Contacts of the strand formed by residues 1457 - 1462 (chain A) in PDB entry 2REA
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 SER1457 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1447A ARG* 3.4 3.6 - - - -
1448A ILE* 2.7 45.3 + - - +
1450A ARG* 3.3 29.3 + - - +
1453A GLN* 4.0 11.3 + - - -
1455A GLU 3.8 0.8 + - - -
1456A PRO* 1.3 74.9 - - - +
1458A PHE* 1.3 65.8 + - - +
1459A VAL* 5.3 3.6 - - - -
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Residues in contact with PHE1458 (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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1430A PHE* 4.0 26.5 - + - -
1445A VAL* 4.3 21.5 - - + -
1446A VAL 3.2 5.8 - - - +
1447A ARG* 3.4 40.4 - - + -
1456A PRO* 3.8 34.3 - - + -
1457A SER* 1.3 75.2 - - - +
1459A VAL* 1.4 65.4 + - - +
1460A PHE* 3.9 17.5 - - + -
1534A SER* 3.9 10.6 - - - -
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Residues in contact with VAL1459 (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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1444A TYR 3.7 0.5 - - - +
1445A VAL* 3.5 4.0 - - - +
1446A VAL* 2.9 50.5 + - + +
1448A ILE* 3.8 22.9 - - + -
1450A ARG* 5.9 0.2 - - - +
1457A SER* 5.3 4.3 - - - -
1458A PHE* 1.4 79.4 - - - +
1460A PHE* 1.3 66.5 + - - +
1461A ARG* 3.7 30.5 - - + +
1530A PHE* 4.6 3.6 - - + +
1531A PHE* 3.8 17.5 - - + +
1533A GLY 4.5 2.5 - - - +
1534A SER* 3.5 21.3 - - - +
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Residues in contact with PHE1460 (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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1433A HIS* 4.9 9.6 - + - -
1443A ILE* 3.5 24.3 - - + +
1444A TYR 3.4 4.3 - - - -
1445A VAL* 3.7 38.6 - - + -
1458A PHE* 3.9 21.8 - - + -
1459A VAL* 1.3 78.3 - - - +
1461A ARG* 1.3 73.8 + - - +
1465A GLU* 3.9 2.8 - - - +
1534A SER* 2.7 28.4 + - - +
1535A HIS* 3.8 39.8 + + + +
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Residues in contact with ARG1461 (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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1443A ILE* 3.8 2.1 - - - +
1444A TYR* 2.9 34.9 + - - +
1446A VAL* 4.8 2.5 - - + -
1459A VAL* 3.7 22.4 - - + +
1460A PHE* 1.3 90.2 + - - +
1462A THR* 1.3 65.0 + - - +
1465A GLU* 2.8 29.4 - - - +
1466A PHE* 3.5 21.5 - - + -
1530A PHE* 2.6 57.6 + - + -
1532A HIS 3.0 25.7 + - - +
1533A GLY 3.1 9.5 + - - -
1534A SER 3.1 17.2 + - - -
1535A HIS 4.1 0.4 - - - -
1536A HIS* 3.2 23.8 + - - +
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Residues in contact with THR1462 (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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1435A LYS* 4.4 15.9 - - - +
1441A HIS* 5.1 11.6 - - + -
1442A TYR 3.6 17.9 - - - +
1443A ILE* 3.8 22.9 - - + -
1461A ARG* 1.3 74.5 - - - +
1463A PHE* 1.3 68.2 + - - +
1464A ASP* 2.9 18.5 + - - +
1465A GLU* 2.9 31.8 + - - +
1466A PHE* 3.1 13.4 + - - -
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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