Contacts of the strand formed by residues 21 - 27 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ILE* 4.6 2.2 - - + -
11A TYR 3.3 8.7 - - - +
12A LEU* 3.7 10.1 - - + -
19A HIS 3.6 15.0 - - - +
20A PRO* 1.3 71.4 - - - +
22A LEU* 1.3 64.7 + - - +
36A GLU* 3.4 5.9 - - - +
37A ALA* 3.0 38.6 + - + +
39A ILE 4.2 9.6 - - - +
40A ALA* 5.2 0.4 - - - +
45A GLY* 3.5 21.8 - - - +
48A ALA* 4.1 8.7 - - + -
49A ALA* 3.9 23.3 - - + +
52A ILE* 3.8 24.6 - - + +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 3.5 7.8 - - - +
11A TYR* 2.8 41.4 + - + +
13A LEU* 3.9 26.5 - - + -
20A PRO* 4.2 7.6 - - + -
21A VAL* 1.3 75.4 - - - +
23A VAL* 1.3 63.8 + - - +
35A GLY 3.4 6.5 - - - +
36A GLU* 3.5 40.2 - - + +
52A ILE* 4.9 2.9 - - - -
311A SER* 3.8 7.2 - - - +
313A LEU* 4.3 6.5 - - + -
346A VAL* 4.0 23.3 - - + -
370A LEU* 4.6 13.5 - - + -
375A ILE* 4.0 15.7 - - + -
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.3 30.5 - - + -
9A ASN 3.2 6.1 - - - +
11A TYR* 4.9 1.3 - - - -
22A LEU* 1.3 76.3 - - - +
24A GLU* 1.3 66.4 + - - +
25A ILE* 4.4 5.2 - - + -
34A ALA* 3.4 4.7 - - - +
35A GLY 2.9 41.0 + - - +
52A ILE* 3.7 24.7 - - + -
95A ALA* 3.5 36.1 - - + +
96A ILE* 4.2 6.5 - - + +
99A ALA* 4.4 6.7 - - + -
313A LEU* 5.2 0.3 - - - +
370A LEU* 5.2 1.3 - - - +
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Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLY 3.9 0.5 - - - +
8A VAL* 3.4 3.5 - - - -
9A ASN* 2.9 42.9 + - + +
11A TYR* 3.4 28.2 + - + -
23A VAL* 1.3 75.7 - - - +
25A ILE* 1.3 65.2 + - - +
26A SER* 3.9 12.6 + - - +
32A THR* 4.5 21.8 + - - +
33A GLY 3.3 8.7 - - - +
34A ALA* 4.5 0.2 - - - +
370A LEU* 4.0 18.5 - - + +
372A LYS* 3.0 36.5 - - - +
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 3.7 37.9 - - + -
7A GLY 3.6 3.6 - - - +
8A VAL* 4.2 10.8 - - + -
23A VAL* 4.4 8.1 - - + -
24A GLU* 1.3 75.6 - - - +
26A SER* 1.3 64.0 + - - +
32A THR* 3.1 6.4 - - - -
33A GLY 2.7 38.9 + - - +
60A LEU* 4.4 7.6 - - + -
96A ILE* 3.9 24.5 - - + +
99A ALA* 3.4 26.7 - - + -
100A LEU* 4.2 15.9 - - + -
103A ILE* 3.9 16.2 - - + +
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Residues in contact with SER 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 3.5 6.6 - - - +
6A THR* 2.9 29.6 + - - -
7A GLY* 2.7 20.5 + - - +
9A ASN* 5.5 1.9 + - - -
24A GLU* 3.9 14.3 + - - +
25A ILE* 1.3 75.4 - - - +
27A THR* 1.3 63.9 + - - +
32A THR* 3.9 20.3 - - - +
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Residues in contact with THR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.2 13.1 - - + +
4A LYS 3.1 15.5 - - - +
5A ILE* 4.3 3.8 - - + -
6A THR* 3.4 9.4 + - - -
26A SER* 1.3 78.2 - - - +
28A ASP* 1.3 70.3 + - - +
29A GLU 3.8 3.8 + - - -
30A GLY* 3.2 12.6 + - - -
31A ILE* 2.7 43.1 + - - +
32A THR* 5.2 0.4 - - - +
65A PRO* 4.2 18.6 - - + -
103A ILE* 4.0 19.3 - - + -
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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