Contacts of the strand formed by residues 36 - 40 (chain A) in PDB entry 2OQ1
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 PHE 36 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.6 35.3 - + - +
26A LEU* 4.2 1.8 - - - -
34A GLY 3.5 12.3 - - - -
35A LEU* 1.3 76.6 - - - +
37A LEU* 1.3 67.3 + - - +
50A LEU* 3.9 22.9 - - + -
51A SER 3.1 12.8 - - - +
52A LEU* 3.9 7.2 - - + -
86A CYS* 4.0 14.8 - - + -
90A SER* 5.1 4.5 - - - -
100A LEU* 3.7 36.3 - - + -
102A LYS 3.4 7.6 + - - -
103A PRO* 3.5 32.9 - - + +
104A CYS* 2.7 35.2 + - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.6 6.1 - - - -
14A TYR* 3.7 35.9 - - + -
17A ILE* 4.5 1.8 - - + -
22A ALA* 3.7 37.9 - - + +
25A HIS* 4.1 11.4 - - + +
26A LEU* 4.0 14.1 - - + -
36A PHE* 1.3 84.4 - - - +
38A LEU* 1.3 73.3 + - - +
39A ARG* 4.3 8.7 - - + +
50A LEU* 3.8 5.5 - - - +
51A SER* 2.9 49.3 + - - -
104A CYS* 4.2 3.8 - - + +
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 4.3 15.0 - - + -
10A LEU* 5.6 2.2 - - + -
12A PHE* 2.9 26.9 + - + +
13A PHE* 3.3 11.5 - - + -
14A TYR* 2.8 26.7 + - - -
37A LEU* 1.3 78.2 - - - +
39A ARG* 1.3 61.2 + - - +
48A TYR* 4.0 12.1 - - + -
49A VAL 3.4 16.6 - - - +
50A LEU* 4.0 10.5 - - + -
63A ILE* 3.8 26.7 - - + -
82A PRO* 3.8 30.3 - - + -
86A CYS* 4.5 15.5 - - - -
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Residues in contact with ARG 39 (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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13A PHE* 4.0 7.2 - - - -
14A TYR* 4.9 0.2 - - + -
15A GLY 3.4 13.7 - - - +
17A ILE* 3.8 29.3 + - + +
18A SER 4.4 0.2 - - - -
19A ARG* 3.7 19.5 - - - +
22A ALA* 3.7 25.8 - - - +
37A LEU* 4.3 4.3 - - + -
38A LEU* 1.3 76.3 - - - +
40A GLN* 1.3 66.2 + - - +
42A LEU* 5.4 1.4 - - - +
48A TYR* 3.3 7.1 - - - +
49A VAL* 2.9 57.7 + - + +
51A SER* 4.2 6.1 - - - -
60A HIS* 3.1 27.5 + - - -
315B PTR 2.8 43.2 + - - -
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Residues in contact with GLN 40 (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 ASP* 4.3 15.1 + - - +
13A PHE* 3.9 11.4 - - + -
15A GLY 2.8 23.2 + - - +
16A SER* 3.4 25.4 + - - +
17A ILE 4.7 3.3 - - - +
39A ARG* 1.3 79.6 + - - +
41A CYS* 1.3 74.6 + - - +
42A LEU* 3.5 12.2 + - - +
46A GLY* 5.6 8.4 - - - +
47A GLY 3.9 11.2 - - - +
48A TYR* 4.1 5.6 - - + -
49A VAL* 4.6 1.5 - - - +
115A GLY* 4.0 10.7 + - - -
118A ASP* 3.0 33.5 + - - +
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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
------------------------------------------------------------
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