Contacts of the strand formed by residues 1490 - 1494 (chain A) in PDB entry 2IG0
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 ARG1490 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1488A GLY 3.5 2.5 + - - +
1489A LEU* 1.3 73.3 - - - +
1491A VAL* 1.3 66.1 + - - +
1503A SER* 4.5 3.8 - - - -
1504A GLY 3.4 20.8 + - - +
1505A LYS* 3.5 31.7 - - + +
1520A ASP* 3.0 43.1 + - - -
1534A LEU* 3.9 11.4 - - - +
1535A CYS 4.5 1.9 + - - -
1536A ASP* 3.3 47.3 + - + +
1583A ARG* 3.6 31.3 - - - +
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Residues in contact with VAL1491 (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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1489A LEU* 3.9 8.3 - - + +
1490A ARG* 1.3 82.0 + - - +
1492A VAL* 1.3 69.1 + - - +
1493A ALA* 4.4 2.2 - - + +
1503A SER* 3.3 5.0 - - - -
1504A GLY 2.9 34.9 + - - +
1506A ILE* 4.1 16.2 - - + -
1517A LEU* 3.7 31.0 - - + -
1532A ILE* 3.6 25.4 - - + -
1533A LEU 3.2 15.5 - - - +
1534A LEU* 3.9 18.2 - - + -
1535A CYS 4.6 3.1 - - - +
1602A LEU* 4.8 0.9 - - + -
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Residues in contact with VAL1492 (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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1491A VAL* 1.3 81.5 - - - +
1493A ALA* 1.3 58.4 + - - +
1501A PHE* 3.8 25.1 - - + +
1502A TYR* 3.2 20.6 - - - -
1503A SER* 4.1 7.4 - - - +
1533A LEU* 2.8 41.6 + - + +
1535A CYS* 3.6 24.9 - - - +
1538A ILE* 3.9 24.9 - - + -
1586A VAL 5.8 0.9 - - - +
1587A ILE* 5.7 1.1 - - - -
1588A LEU* 4.0 14.8 - - + -
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Residues in contact with ALA1493 (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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1491A VAL* 4.4 2.0 - - + +
1492A VAL* 1.3 75.1 - - - +
1494A LYS* 1.3 65.7 + - - +
1495A TRP 3.5 0.3 + - - -
1501A PHE* 3.1 4.8 - - - -
1502A TYR 2.8 28.0 + - - +
1517A LEU* 3.4 37.9 - - + -
1519A PHE* 3.5 14.6 - - + -
1527A VAL* 4.4 3.1 - - + -
1531A ASP 3.5 8.1 - - - +
1532A ILE* 4.1 11.9 - - + -
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Residues in contact with LYS1494 (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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1493A ALA* 1.3 74.1 - - - +
1495A TRP* 1.3 67.4 + - - +
1496A SER* 3.8 13.6 + - - +
1499A GLY* 3.8 25.4 - - - +
1500A TYR 3.4 5.6 - - - +
1501A PHE* 3.6 19.0 - - + -
1519A PHE* 4.2 2.4 - - - -
1525A CYS* 5.0 0.9 - - - -
1527A VAL* 3.8 22.6 - - - +
1530A LYS* 4.6 6.7 - - - +
1531A ASP* 3.0 50.0 + - + +
1590A LEU* 3.5 29.1 - - - +
1594A ASN* 5.0 2.5 + - - -
1597A ARG* 5.9 0.2 - - - +
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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