Contacts of the strand formed by residues 24 - 34 (chain B) in PDB entry 2PQA
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 PRO 24 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B MET* 3.9 19.3 - - + -
7B LEU* 3.9 23.3 - - + -
8B PRO 3.8 13.6 - - - +
9B ARG* 3.7 20.9 - - + -
10B SER* 3.4 17.0 + - - -
23B LYS* 1.3 90.3 - - + +
25B VAL* 1.3 63.3 + - - +
71B GLY 3.6 6.1 - - - +
72B ARG* 4.1 14.8 - - - +
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Residues in contact with VAL 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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9B ARG* 4.0 5.6 - - - +
10B SER* 3.4 11.7 - - - +
12B ILE* 3.8 32.3 - - + -
20B PHE* 4.2 13.7 - - + -
23B LYS 4.0 3.1 - - - +
24B PRO* 1.3 80.3 - - - +
26B CYS* 1.3 62.3 + - - +
69B VAL 3.9 0.4 - - - +
70B VAL* 3.4 6.9 - - - +
71B GLY 2.7 49.4 + - - +
73B VAL* 3.7 29.2 - - + +
79B ILE* 4.0 21.3 - - + -
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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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97A MET* 3.8 32.5 - - + -
9B ARG* 4.2 2.9 - - - +
10B SER 2.8 12.0 + - - +
11B ARG* 3.4 27.2 - - + +
12B ILE* 3.3 22.7 + - - +
25B VAL* 1.3 73.8 - - - +
27B PHE* 1.3 59.2 + - - +
28B VAL* 4.2 1.4 + - - -
68B GLU* 3.3 41.7 - - - -
69B VAL 3.3 5.8 - - - +
70B VAL* 4.6 1.3 - - - -
99B TYR* 4.8 1.2 + - - -
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Residues in contact with PHE 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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12B ILE* 4.0 22.0 - - + +
13B ASN* 4.0 5.8 - - - -
14B ALA* 3.6 30.3 - - + -
17B LEU* 4.8 2.5 - - + -
25B VAL* 4.2 0.6 - - + -
26B CYS* 1.3 73.2 - - - +
28B VAL* 1.3 76.0 + - - +
29B GLY* 3.8 1.6 - - - -
43B LEU* 3.5 47.1 - - + -
45B ASP* 4.1 17.5 - - + -
51B GLY* 4.3 15.5 - - - -
53B ILE* 4.7 3.1 - - + -
67B VAL 3.7 1.9 - - - +
68B GLU* 3.7 0.7 - - - -
69B VAL* 2.8 41.4 + - + +
79B ILE* 3.7 31.9 - - + -
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Residues in contact with VAL 28 (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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11B ARG* 3.6 14.6 - - - +
12B ILE 4.5 5.5 + - - +
26B CYS* 4.2 1.4 + - - -
27B PHE* 1.3 82.6 - - - +
29B GLY* 1.3 59.8 + - - +
45B ASP* 4.0 13.5 - - - +
66B ILE* 3.6 26.9 - - + -
67B VAL 3.6 5.2 - - - +
68B GLU* 3.7 20.6 - - + +
87B PHE* 4.4 13.9 - - + -
94B PHE* 4.5 2.0 - - + -
96B LEU* 4.1 16.0 - - + +
99B TYR* 3.3 44.3 - - + +
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Residues in contact with GLY 29 (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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27B PHE* 3.8 10.2 - - - -
28B VAL* 1.3 76.2 - - - +
30B ARG* 1.3 61.6 + - - -
31B LEU 3.9 0.3 + - - -
43B LEU* 4.0 7.9 - - - +
44B SER 2.9 16.6 - - - -
66B ILE* 3.7 4.2 - - - -
67B VAL* 3.0 33.1 + - - +
96B LEU* 4.3 9.2 - - - -
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Residues in contact with ARG 30 (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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29B GLY* 1.3 72.4 - - - -
31B LEU* 1.3 71.5 + - - +
32B GLU* 3.2 16.3 + - - +
43B LEU* 3.2 2.2 - - - -
44B SER* 2.6 48.0 + - - +
65B GLY* 3.7 22.5 - - - +
66B ILE* 3.7 29.6 - - + +
89B GLU* 4.7 7.7 + - - -
94B PHE 4.6 10.7 + - - -
96B LEU* 4.0 14.2 - - + +
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Residues in contact with LEU 31 (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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30B ARG* 1.3 75.3 - - - +
32B GLU* 1.3 63.4 + - - +
33B LYS* 4.0 5.6 - - - +
34B ILE* 3.8 24.0 - - + -
41B PHE* 3.7 22.2 - - + -
42B ILE 3.9 4.3 - - - +
43B LEU* 3.7 11.1 - - + +
63B ILE* 3.1 52.3 - - + +
64B SER* 3.9 14.6 - - - -
65B GLY 3.1 20.5 + - - +
67B VAL* 4.3 3.8 - - + -
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Residues in contact with GLU 32 (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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30B ARG* 3.5 29.7 - - - +
31B LEU* 1.3 77.4 - - - +
33B LYS* 1.3 65.8 + - + +
42B ILE* 2.9 21.2 + - + +
43B LEU 4.4 0.4 - - - -
44B SER* 3.0 34.6 + - - +
50B ASN* 4.2 9.4 - - - +
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Residues in contact with LYS 33 (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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31B LEU* 3.7 4.3 - - - +
32B GLU* 1.3 83.4 - - + +
34B ILE* 1.3 75.8 + - - +
35B HIS 4.3 0.4 - - - +
40B MET* 5.3 0.4 - - - +
41B PHE* 3.0 6.2 - - - +
42B ILE* 2.8 53.2 + - + +
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Residues in contact with ILE 34 (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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31B LEU* 3.8 25.1 - - + -
33B LYS* 1.3 90.3 - - - +
35B HIS* 1.3 77.3 + - - +
36B PRO* 3.5 4.7 - - - +
38B GLY* 4.3 5.6 - - - -
40B MET 4.1 5.4 - - - +
41B PHE* 3.9 6.3 - - + -
59B LEU* 3.9 21.3 - - + -
61B GLU 5.8 0.4 - - - +
62B GLU* 5.8 1.6 - - - +
63B ILE* 3.7 32.5 - - + +
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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