Contacts of the strand formed by residues 21 - 29 (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 TYR 21 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 4.1 1.6 - - - +
17B VAL* 3.4 42.7 - - + +
18B LYS 3.4 20.4 - - - -
19B ALA* 3.7 3.1 - - - -
20B PRO* 1.3 76.2 - - - +
22B VAL* 1.3 68.9 - - - +
23B ARG* 3.6 17.0 + - + -
40B ASP* 2.7 34.3 + - - +
41B LEU* 3.8 0.7 - - - -
42B ARG* 3.0 66.9 + - + +
103B PHE* 4.5 0.5 - - - -
148B LEU* 3.8 8.8 - - - +
149B LYS* 3.3 21.1 - - + +
151B GLN* 3.4 24.9 - - + -
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Residues in contact with VAL 22 (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* 1.3 76.7 - - - +
23B ARG* 1.3 64.4 + - - +
39B TYR* 4.3 7.4 - - + -
40B ASP 3.6 3.1 - - - -
41B LEU* 3.9 12.1 - - + -
96B GLU* 3.9 19.3 - - + +
99B VAL* 3.7 25.8 - - + -
100B MET* 3.9 26.2 - - + -
103B PHE* 3.5 33.2 - - + -
148B LEU* 4.6 1.3 - - + -
149B LYS 3.0 7.1 + - - +
150B VAL* 3.4 9.0 - - - +
151B GLN 2.9 22.5 + - - -
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Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE* 4.1 8.5 + - - +
12B LEU* 3.6 36.3 - - - +
14B HIS* 5.8 0.6 - - - -
21B TYR* 3.6 13.7 - - + -
22B VAL* 1.3 78.9 - - - +
24B LEU* 1.3 78.1 + - - +
25B ALA* 3.2 28.2 + - - +
39B TYR* 3.4 7.0 - - - -
40B ASP* 2.8 66.3 + - - +
42B ARG* 4.8 2.0 - - - +
96B GLU* 3.6 5.8 - - - +
151B GLN* 3.4 33.0 - - - +
152B GLU 4.4 0.9 - - - -
153B THR* 2.9 36.4 + - - +
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Residues in contact with LEU 24 (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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10B PHE* 3.2 33.8 - - + -
23B ARG* 1.3 81.9 + - - +
25B ALA* 1.3 58.0 + - - +
26B GLY 3.7 12.6 - - - +
27B VAL* 3.9 10.5 - - + -
37B SER* 3.9 18.8 - - - +
38B LYS 3.4 16.6 - - - +
39B TYR* 3.8 18.2 - - + -
94B PRO* 3.8 27.6 - - + -
96B GLU* 2.7 31.8 + - + +
153B THR* 3.5 2.1 + - - -
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Residues in contact with ALA 25 (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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8B GLU 4.6 0.2 - - - -
9B SER* 3.5 5.5 + - - -
10B PHE* 2.9 30.1 + - - +
23B ARG* 3.2 28.5 + - - +
24B LEU* 1.3 72.1 - - - +
26B GLY* 1.3 58.6 + - - +
38B LYS* 2.7 23.2 + - + +
39B TYR 4.4 0.9 - - - -
40B ASP* 4.1 15.7 - - + +
87B TYR* 5.7 3.8 - - + -
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Residues in contact with GLY 26 (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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7B VAL 3.4 8.5 - - - -
8B GLU 3.3 17.3 - - - -
10B PHE* 3.6 9.1 - - - -
24B LEU* 3.5 4.5 - - - +
25B ALA* 1.3 81.7 - - - +
27B VAL* 1.3 70.8 + - - +
38B LYS* 2.9 30.1 + - - +
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Residues in contact with VAL 27 (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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7B VAL* 2.8 30.9 + - + +
8B GLU* 3.3 14.2 + - - +
10B PHE* 4.8 4.0 - - + -
24B LEU* 3.9 15.3 - - + -
26B GLY* 1.3 80.6 - - - +
28B LYS* 1.3 67.6 + - - +
29B THR* 4.3 1.3 - - - +
35B GLN* 3.9 36.3 - - + +
36B ILE 3.4 11.2 - - - +
37B SER* 4.3 2.9 - - - +
38B LYS* 5.4 0.4 - - - -
94B PRO* 3.8 24.0 - - + -
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Residues in contact with LYS 28 (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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73A GLY* 3.8 22.5 - - - +
74A VAL 3.6 22.9 + - - +
75A VAL* 4.5 6.5 - - + +
91A ILE* 3.4 30.3 - - + -
8B GLU* 2.8 47.3 + - + +
27B VAL* 1.3 78.1 - - - +
29B THR* 1.3 67.5 + - - +
36B ILE* 2.8 46.0 + - + +
38B LYS* 4.9 9.3 - - - +
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Residues in contact with THR 29 (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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91A ILE* 3.4 14.6 - - - +
27B VAL* 4.3 1.9 + - - +
28B LYS* 1.3 80.8 + - + +
30B THR* 1.3 74.7 + - - +
31B PRO* 4.6 1.2 - - - +
33B GLY* 4.0 9.7 + - - -
34B ASP 3.3 11.8 + - - -
35B GLN* 4.4 8.3 - - - +
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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