Contacts of the helix formed by residues 94 - 110 (chain B) in PDB entry 6WNX
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 ILE 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLN* 4.0 11.9 - - + +
24B SER* 3.6 24.0 - - - -
52B VAL* 3.7 30.7 - - + -
55B TRP* 3.7 21.3 - - + -
56B CYS* 4.2 10.5 - - - -
62B ASP* 5.2 1.8 - - - +
89B ALA* 3.0 10.5 + - - +
92B LEU* 3.7 21.1 - - + -
93B ASP* 1.3 75.8 - - - +
95B LYS* 1.3 65.6 + - - +
96B GLY 4.5 1.1 - - - +
97B LEU* 3.6 26.4 - - + +
98B LEU* 3.0 23.5 + - - +
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Residues in contact with LYS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ASP* 3.8 9.2 + - - +
94B ILE* 1.3 71.7 - - - +
96B GLY* 1.3 52.1 + - - +
98B LEU* 3.1 13.1 + - + +
99B ASP* 2.7 66.5 + - - +
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Residues in contact with GLY 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TRP* 3.6 11.6 - - - -
62B ASP* 4.4 3.6 + - - -
64B PRO* 3.9 23.0 - - - +
94B ILE* 3.3 2.8 - - - +
95B LYS* 1.3 78.2 - - - +
97B LEU* 1.3 55.9 + - - +
99B ASP* 3.3 10.5 + - - +
100B VAL* 3.0 33.1 + - - +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 4.3 35.0 - - + -
55B TRP* 3.4 45.6 - - + +
74B PHE* 4.4 10.5 - - + -
85B LEU* 4.5 10.5 - - + +
89B ALA* 3.8 24.0 - - + -
94B ILE* 3.2 23.1 + - + +
96B GLY* 1.3 73.2 - - - +
98B LEU* 1.3 57.3 + - - +
100B VAL* 3.2 7.0 - - + +
101B THR* 2.6 52.6 + - + +
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 4.2 18.8 - - + -
21A ASN* 5.2 7.4 - - - +
86B ILE* 3.8 38.8 - - + +
89B ALA* 3.7 10.7 - - + +
90B ASN* 4.0 23.1 - - - +
93B ASP* 6.5 0.7 - - - -
94B ILE 3.0 13.0 + - - +
95B LYS* 3.4 15.0 - - + +
97B LEU* 1.3 78.9 - - - +
99B ASP* 1.3 59.5 + - - +
101B THR* 2.7 16.7 + - - -
102B CYS* 3.0 32.0 + - - -
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Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.7 19.7 + - - +
64B PRO* 6.3 0.9 - - + -
95B LYS* 2.7 60.7 + - - +
96B GLY* 3.5 9.0 - - - +
97B LEU 3.1 0.2 - - - -
98B LEU* 1.3 78.0 - - - +
100B VAL* 1.3 57.8 + - + +
102B CYS* 3.4 2.6 + - - +
103B LYS* 3.0 28.8 + - - +
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TRP* 4.0 13.7 - - - +
64B PRO* 4.2 15.7 - - + -
66B ASP 4.0 19.3 - - - +
67B ILE* 4.1 13.8 - - + +
71B ASP* 4.2 17.7 - - + +
75B LEU* 3.8 20.9 - - + -
96B GLY 3.0 19.4 + - - +
97B LEU* 3.2 22.7 - - + +
99B ASP* 1.3 72.6 - - + +
101B THR* 1.3 64.5 + - - +
103B LYS* 3.2 3.3 + - - +
104B THR* 2.7 40.4 + - - -
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Residues in contact with THR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LEU* 3.9 23.6 - - + -
82B LEU* 4.0 13.1 - - + +
85B LEU* 4.1 16.2 - - + -
86B ILE* 3.5 24.0 - - + +
97B LEU* 2.6 37.5 + - + +
98B LEU* 2.7 18.4 + - - -
100B VAL* 1.3 78.0 - - + +
102B CYS* 1.3 59.5 + - - +
104B THR* 3.3 9.5 + - - -
105B VAL* 3.2 25.6 + - - +
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Residues in contact with CYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 3.9 25.8 - - - -
21A ASN* 4.9 7.4 - - + -
22A ILE* 3.7 32.7 - - + +
25A TYR* 4.1 14.1 - - + +
86B ILE* 4.7 4.3 - - - -
98B LEU* 3.0 34.8 + - - +
99B ASP* 3.7 5.6 - - - +
100B VAL 3.1 0.2 - - - -
101B THR* 1.3 73.4 + - - +
103B LYS* 1.3 60.3 + - - +
104B THR 3.1 1.1 - - - -
105B VAL* 3.0 7.3 + - - +
106B ALA* 3.0 26.2 + - - +
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.7 46.7 + - + +
66B ASP* 5.7 8.6 - - - +
67B ILE* 3.3 31.0 - - + -
99B ASP 3.0 18.4 + - - +
100B VAL 3.7 3.8 - - - +
102B CYS* 1.3 74.9 - - - +
104B THR* 1.3 57.1 + - - +
106B ALA* 3.4 2.0 + - + +
107B ASN* 2.9 54.4 + - - +
110B LYS* 5.7 1.6 - - - +
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Residues in contact with THR 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 4.7 7.9 - - - +
75B LEU* 3.3 35.5 - - + +
82B LEU* 4.2 17.5 - - + -
100B VAL 2.7 22.7 + - - -
101B THR* 3.4 11.4 - - - -
102B CYS 3.1 0.2 - - - -
103B LYS* 1.3 74.3 - - - +
105B VAL* 1.3 63.0 + - - +
107B ASN* 3.3 11.5 + - + +
108B MET* 3.2 25.7 + - + +
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 3.7 48.0 - - + -
22A ILE* 4.0 19.5 - - + -
82B LEU* 3.8 20.0 - - + -
86B ILE* 4.0 7.6 - - + -
101B THR 3.2 12.5 + - - +
102B CYS 3.0 7.0 + - - +
104B THR* 1.3 71.7 - - - +
106B ALA* 1.3 67.4 + - - +
108B MET* 2.9 20.3 + - - +
109B ILE* 3.1 20.4 + - + +
121B PHE* 4.3 7.6 - - + -
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.6 31.0 - - - +
25A TYR* 3.6 22.0 - - + -
26A LEU* 3.7 14.3 - - + +
102B CYS 3.0 11.4 + - - +
103B LYS* 3.4 11.4 - - + +
105B VAL* 1.3 75.6 - - - +
107B ASN* 1.3 58.9 + - - +
109B ILE* 2.9 20.0 + - - +
110B LYS* 2.9 13.9 + - - +
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Residues in contact with ASN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ILE* 4.4 10.5 - - - +
72B GLN* 6.1 0.4 - - - +
103B LYS* 2.9 50.8 + - - +
104B THR* 3.6 9.4 - - + +
105B VAL 3.1 0.4 - - - -
106B ALA* 1.3 76.6 - - - +
108B MET* 1.3 62.1 + - - +
109B ILE 3.3 0.3 + - - -
110B LYS* 3.2 53.4 + - - +
112B LYS* 5.2 1.4 - - - -
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Residues in contact with MET 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 5.2 0.4 - - - -
79B GLN* 3.4 39.3 - - + +
82B LEU* 4.3 17.7 - - - -
104B THR* 3.2 17.9 + - + +
105B VAL* 2.9 20.2 + - - +
107B ASN* 1.3 77.9 - - + +
109B ILE* 1.3 56.7 + - - +
112B LYS* 2.7 35.4 + - - +
117B ILE* 5.5 0.2 - - - +
120B THR* 4.4 6.1 - - + -
121B PHE* 3.8 22.5 - - + -
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.6 6.1 - - + -
22A ILE* 4.1 22.4 - - + -
23A LEU* 4.7 5.8 - - + -
26A LEU* 3.9 23.1 - - + -
30A SER* 4.9 4.7 - - - +
34A ALA* 4.7 3.1 - - + -
41A TRP* 3.9 26.2 - - + -
105B VAL* 3.6 20.9 - - + +
106B ALA* 2.9 8.3 + - - +
108B MET* 1.3 77.0 - - - +
110B LYS* 1.3 67.2 + - - +
111B GLY 3.6 1.2 + - - -
112B LYS* 3.7 16.9 + - - +
117B ILE* 3.9 25.7 - - + +
121B PHE* 3.8 19.5 - - + -
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.2 9.4 - - + +
27A ASP* 4.8 3.6 - - - +
30A SER* 3.6 16.2 - - - +
103B LYS* 5.7 1.6 - - - +
106B ALA 2.9 9.4 + - - +
107B ASN* 3.2 53.6 + - - +
109B ILE* 1.3 79.5 - - - +
111B GLY* 1.3 63.0 + - - +
112B LYS* 3.4 8.8 + - - +
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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