Contacts of the strand formed by residues 70 - 75 (chain B) in PDB entry 2OOR
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 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 5.1 3.8 - - + -
2B LYS 3.1 4.1 + - - +
3B ILE* 3.3 30.7 - - + -
4B ALA 2.9 24.2 + - - -
31B PHE* 4.1 21.8 - - + -
68B ALA* 3.6 3.1 - - - +
69B ASP* 1.3 84.2 - - + +
71B VAL* 1.3 69.2 + - - +
72B TRP* 3.8 16.2 - - + +
95B VAL* 3.4 18.2 - - + +
97B MET* 4.7 6.5 - - + -
343B LEU* 4.9 2.7 - - + -
354B LEU* 4.0 24.7 - - + -
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Residues in contact with VAL 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 ALA* 3.4 9.0 - - + +
6B PRO* 4.6 6.3 - - + -
65B LEU* 4.4 27.4 - - + +
68B ALA* 4.2 18.4 - - + +
70B VAL* 1.3 79.8 - - - +
72B TRP* 1.3 74.4 + - - +
73B LYS* 4.8 4.5 - - + -
90B ILE* 4.2 24.9 - - + -
91B LYS 5.6 0.2 - - - +
94B ALA* 5.1 0.7 - - + -
95B VAL 2.7 15.4 + - - +
96B LEU* 3.5 24.0 - - + +
97B MET 3.0 26.2 + - - -
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Residues in contact with TRP 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 ILE* 3.6 26.0 - - + +
4B ALA 3.0 5.9 + - - -
5B ILE* 3.5 19.7 - - + +
6B PRO* 3.2 19.1 - - - +
17B ALA* 3.4 22.0 - - - +
18B ILE* 4.4 6.3 - - + -
22B VAL* 3.6 21.5 - - + -
26B LEU* 3.9 18.6 - - + -
70B VAL* 3.8 6.6 - - + +
71B VAL* 1.3 81.8 - - - +
73B LYS* 1.3 63.9 + - - +
97B MET* 3.5 33.3 - - + -
336B ALA 3.8 9.0 - - - -
339B LEU* 3.5 37.2 - - + -
340B LEU* 3.4 25.8 - - + -
343B LEU* 3.8 17.2 - - + +
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Residues in contact with LYS 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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5B ILE* 5.3 0.2 - - - -
6B PRO* 4.1 23.8 - - + -
7B LYS 5.4 0.7 - - - -
8B GLU* 3.4 27.8 + - - +
9B ARG 5.7 1.0 - - - +
10B ARG* 6.1 0.6 - - - +
17B ALA* 3.5 12.9 - - - +
65B LEU* 6.3 1.1 - - + -
71B VAL* 4.3 4.2 - - + -
72B TRP* 1.3 75.8 - - - +
74B VAL* 1.3 58.5 + - - +
75B GLN 2.7 29.5 + - - +
76B ARG 4.0 5.1 + - - -
77B PRO* 4.2 24.7 - - + -
86B GLU* 4.2 16.8 + - - -
90B ILE* 5.7 1.1 - - + -
96B LEU* 4.1 18.2 - - + -
97B MET 3.3 4.2 + - - +
98B CYS* 3.0 32.3 - - + +
335B PHE* 3.8 6.6 - - - -
339B LEU* 4.4 0.2 - - - +
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Residues in contact with VAL 74 (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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8B GLU* 3.1 23.6 + - + +
13B GLU* 3.9 6.5 - - - +
15B ARG* 3.5 42.6 - - + +
16B VAL* 3.7 35.9 - - - +
17B ALA* 3.8 2.0 - - + +
73B LYS* 1.3 70.6 - - - +
75B GLN* 1.3 70.3 + - + +
99B HIS* 2.9 36.6 + - + +
335B PHE* 3.7 21.9 - - + -
700B GOL 5.6 0.4 - - - -
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Residues in contact with GLN 75 (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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8B GLU* 3.1 14.3 + - - +
10B ARG* 3.8 31.0 + - - +
11B PRO 5.7 1.2 + - - -
13B GLU* 2.6 39.2 + - - +
73B LYS* 2.7 30.2 + - - +
74B VAL* 1.3 83.0 - - + +
76B ARG* 1.3 67.5 + - - +
98B CYS* 4.5 0.9 - - - -
99B HIS* 3.6 4.7 - - - -
322B ASN* 3.6 12.1 - - - +
700B GOL 3.6 34.5 + - - +
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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