Contacts of the strand formed by residues 18 - 26 (chain A) in PDB entry 4OIB
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 GLY 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.2 6.5 - - - -
15A GLU* 2.8 28.5 + - - -
16A ARG 3.1 0.4 - - - -
17A GLY* 1.3 81.0 - - - +
19A SER* 1.3 60.0 + - - -
58A ASP 2.9 20.4 + - - -
59A ILE* 3.1 14.5 + - - +
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Residues in contact with SER 19 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.4 14.7 - - - +
18A GLY* 1.3 75.9 - - - -
20A LEU* 1.3 68.4 + - - +
55A GLN* 4.5 9.7 + - - -
56A LEU 3.1 12.8 - - - -
57A VAL* 3.6 24.0 - - - -
59A ILE* 4.4 1.3 - - - -
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Residues in contact with LEU 20 (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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9A PRO* 5.0 4.9 - - + -
12A ALA* 3.6 29.2 - - + -
13A PHE 5.6 1.1 - - - +
14A VAL* 4.7 12.1 - - + -
19A SER* 1.3 77.2 - - - +
21A TRP* 1.3 80.3 + - - +
22A LEU* 4.2 13.6 - - + +
54A ARG 3.8 0.2 - - - +
55A GLN* 3.3 6.2 - - - +
56A LEU* 2.9 39.1 + - + +
59A ILE* 3.6 26.2 - - + -
83A ILE* 4.9 12.3 - - + -
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Residues in contact with TRP 21 (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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9A PRO* 4.0 8.1 - - - +
20A LEU* 1.3 86.1 - - - +
22A LEU* 1.3 75.5 + - - +
44A GLY* 4.6 1.1 - - - -
45A THR* 4.6 7.6 - - - -
46A GLN* 4.3 42.0 - - + -
53A ALA* 4.6 6.3 - - + -
54A ARG* 3.5 25.6 - - - -
55A GLN* 3.7 45.6 - - + +
1B NAG 5.3 5.4 - - + -
1C NAG 6.1 4.5 - - + -
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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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7A LEU* 4.5 14.4 - - + -
8A GLN 3.4 14.6 - - - +
9A PRO* 3.7 19.3 - - + +
20A LEU* 4.2 19.5 - - + +
21A TRP* 1.3 84.7 - - - +
23A ASN* 1.3 61.0 + - - +
24A CYS* 4.0 2.0 - - + +
36A LEU* 4.9 11.9 - - + -
52A LEU 4.0 0.7 - - - +
53A ALA* 3.2 6.4 - - - +
54A ARG* 2.9 40.6 + - + +
56A LEU* 4.6 21.1 - - + -
66A PRO* 4.6 14.4 - - + -
83A ILE* 4.6 20.4 - - + -
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Residues in contact with ASN 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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6A ASP* 4.3 1.0 - - - +
7A LEU* 4.0 0.2 - - - -
8A GLN* 2.9 46.9 + - + +
21A TRP 4.4 0.4 - - - -
22A LEU* 1.3 70.8 - - - +
24A CYS* 1.3 61.3 + - - +
25A SER* 4.1 6.2 + - - -
51A TRP* 3.2 19.9 - - - +
52A LEU 3.7 3.0 - - - +
53A ALA* 3.8 1.4 - - - +
1B NAG 1.4 78.9 + - - +
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Residues in contact with CYS 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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6A ASP 3.2 22.0 - - - -
7A LEU* 4.2 9.9 - - + +
22A LEU* 4.0 2.8 - - + +
23A ASN* 1.3 71.8 + - - +
25A SER* 1.3 61.5 + - - +
36A LEU* 5.9 0.9 - - + -
52A LEU* 2.9 37.1 + - + +
68A CYS* 2.0 61.0 - - + -
70A PHE* 3.2 12.2 - - - -
79A ALA* 4.8 2.0 - - - -
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Residues in contact with SER 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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4A TRP* 4.6 4.9 - - - -
6A ASP* 2.9 39.9 + - - +
23A ASN* 4.1 7.2 + - - -
24A CYS* 1.3 77.0 - - - +
26A THR* 1.3 65.0 + - - +
50A ARG* 3.4 12.1 - - - -
51A TRP* 3.4 17.4 - - - +
70A PHE* 3.5 8.8 - - - -
1B NAG 3.9 19.1 + - - -
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Residues in contact with THR 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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4A TRP* 2.3 39.9 + - - -
5A ALA* 4.3 0.9 - - - -
25A SER* 1.3 78.3 - - - +
27A ASN* 1.3 62.7 + - - +
28A CYS* 3.7 23.3 + - + +
31A PRO* 5.3 2.5 - - + -
50A ARG* 3.2 30.2 + - + +
70A PHE* 3.5 38.6 - - + -
77A LEU* 3.5 10.4 - - - +
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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