Contacts of the strand formed by residues 35 - 42 (chain B) in PDB entry 1VGX
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 GLN 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL* 3.9 21.3 - - + +
28B LYS 3.8 3.4 - - - -
29B THR* 4.4 8.1 - - - +
33B GLY 4.6 6.0 - - - +
34B ASP* 1.3 78.3 - - - +
36B ILE* 1.3 62.0 + - - +
37B SER 3.7 0.7 - - - -
91B ILE* 3.6 5.0 - - - +
92B GLY* 2.9 41.8 + - - +
93B GLU* 3.3 23.6 + - - +
94B PRO* 3.4 21.0 - - - +
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Residues in contact with ILE 36 (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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30A THR* 4.9 1.1 - - + -
36A ILE* 3.6 29.8 - - + -
75A VAL* 4.0 28.3 - - + -
91A ILE* 4.4 11.2 - - + -
27B VAL* 3.4 3.7 - - - -
28B LYS* 2.8 46.0 + - + +
30B THR* 4.1 21.5 - - + -
35B GLN* 1.3 75.6 - - - +
37B SER* 1.3 61.8 + - - +
38B LYS* 3.7 4.3 + - + +
75B VAL* 4.7 4.3 - - + -
89B ALA* 4.1 18.2 - - + -
90B VAL 3.4 5.8 - - - +
91B ILE* 3.7 19.5 - - + -
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Residues in contact with SER 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.9 4.3 - - - -
26B GLY 3.8 5.4 - - - -
27B VAL* 4.3 3.9 - - - +
35B GLN 3.7 1.0 - - - -
36B ILE* 1.3 71.3 - - - +
38B LYS* 1.3 60.1 + - - +
39B TYR* 3.5 31.7 - - - -
89B ALA* 3.4 1.7 - - - -
90B VAL* 2.8 39.9 + - - -
92B GLY 2.8 23.1 + - - -
93B GLU 4.6 0.2 - - - -
94B PRO* 3.3 26.2 - - - +
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Residues in contact with LYS 38 (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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68A ARG* 3.9 6.7 - - - +
75A VAL* 2.9 35.8 + - + +
76A ASP* 2.9 25.5 + - - +
8B GLU* 2.8 39.7 + - - +
9B SER* 4.4 5.3 - - - -
24B LEU* 3.4 9.7 - - - +
25B ALA* 2.7 34.5 + - + +
26B GLY* 2.9 22.7 + - - +
28B LYS* 4.9 10.7 - - - +
36B ILE 4.4 5.4 - - - +
37B SER* 1.3 75.3 - - - +
39B TYR* 1.3 57.2 + - - +
87B TYR* 3.6 22.9 - - + +
88B MET 3.6 4.5 - - - -
89B ALA* 4.4 2.9 - - + +
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Residues in contact with TYR 39 (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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22B VAL* 4.3 3.8 - - + -
23B ARG 3.4 13.0 - - - +
24B LEU* 3.8 15.3 - - + -
25B ALA* 4.4 2.9 - - - -
37B SER* 3.5 31.5 - - - -
38B LYS* 1.3 78.4 - - - +
40B ASP* 1.3 59.6 + - - +
41B LEU* 3.7 20.3 + - + +
87B TYR* 3.5 11.3 - - - -
88B MET* 2.8 41.6 + - + +
90B VAL* 3.8 22.4 - - + -
93B GLU 4.1 2.1 + - - -
94B PRO* 3.5 8.0 - - - +
95B ASP* 2.8 27.4 + - - +
96B GLU* 4.1 17.7 - - + -
99B VAL* 3.5 36.2 - - + +
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Residues in contact with ASP 40 (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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12B LEU* 4.1 0.2 - - - +
21B TYR* 2.7 27.9 + - - +
22B VAL* 3.6 4.3 - - - -
23B ARG* 2.8 65.2 + - + +
25B ALA* 4.1 4.9 - - + +
39B TYR* 1.3 69.5 - - - +
41B LEU* 1.3 58.8 + - - +
42B ARG* 2.9 44.0 + - - +
80B MET* 3.3 17.3 - - + +
87B TYR* 6.0 0.2 - - - -
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Residues in contact with LEU 41 (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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21B TYR 3.8 4.5 - - - -
22B VAL* 3.9 23.8 - - + -
39B TYR* 4.1 24.0 - - + +
40B ASP* 1.3 71.2 + - - +
42B ARG* 1.3 60.5 + - - +
43B PHE* 3.6 6.4 - - - -
63B LEU* 5.8 0.7 - - + -
67B MET* 4.6 5.2 - - + -
77B VAL* 4.8 6.3 - - + -
85B GLY* 3.3 3.4 - - - -
86B MET* 2.9 48.9 + - + +
88B MET* 4.0 29.8 - - + -
99B VAL* 4.1 12.1 - - + -
103B PHE* 3.9 36.1 - - + -
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Residues in contact with ARG 42 (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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126A GLY* 4.2 0.6 - - - -
12B LEU* 4.4 2.6 - - - +
14B HIS* 3.8 21.6 + - - -
19B ALA* 4.1 4.7 - - + -
20B PRO* 3.1 9.2 - - - +
21B TYR* 3.0 74.7 + - + +
23B ARG* 4.8 1.4 - - - +
40B ASP* 2.9 36.8 + - - -
41B LEU* 1.3 72.0 - - - +
43B PHE* 1.3 57.9 + - - +
44B LEU 3.3 20.0 - - - +
46B PRO* 4.0 18.3 - - + +
80B MET* 3.9 12.7 - - - +
82B CSD 2.9 20.2 + - - -
84B THR* 2.8 43.3 + - - -
85B GLY* 4.3 0.9 - - - +
103B PHE* 5.1 1.5 - - - -
143B VAL* 5.2 0.2 - - - +
148B LEU* 4.9 1.4 - - - +
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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