Contacts of the helix formed by residues 1440 - 1452 (chain A) in PDB entry 5M64
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 ASN1440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1438A ASN 3.5 3.4 + - - +
1439A MET* 1.3 74.0 - - - +
1441A LYS* 1.3 66.7 + - - +
1442A VAL* 3.5 22.5 - - + +
1443A GLN* 3.2 26.1 + - - +
1444A ARG* 3.0 23.2 + - - +
1464A ASP* 4.3 16.2 + - - -
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Residues in contact with LYS1441 (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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1440A ASN* 1.3 72.4 - - - +
1442A VAL* 1.3 66.9 + - + +
1444A ARG* 3.0 29.2 + - + +
1445A ASP* 3.1 26.8 + - + +
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Residues in contact with VAL1442 (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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1440A ASN* 3.5 27.8 - - + +
1441A LYS* 1.3 79.5 - - + +
1443A GLN* 1.3 60.3 + - + +
1445A ASP* 4.6 3.1 - - - +
1446A ARG* 3.1 27.9 + - - +
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Residues in contact with GLN1443 (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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1439A MET* 4.3 18.4 - - + +
1440A ASN* 3.2 24.3 + - - +
1441A LYS 3.1 0.4 - - - -
1442A VAL* 1.3 80.1 - - + +
1444A ARG* 1.3 61.5 + - - +
1445A ASP 3.6 0.2 - - - -
1446A ARG* 4.0 31.5 - - + +
1447A GLN* 2.9 32.3 + - + +
1460A TYR* 4.1 9.3 + - + +
1461A ASN* 3.2 20.4 + - - +
1462A PHE* 3.1 38.6 + - - +
1464A ASP* 5.5 5.0 - - - +
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Residues in contact with ARG1444 (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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1439A MET* 4.5 20.6 + - - +
1440A ASN 3.0 22.2 + - - +
1441A LYS* 3.0 26.7 + - + +
1443A GLN* 1.3 75.8 - - - +
1445A ASP* 1.3 60.6 + - - +
1447A GLN* 3.4 18.2 + - - +
1448A SER* 3.0 31.1 + - - -
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Residues in contact with ASP1445 (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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1441A LYS* 3.1 24.7 + - + +
1442A VAL* 4.7 3.1 - - - +
1444A ARG* 1.3 77.6 - - - +
1446A ARG* 1.3 58.7 + - - +
1448A SER* 3.5 8.6 + - - -
1449A ALA* 2.9 26.6 + - - +
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Residues in contact with ARG1446 (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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1314A GLN* 3.1 46.4 - - - +
1442A VAL 3.1 21.1 + - - +
1443A GLN* 4.0 24.3 - - - +
1444A ARG 3.2 0.6 - - - -
1445A ASP* 1.3 77.4 - - - +
1447A GLN* 1.3 60.3 + - - +
1449A ALA* 3.1 9.9 + - + +
1450A ILE* 3.0 36.3 + - + +
1460A TYR* 3.6 11.0 - - + -
1462A PHE* 3.3 29.7 - - - +
1464A ASP* 5.9 4.2 - - - +
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Residues in contact with GLN1447 (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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1439A MET* 5.6 4.9 - - - +
1443A GLN* 2.9 22.9 + - + +
1444A ARG* 3.6 21.6 + - - +
1445A ASP 3.3 0.2 - - - -
1446A ARG* 1.3 78.1 - - - +
1448A SER* 1.3 57.3 + - - +
1450A ILE* 3.0 10.1 + - - +
1451A ILE* 2.9 42.6 + - + +
1458A THR 3.4 21.2 + - - -
1459A LYS* 3.5 23.4 - - - +
1460A TYR* 3.6 32.1 + - + +
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Residues in contact with SER1448 (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 ARG 3.0 17.5 + - - -
1445A ASP* 3.7 11.3 - - - -
1447A GLN* 1.3 76.8 - - - +
1449A ALA* 1.3 57.1 + - - +
1451A ILE* 3.3 14.2 + - - +
1452A SER* 2.9 27.4 + - - -
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Residues in contact with ALA1449 (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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1445A ASP* 2.9 16.4 + - - +
1446A ARG* 3.1 14.1 + - + +
1448A SER* 1.3 76.5 - - - +
1450A ILE* 1.3 63.8 + - + +
1452A SER* 2.3 27.8 + - - +
1453A HIS* 3.8 5.9 + - - +
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Residues in contact with ILE1450 (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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1314A GLN* 5.5 0.7 - - - +
1318A SER* 3.7 36.1 - - - +
1319A ASN* 5.9 2.0 - - - +
1322A ILE* 5.4 6.5 - - + -
1446A ARG* 3.0 23.2 + - + +
1447A GLN* 3.0 10.9 + - - +
1449A ALA* 1.3 79.5 - - + +
1451A ILE* 1.3 64.2 + - + +
1453A HIS* 3.2 12.1 + - - +
1454A HIS* 3.5 25.0 + - + +
1457A ILE* 4.3 20.8 - - + +
1460A TYR* 4.7 30.1 - - + -
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Residues in contact with ILE1451 (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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1447A GLN* 2.9 27.7 + - + +
1448A SER* 3.3 15.5 + - - +
1450A ILE* 1.3 76.3 - - + +
1452A SER* 1.3 58.0 + - - +
1454A HIS 2.7 27.2 - - - +
1455A ARG* 5.9 0.7 - - - +
1457A ILE* 4.3 24.9 - - + +
1458A THR* 3.6 24.5 - - - +
1460A TYR* 6.5 0.2 - - + -
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Residues in contact with SER1452 (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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1448A SER 2.9 13.1 + - - -
1449A ALA* 2.3 32.9 + - - +
1451A ILE* 1.3 78.0 - - - +
1453A HIS* 1.3 56.2 + - - +
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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