Contacts of the strand formed by residues 22 - 27 (chain B) in PDB entry 1VDG
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 VAL 22 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA* 4.3 0.2 - - + -
11B GLU 3.3 15.5 - - - +
12B PRO* 4.4 0.4 - - - -
13B GLY 3.6 22.9 - - - +
16B ILE* 3.7 15.0 - - + -
21B PRO* 1.3 78.1 - - - +
23B THR* 1.3 66.2 + - - +
24B LEU* 4.0 17.0 - - + -
61B PRO 3.6 0.2 - - - -
62B ILE* 2.7 56.1 + - + +
65B ILE* 3.7 27.4 - - + -
93B LEU* 4.4 4.9 - - + -
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Residues in contact with THR 23 (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 ALA* 3.4 0.7 - - - -
11B GLU* 2.7 53.0 + - - +
22B VAL* 1.3 73.9 - - - +
24B LEU* 1.3 67.8 + - - +
25B ARG* 3.7 26.3 + - + -
59B GLN* 4.8 7.0 - - + +
60B PHE 4.0 5.8 - - - +
61B PRO* 3.5 26.2 - - + +
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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
----------------------------------------------------------
8B LEU* 4.8 4.7 - - + -
9B TRP 3.5 4.3 - - - +
10B ALA* 3.4 26.2 - - + -
22B VAL* 4.0 13.5 - - + +
23B THR* 1.3 75.1 - - - +
25B ARG* 1.3 62.1 + - - +
37B LEU* 4.2 18.6 - - + -
46B TRP* 3.9 21.3 - - + -
58B GLY 3.8 1.6 - - - +
59B GLN* 3.9 0.9 - - - -
60B PHE* 3.0 43.6 + - - +
62B ILE* 4.7 2.7 - - + -
73B TYR* 4.5 6.7 - - + -
91B LEU* 4.1 19.5 - - + -
93B LEU* 3.7 29.8 - - + -
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Residues in contact with ARG 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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162A GLY 3.1 27.0 + - - +
163A PRO* 4.6 8.5 - - - +
8B LEU* 2.9 9.3 - - - +
9B TRP* 2.7 83.5 + - + +
11B GLU* 3.1 36.3 + - + +
23B THR* 3.8 20.4 - - - +
24B LEU* 1.3 75.4 - - - +
26B CYS* 1.3 59.9 + - - +
27B GLN* 3.4 24.2 + - - +
57B LYS 4.9 3.8 + - - -
58B GLY 3.5 3.9 + - - -
59B GLN* 3.8 30.1 - - - +
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Residues in contact with CYS 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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6B PRO* 4.1 6.7 - - - -
7B THR 3.4 4.9 - - - -
8B LEU* 3.9 6.3 - - + -
25B ARG* 1.3 74.0 - - - +
27B GLN* 1.3 61.1 + - - +
35B TYR* 3.5 32.0 - - + -
37B LEU* 5.3 0.4 - - + -
58B GLY* 3.0 31.8 + - - +
60B PHE* 4.2 13.2 - - + -
75B CYS* 2.0 49.1 - - + -
76B TYR 4.4 1.8 - - - -
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Residues in contact with GLN 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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145A LEU* 3.2 31.8 - - + +
146A ASN 5.5 0.3 + - - -
160A SER* 2.7 38.5 + - - +
161A VAL* 5.0 2.3 - - - +
6B PRO* 3.4 2.8 - - - +
7B THR* 2.9 37.2 + - - +
9B TRP* 3.7 22.4 - - + -
25B ARG* 3.4 24.9 + - + +
26B CYS* 1.3 75.9 - - - +
28B GLY* 1.3 65.5 + - - +
30B GLN 4.8 4.1 + - - +
35B TYR* 3.3 13.7 - - + +
57B LYS 4.7 10.8 - - - +
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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