Contacts of the strand formed by residues 21 - 28 (chain G) in PDB entry 1S7X
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 ARG 21 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G THR 3.7 1.2 - - - +
11G ALA* 3.1 4.3 - - - -
12G VAL* 2.9 38.2 + - + +
17G LEU* 6.2 4.2 - - + +
19G GLU 3.8 1.2 + - - -
20G PRO* 1.3 72.3 - - - +
22G TYR* 1.3 61.0 + - - +
23G ILE* 3.6 20.9 - - + +
37G ASP* 2.8 37.7 + - - +
38G SER* 3.7 9.9 - - - +
39G ASP* 3.5 39.0 + - - +
54H MET* 5.1 12.3 - - - +
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Residues in contact with TYR 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G GLU* 2.3 46.7 + - + +
10G THR 3.3 12.6 - - - -
11G ALA* 4.3 4.0 - - + +
20G PRO* 3.8 1.5 + - + +
21G ARG* 1.3 72.1 - - - +
23G ILE* 1.3 65.0 + - - +
24G SER* 3.6 19.0 + - - -
36G PHE* 3.7 26.5 - + - -
37G ASP* 3.7 0.7 - - - -
38G SER* 3.1 34.1 + - - +
45G TYR* 4.7 1.4 + - - -
67G ALA* 3.6 19.4 - - + -
70G GLN* 3.1 16.1 - - + +
71G GLU* 3.9 32.5 - - + +
74G PHE* 3.8 31.2 - + + -
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Residues in contact with ILE 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G PHE 3.8 1.1 - - - +
9G GLU* 3.3 2.9 - - - +
10G THR* 2.8 38.8 + - - +
21G ARG* 3.6 29.8 - - + +
22G TYR* 1.3 83.3 - - - +
24G SER* 1.3 63.8 + - - +
25G VAL* 4.0 10.3 - - + -
35G ARG* 3.7 26.2 - - - +
36G PHE 3.3 10.8 - - - +
37G ASP* 3.7 20.9 - - - +
54H MET* 3.4 42.2 - - + +
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Residues in contact with SER 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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7G TYR* 3.9 8.0 - - - +
8G PHE 3.5 4.0 - - - -
9G GLU* 3.5 15.4 - - - +
22G TYR* 3.6 22.8 + - - -
23G ILE* 1.3 74.0 - - - +
25G VAL* 1.3 69.1 + - - +
26G GLY 4.3 0.2 - - - -
35G ARG* 3.4 2.9 - - - +
36G PHE* 3.0 32.7 + - - +
45G TYR* 2.5 35.0 + - - -
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Residues in contact with VAL 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G TYR* 3.3 4.5 - - - -
8G PHE* 2.9 41.7 + - + +
23G ILE* 4.0 7.0 - - + -
24G SER* 1.3 81.3 + - - +
26G GLY* 1.3 57.3 + - - +
27G TYR* 3.3 33.0 - - + +
32G GLU* 3.4 42.2 - - + +
34G VAL 3.7 4.7 - - - +
35G ARG* 3.6 28.7 - - - +
54H MET 4.7 3.4 - - - +
55H SER* 5.3 2.0 - - - +
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Residues in contact with GLY 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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6G ARG 3.3 7.4 - - - -
7G TYR* 3.8 10.3 - - - -
24G SER 4.3 0.4 - - - -
25G VAL* 1.3 71.3 - - - +
27G TYR* 1.3 61.9 + - - -
32G GLU* 3.5 7.1 - - - +
33G PHE* 3.0 37.6 + - - -
34G VAL* 3.1 25.0 + - - +
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Residues in contact with TYR 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 MET* 3.2 13.2 - - - +
6G ARG* 2.8 49.7 + - + +
8G PHE* 4.0 28.1 - + - +
25G VAL* 3.3 40.6 - - + +
26G GLY* 1.3 75.4 - - - -
28G VAL* 1.3 59.2 + - - +
29G ASP 4.2 0.2 - - - -
30G ASN* 3.8 21.1 - - - +
31G LYS 3.2 12.8 - - - +
32G GLU* 3.7 31.3 + - + -
33G PHE* 3.2 6.6 - - - -
55H SER* 3.8 23.4 + - - -
56H PHE 4.8 0.7 + - - -
63H TYR* 4.3 10.3 + - - -
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Residues in contact with VAL 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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4G SER 3.4 3.4 - - - -
5G MET* 4.5 2.5 - - - -
27G TYR* 1.3 77.9 - - - +
29G ASP* 1.3 82.4 + - + +
30G ASN 3.1 1.1 - - - -
31G LYS* 2.9 23.5 + - + +
33G PHE* 3.5 29.2 - - + -
51G TRP* 4.3 11.4 - - + -
168G LEU* 3.8 24.7 - - + -
171G TYR* 4.0 25.1 - - + -
172G LEU* 4.1 11.4 - - + +
179G LEU* 4.0 11.7 - - + +
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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