Contacts of the strand formed by residues 66 - 73 (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 ILE 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 3.6 28.5 - - + -
29B GLY 3.7 3.8 - - - +
30B ARG* 3.7 42.2 - - + +
64B SER 3.6 2.6 + - - +
65B GLY* 1.3 70.3 - - - -
67B VAL* 1.3 62.6 + - - +
86B GLN* 3.6 3.5 - - - -
87B PHE* 2.9 55.4 + - + +
89B GLU* 3.5 21.6 + - - +
94B PHE* 4.0 26.5 - - + +
96B LEU* 4.2 13.9 - - + -
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Residues in contact with VAL 67 (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 3.7 2.4 - - - +
28B VAL* 3.6 2.4 - - - +
29B GLY 3.0 31.5 + - - +
31B LEU* 4.3 14.1 - - + -
41B PHE* 4.9 7.0 - - + -
43B LEU* 4.1 12.9 - - + +
63B ILE* 4.7 11.2 - - + -
64B SER 3.9 10.3 - - - +
65B GLY 3.6 11.2 - - - +
66B ILE* 1.3 82.9 - - - +
68B GLU* 1.3 62.7 + - - +
69B VAL* 3.9 18.2 - - + -
84B TYR* 4.0 24.0 - - + -
85B VAL 3.6 9.4 - - - +
86B GLN* 4.0 9.6 - - + +
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Residues in contact with GLU 68 (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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79A ILE* 5.7 1.4 - - - +
81A ARG* 5.8 1.7 + - - -
97A MET* 5.0 4.0 - - - +
125A TYR* 2.6 28.9 + - - -
11B ARG* 2.6 36.6 + - - -
26B CYS* 3.5 23.3 - - - -
27B PHE 3.7 2.5 - - - -
28B VAL* 3.7 12.5 - - + +
67B VAL* 1.3 71.8 - - - +
69B VAL* 1.3 61.1 + - - +
70B VAL* 5.3 4.3 - - + +
84B TYR* 3.0 4.2 - - - -
85B VAL* 2.7 51.3 + - + +
87B PHE* 3.6 21.8 - - + -
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Residues in contact with VAL 69 (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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25B VAL* 3.9 0.5 - - - +
26B CYS* 3.3 3.6 - - - -
27B PHE* 2.8 43.3 + - + +
41B PHE* 3.8 28.9 - - + -
43B LEU* 3.8 18.6 - - + -
53B ILE* 3.7 28.0 - - + -
67B VAL* 4.1 3.4 - - + -
68B GLU* 1.3 74.5 - - - +
70B VAL* 1.3 75.1 + - - +
79B ILE* 4.2 10.4 - - + +
81B CYS* 4.0 8.3 - - + -
83B SER 3.6 2.9 - - - -
84B TYR* 3.9 13.9 - - + -
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Residues in contact with VAL 70 (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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81A ARG* 4.6 11.0 - - - +
97A MET* 3.4 29.2 - - + -
4B MET* 4.5 4.5 - - + +
5B MET* 6.0 3.1 - - + -
9B ARG* 3.6 29.6 - - + +
25B VAL 3.4 5.6 - - - +
26B CYS* 4.6 5.4 - - + -
68B GLU* 5.3 5.4 - - + +
69B VAL* 1.3 79.7 - - - +
71B GLY* 1.3 56.2 + - - +
81B CYS* 3.6 3.5 - - - -
82B THR* 2.8 48.5 + - + -
83B SER* 2.6 26.5 + - - +
84B TYR* 5.8 0.2 - - - -
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Residues in contact with GLY 71 (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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4B MET* 3.9 16.2 - - - -
24B PRO* 3.6 0.9 - - - +
25B VAL* 2.7 43.7 + - - +
69B VAL 4.2 0.2 - - - -
70B VAL* 1.3 75.9 - - - +
72B ARG* 1.3 58.2 + - - -
79B ILE* 3.7 11.0 - - - +
80B LEU 3.0 14.6 - - - -
82B THR 4.0 3.4 - - - -
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Residues in contact with ARG 72 (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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3B ASP 5.8 0.6 + - - -
4B MET* 3.7 32.2 - - + +
7B LEU* 4.8 8.3 - - - +
22B ASP* 2.9 52.1 + - - +
23B LYS 3.5 4.0 - - - +
24B PRO* 4.1 19.2 - - - +
71B GLY* 1.3 74.3 - - - -
73B VAL* 1.3 68.6 + - - +
74B THR* 3.4 1.2 + - - -
79B ILE* 3.5 2.5 - - - -
80B LEU* 2.9 40.1 + - + +
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Residues in contact with VAL 73 (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* 4.4 1.3 - - + -
17B LEU* 3.6 35.0 - - + +
20B PHE* 2.2 43.1 - - + +
21B ILE* 3.3 3.4 - - + -
22B ASP* 2.8 49.5 + - - +
23B LYS 3.1 10.9 + - - +
25B VAL* 3.7 25.1 - - + -
71B GLY 4.0 0.4 + - - -
72B ARG* 1.3 75.2 - - - +
74B THR* 1.3 61.5 + - - +
77B ALA* 5.4 1.6 - - - -
78B THR 3.2 6.1 - - - +
79B ILE* 4.1 1.6 - - + +
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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