Contacts of the strand formed by residues 85 - 93 (chain B) in PDB entry 2VCK
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 ASP 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LYS 4.7 1.6 - - - +
22B THR* 2.7 34.4 + - - -
23B ILE* 3.7 8.8 + - + +
24B TRP* 2.9 19.5 + - - -
78B HIS* 2.6 30.2 + - - -
79B ILE 3.4 4.0 - - - -
80B VAL* 3.8 12.1 - - + +
84B SER* 1.3 76.2 - - - +
86B ILE* 1.3 59.1 + - - +
108B LYS* 2.8 45.4 + - + +
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Residues in contact with ILE 86 (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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77B ALA 3.7 0.9 - - - +
78B HIS* 3.3 8.0 - - - -
79B ILE* 2.8 42.1 + - + +
84B SER* 4.8 0.4 - - - -
85B ASP* 1.3 79.4 + - - +
87B TYR* 1.3 64.4 + - - +
88B ASN* 4.7 0.4 - - + -
105B ASP* 3.7 10.3 - - - +
106B LEU 3.3 2.2 - - - -
107B MSE 3.9 14.1 - - + -
108B LYS 4.2 10.3 - - - +
109B PHE* 3.7 28.0 - - + -
211B TYR* 4.1 26.0 - - + +
1234B BLA 3.6 48.7 - - + +
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Residues in contact with TYR 87 (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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24B TRP* 4.0 19.7 - - + +
27B TYR 6.0 0.7 - - - -
28B ILE* 3.6 36.3 - - + +
31B LEU* 3.8 7.4 - - + +
32B PHE* 3.5 16.6 - - - -
76B GLU* 2.5 42.4 + - + +
77B ALA 3.4 8.5 - - - -
78B HIS* 4.0 17.3 - + + -
86B ILE* 1.3 74.7 - - - +
88B ASN* 1.3 58.8 + - - +
89B THR* 3.1 22.9 + - - -
104B MSE 3.7 16.9 - - - +
105B ASP* 3.5 1.7 - - - -
106B LEU* 2.8 57.4 + - + +
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Residues in contact with ASN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ARG* 2.8 43.8 + - - +
77B ALA* 2.9 41.4 + - + +
86B ILE* 4.7 1.3 - - + -
87B TYR* 1.3 71.9 - - - +
89B THR* 1.3 61.1 + - - +
104B MSE 3.4 3.8 - - - -
105B ASP* 3.4 5.2 + - - +
206B ASP* 4.7 0.4 + - - -
208B VAL* 6.1 0.2 - - - +
229B LEU* 4.4 11.8 - - - +
1234B BLA 2.7 71.0 + - + +
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Residues in contact with THR 89 (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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31B LEU* 4.3 4.5 - - + -
32B PHE* 5.3 1.6 - - + -
74B ALA* 5.0 3.6 - - + -
75B ARG* 3.4 12.3 - - - +
76B GLU* 3.4 16.5 - - + +
77B ALA 4.0 0.2 + - - -
87B TYR* 3.1 41.9 - - - +
88B ASN* 1.3 77.6 + - - +
90B ILE* 1.3 67.1 + - - +
91B LEU* 4.1 21.8 - - + -
103B GLY* 3.4 1.9 - - - -
104B MSE 2.9 46.9 + - + +
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Residues in contact with ILE 90 (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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74B ALA* 3.2 2.6 - - - -
75B ARG* 3.1 59.1 + - - +
89B THR* 1.3 80.0 - - - +
91B LEU* 1.3 67.6 + - - +
92B TYR* 3.6 34.3 - - + +
101B CYS* 3.7 26.5 - - + -
102B PHE 3.4 6.5 - - - +
103B GLY* 4.1 4.9 - - - -
121B GLN* 4.0 1.1 - - - +
198B PHE* 3.8 23.3 - - + -
202B MSE 5.2 0.2 - - + -
230B PHE* 3.9 6.7 - - + -
1234B BLA 3.7 21.5 - - + -
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Residues in contact with LEU 91 (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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31B LEU* 4.0 24.0 - - + -
32B PHE* 5.6 0.7 - - + -
35B PHE* 3.8 23.3 - - + -
38B LEU* 3.8 25.4 - - + -
71B PHE* 3.7 26.5 - - + -
73B LYS 3.8 3.4 - - - -
74B ALA* 3.9 13.2 - - + +
89B THR* 4.1 13.2 - - + -
90B ILE* 1.3 75.9 - - - +
92B TYR* 1.3 59.9 + - - +
93B PRO* 3.5 2.2 - - - +
101B CYS* 3.0 29.8 - - - +
102B PHE* 2.8 20.3 + - + +
104B MSE 4.4 3.4 - - + -
178B TYR* 4.0 13.2 - - + -
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Residues in contact with TYR 92 (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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71B PHE* 3.5 4.6 - - - -
72B LEU* 2.8 25.4 + - + -
73B LYS* 2.8 50.2 + - + +
75B ARG* 3.9 8.3 - - - -
90B ILE* 3.6 37.9 - - + +
91B LEU* 1.3 70.9 - - - +
93B PRO* 1.3 66.5 - - - +
101B CYS* 3.5 12.3 - - - -
195B TYR* 3.7 23.3 - + + -
198B PHE* 3.7 20.8 - + - -
199B ASP* 2.7 31.6 + - - -
229B LEU 3.4 15.6 + - - -
230B PHE* 4.1 0.5 - - - -
232B TYR* 3.8 22.9 - + + -
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Residues in contact with PRO 93 (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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70B HIS 3.7 6.5 - - - +
71B PHE* 3.7 4.9 - - + -
72B LEU* 3.8 2.7 - - - +
91B LEU 3.5 3.4 - - - +
92B TYR* 1.3 87.3 - - - +
94B LYS* 1.3 68.2 + - - +
99B LEU* 3.9 20.6 - - + +
100B PRO 3.4 21.1 - - - +
101B CYS* 3.9 6.3 - - - -
178B TYR* 3.3 14.1 - - - +
182B ILE* 3.8 26.0 - - + -
187B PRO* 4.7 0.2 - - + -
195B TYR* 2.7 46.6 + - - +
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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