Contacts of the strand formed by residues 21 - 30 (chain G) in PDB entry 2VLR
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 ASN 21 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11G SER* 4.2 5.0 + - - -
12G ARG* 3.4 9.9 + - - +
13G HIS* 3.2 56.0 + - - +
14G PRO 4.3 6.9 + - - -
15G ALA* 4.4 7.5 - - - +
16G GLU 5.1 2.0 - - - +
19G LYS* 4.4 7.6 + - - +
20G SER* 1.3 76.8 + - - +
22G PHE* 1.3 79.9 + - - +
69G GLU* 3.1 26.9 - - - +
70G PHE* 3.2 33.0 + - + +
72G PRO* 4.4 5.3 - - + +
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Residues in contact with PHE 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G SER* 3.3 8.8 - - - -
12G ARG* 3.2 77.5 + - + +
13G HIS* 6.0 1.3 - + - -
21G ASN* 1.3 94.0 + - - +
23G LEU* 1.3 59.2 + - - +
24G ASN* 4.3 9.1 + - - +
67G TYR* 4.3 20.0 - + - -
68G THR* 3.5 19.5 - - - -
69G GLU* 3.6 36.3 - - + -
70G PHE* 3.4 7.2 - - - -
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Residues in contact with LEU 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 4.1 21.1 - - + -
10G TYR 3.9 9.9 - - - +
22G PHE* 1.3 72.5 - - - +
24G ASN* 1.3 62.3 + - - +
39G LEU* 4.0 25.6 - - + +
40G LEU 5.2 1.8 - - - +
46G ILE* 4.9 7.9 - - + -
66G TYR 3.9 0.2 - - - +
67G TYR* 3.2 5.2 - - - -
68G THR* 2.8 40.7 + - + +
70G PHE* 3.5 25.4 - - + -
78G TYR* 3.5 38.4 - - + -
79G ALA 5.2 3.1 - - - +
95G TRP* 4.3 19.5 - - + -
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Residues in contact with ASN 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235F PRO 4.3 0.2 + - - -
236F ALA 3.5 24.0 + - - +
237F GLY* 5.5 0.3 - - - -
8G GLN 4.3 0.2 - - - -
9G VAL* 3.4 12.5 - - - +
10G TYR* 2.9 61.9 + - + +
12G ARG* 3.8 16.5 + - - +
22G PHE* 4.3 8.2 - - - +
23G LEU* 1.3 76.2 - - - +
25G CYS* 1.3 60.6 + - - +
26G TYR 4.1 0.7 - - - -
39G LEU* 4.6 3.4 - - - -
65G LEU* 3.7 22.8 - - + +
66G TYR 3.2 2.9 - - - -
67G TYR* 3.4 21.3 - - - +
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Residues in contact with CYS 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ILE* 3.7 20.6 - - - -
8G GLN 3.4 4.0 - - - -
9G VAL* 4.7 0.7 - - + -
24G ASN* 1.3 72.7 - - - +
26G TYR* 1.3 62.4 + - - +
27G VAL* 3.7 9.8 + - - +
37G VAL* 4.1 10.3 - - + -
39G LEU* 3.7 13.4 - - + +
64G LEU 3.8 0.5 - - - +
65G LEU* 3.7 2.7 - - - -
66G TYR* 2.7 41.4 + - + +
80G CYS* 2.1 50.7 - - + -
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Residues in contact with TYR 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F GLU* 4.0 16.1 + - - -
233F THR 4.1 19.5 + - - -
234F ARG* 4.0 13.5 - - + -
235F PRO* 3.8 29.1 - - + +
6G LYS 3.7 0.9 - - - +
7G ILE* 3.5 5.2 - - - +
8G GLN* 3.0 43.6 + - + +
10G TYR* 3.6 23.6 - - + +
24G ASN 4.1 0.4 - - - -
25G CYS* 1.3 71.9 - - - +
27G VAL* 1.3 59.7 + - - +
28G SER* 4.0 20.2 - - - -
63G TYR* 3.9 41.1 - + + +
64G LEU 3.4 17.5 - - - -
65G LEU* 4.0 5.4 - - + +
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Residues in contact with VAL 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G PRO* 4.4 2.0 - - + -
6G LYS 3.3 4.3 - - - +
7G ILE* 4.1 12.3 - - + -
25G CYS* 3.7 9.8 + - - +
26G TYR* 1.3 75.2 - - - +
28G SER* 1.3 64.0 + - - +
30G PHE* 3.7 16.4 - - + -
35G ILE* 4.0 21.1 - - + -
37G VAL* 4.0 27.1 - - + -
63G TYR* 3.4 2.4 - - - +
64G LEU* 3.0 47.5 + - + +
66G TYR* 4.5 4.3 - - + -
82G VAL* 4.1 19.3 - - + -
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Residues in contact with SER 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F GLU* 3.2 34.2 + - - -
5G PRO* 3.6 1.7 - - - +
6G LYS* 2.8 43.5 + - - +
8G GLN* 5.9 0.2 + - - -
26G TYR* 4.0 15.3 - - - -
27G VAL* 1.3 76.7 - - - +
29G GLY* 1.3 63.8 + - - +
30G PHE* 3.4 5.3 - - - -
62G PHE 3.6 6.3 - - - -
63G TYR* 3.7 15.0 - - - -
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Residues in contact with GLY 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F GLU* 5.5 0.2 + - - -
3G ARG* 3.4 29.2 + - - +
4G THR 3.7 7.0 - - - +
6G LYS* 4.8 10.1 - - - -
28G SER* 1.3 77.5 + - - +
30G PHE* 1.3 57.3 + - - +
61G SER* 3.5 23.3 + - - -
62G PHE 3.1 7.3 + - - -
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Residues in contact with PHE 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G ARG* 3.6 7.6 - - - +
4G THR 4.4 0.2 - - - -
5G PRO* 3.7 25.4 - - + -
27G VAL* 3.5 27.1 - - + -
28G SER* 3.9 12.1 - - - -
29G GLY* 1.3 78.7 - - - +
31G HIS* 1.3 63.5 + - - +
32G PRO 3.6 17.9 - - - -
33G SER* 3.6 22.9 - - - -
35G ILE* 4.1 25.1 - - + -
54G LEU* 5.0 0.2 - - + -
61G SER* 3.8 2.8 - - - -
62G PHE* 3.2 65.3 + - + -
63G TYR* 3.8 1.8 - - - -
64G LEU* 3.9 23.8 - - + -
84G HIS* 4.2 4.9 - + - +
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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