* 1.3 61.8 + - - +
102O HIS* 3.5 8.0 + - - +
103O TYR* 3.2 21.5 + - - +
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Residues in contact with LEU 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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5O THR* 4.1 15.0 - - + -
56O PHE* 3.7 24.0 - - + -
57O LEU* 5.2 2.0 - - + -
60O ILE* 3.9 18.4 - - + -
72O ILE* 4.5 12.6 - - + -
74O HIS* 3.3 46.2 - - + +
96O TYR* 3.0 25.3 + - + +
97O SER 3.6 7.4 - - - +
99O GLU* 1.3 75.5 - - - +
101O LEU* 1.3 66.4 + - - +
103O TYR* 3.1 6.5 + - - +
104O CYS* 2.9 26.5 + - - -
111O PHE* 3.7 13.5 - - + -
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Residues in contact with LEU 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 SER 2.9 16.6 + - - +
98O LYS 3.2 4.2 + - - +
100O LEU* 1.3 76.9 - - - +
102O HIS* 1.3 60.0 + - + +
104O CYS* 3.3 1.2 + - - +
105O LEU* 2.8 40.8 + - + +
111O PHE* 3.8 31.1 - - + -
147O PHE* 4.0 21.1 - - + -
150O TYR* 4.0 29.4 - - + -
151O VAL* 4.3 8.7 - - + -
154O ILE* 4.3 13.2 - - + -
162O ILE* 3.8 30.1 - - + -
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Residues in contact with HIS 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* 3.0 33.8 + - + +
99O GLU* 3.9 8.7 - - - +
100O LEU 3.2 0.2 - - - -
101O LEU* 1.3 77.6 - - + +
103O TYR* 1.3 63.8 + - - +
105O LEU* 3.3 13.6 + - + +
106O GLU* 3.0 30.2 + - - +
150O TYR* 2.6 38.3 + + - -
154O ILE* 4.5 14.8 - - + -
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Residues in contact with TYR 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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3O ILE* 6.0 0.4 - - + -
60O ILE* 3.5 58.6 - - + -
63O GLY* 4.3 0.9 - - - -
64O GLU 2.6 27.9 + - - -
65O GLU* 3.8 4.9 + - - -
66O PHE* 3.3 17.8 + + - -
69O VAL* 5.6 3.2 - - + +
72O ILE* 4.7 7.2 - - + -
99O GLU 3.2 12.9 + - - +
100O LEU* 3.1 9.1 + - - +
102O HIS* 1.3 78.0 - - - +
104O CYS* 1.3 72.0 + - - +
106O GLU* 4.8 1.3 - - - -
107O ARG* 3.1 79.4 + - - +
109O ILE* 4.1 12.9 - - + +
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Residues in contact with CYS 104 (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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72O ILE* 3.4 37.2 - - - -
100O LEU 2.9 14.8 + - - +
101O LEU* 3.6 6.5 - - + +
103O TYR* 1.3 78.6 - - - +
105O LEU* 1.3 56.4 + - + +
107O ARG 3.0 1.7 + - - -
108O GLU 2.7 32.1 + - - -
109O ILE* 2.9 40.8 + - - +
111O PHE* 3.8 26.0 - - + -
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Residues in contact with LEU 105 (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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101O LEU* 2.8 30.4 + - + +
102O HIS* 3.5 15.7 - - + +
104O CYS* 1.3 76.7 - - + +
106O GLU* 1.3 62.0 + - - +
108O GLU* 3.3 17.5 + - - +
109O ILE 6.1 0.4 - - - +
111O PHE* 6.3 0.4 - - + -
154O ILE* 3.6 32.5 - - + -
158O ALA* 4.4 13.7 - - + -
159O ASN* 5.2 3.4 - - - +
160O SER* 4.3 15.2 + - - +
161O GLN 5.7 0.2 - - - +
162O ILE* 3.7 30.3 - - + -
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Residues in contact with GLU 106 (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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102O HIS* 3.0 19.2 + - - +
103O TYR* 3.8 5.6 - - - +
105O LEU* 1.3 78.2 - - - +
107O ARG* 1.3 79.8 + - + +
108O GLU* 3.4 3.4 + - - +
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Residues in contact with ARG 107 (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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63O GLY* 3.5 29.5 + - - -
65O GLU* 3.3 37.8 + - - +
103O TYR* 3.1 64.4 + - - +
104O CYS 3.0 2.6 + - - -
106O GLU* 1.3 102.6 + - + +
108O GLU* 1.3 72.2 + - - +
109O ILE* 3.2 23.6 + - + +
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Residues in contact with GLU 108 (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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104O CYS 2.7 4.6 + - - -
105O LEU 3.3 10.8 + - - +
106O GLU 4.9 2.9 - - - +
107O ARG* 1.3 80.7 - - - +
109O ILE* 1.3 56.8 + - - +
110O PRO* 3.4 10.7 - - - +
159O ASN* 3.9 30.8 + - + +
160O SER* 3.4 28.7 - - - +
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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