Contacts of the strand formed by residues 21 - 27 (chain G) in PDB entry 2POZ
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 21 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10G ILE* 4.4 2.0 - - + -
11G TYR 3.3 8.3 - - - +
12G LEU* 3.6 16.2 - - + -
19G HIS 3.6 6.9 + - - +
20G PRO* 1.3 75.0 - - - +
22G LEU* 1.3 66.1 + - - +
36G GLU* 3.4 5.6 - - - +
37G ALA* 3.0 44.3 + - + +
39G ILE 4.3 4.5 - - - +
40G ALA* 5.1 0.4 - - - +
45G GLY* 3.5 26.2 - - - +
48G ALA* 4.2 6.1 - - + -
49G ALA* 4.1 18.8 - - + +
52G ILE* 4.0 25.1 - - + -
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Residues in contact with LEU 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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10G ILE* 3.5 8.0 - - - +
11G TYR* 2.9 38.9 + - + +
13G LEU* 4.1 13.7 - - + -
20G PRO* 4.4 1.6 - - + -
21G VAL* 1.3 80.6 - - - +
23G VAL* 1.3 64.0 + - - +
35G GLY 3.4 6.7 - - - +
36G GLU* 3.3 39.0 - - + +
52G ILE* 4.7 1.1 - - - +
311G SER* 3.6 11.4 - - - +
313G LEU* 4.2 11.7 - - + -
346G VAL* 3.9 30.7 - - + -
370G LEU* 4.8 8.5 - - + -
375G ILE* 3.9 21.8 - - + -
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Residues in contact with VAL 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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8G VAL* 3.5 28.3 - - + -
9G ASN 3.2 7.4 - - - +
10G ILE* 4.4 0.4 - - + -
11G TYR* 5.0 1.8 - - - -
22G LEU* 1.3 77.9 - - - +
24G GLU* 1.3 66.6 + - - +
25G ILE* 4.6 4.9 - - + -
34G ALA* 3.6 4.5 - - - +
35G GLY* 2.8 36.0 + - - +
52G ILE* 3.7 26.9 - - + -
95G ALA* 3.6 32.3 - - + +
96G ILE* 4.2 4.9 - - + +
99G ALA* 4.4 6.7 - - + -
313G LEU* 5.2 0.2 - - - +
370G LEU* 5.1 2.1 - - - +
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Residues in contact with GLU 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 GLY 3.7 0.7 - - - +
8G VAL* 3.3 3.5 - - - -
9G ASN* 2.8 46.1 + - + +
11G TYR* 3.4 28.8 + - + -
23G VAL* 1.3 76.4 - - - +
25G ILE* 1.3 67.7 + - - +
26G SER* 3.9 12.3 + - - +
32G THR* 4.4 18.1 + - - +
33G GLY 3.3 10.1 - - - +
370G LEU* 4.4 15.4 - - + +
372G LYS* 3.1 31.6 - - - +
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Residues in contact with ILE 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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5G ILE* 3.5 38.6 - - + -
7G GLY 3.4 3.6 - - - +
8G VAL* 4.3 15.5 - - + +
23G VAL* 4.6 4.5 - - + -
24G GLU* 1.3 75.1 - - - +
26G SER* 1.3 63.9 + - - +
32G THR* 3.2 7.3 - - - -
33G GLY 2.9 31.6 + - - +
60G LEU* 4.1 19.7 - - + -
96G ILE* 3.9 17.5 - - + +
99G ALA* 3.6 24.9 - - + -
100G LEU* 4.3 14.4 - - + +
103G ILE* 4.1 16.6 - - + +
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Residues in contact with SER 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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5G ILE* 3.5 6.9 - - - +
6G THR* 2.7 39.6 + - - -
7G GLY* 2.7 22.0 + - - +
9G ASN* 5.7 0.9 + - - -
24G GLU* 4.4 13.0 + - - +
25G ILE* 1.3 74.9 - - - +
27G THR* 1.3 59.3 + - - +
32G THR* 3.6 20.2 - - - +
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Residues in contact with THR 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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3G LEU* 4.0 20.8 - - + +
4G LYS 3.1 14.1 - - - +
5G ILE* 4.8 2.5 - - + -
6G THR* 3.6 6.7 + - - -
26G SER* 1.3 80.5 - - - +
28G ASP* 1.3 59.9 + - - +
29G GLU* 2.8 14.7 + - - +
30G GLY* 2.9 15.1 + - - -
31G ILE* 2.4 41.4 + - - +
32G THR* 4.7 0.6 - - - +
65G PRO* 4.4 10.1 - - + -
103G ILE* 3.7 23.1 - - + -
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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