Contacts of the helix formed by residues 1309 - 1320 (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 SER1309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1299A ASN* 5.8 1.3 - - - -
1302A TYR* 4.8 9.4 - - - -
1303A SER* 4.4 7.9 - - - -
1308A VAL* 1.3 75.9 - - - +
1310A LYS* 1.3 66.0 + - - +
1311A GLU* 2.7 25.2 + - - -
1312A GLU* 2.4 26.9 + - - -
1313A LEU* 2.9 31.3 + - - +
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Residues in contact with LYS1310 (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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1299A ASN* 5.5 3.4 - - - -
1302A TYR* 3.3 26.9 - - + +
1309A SER* 1.3 80.0 - - - +
1311A GLU* 1.3 59.5 + - - +
1313A LEU* 4.7 2.5 - - + -
1314A GLN* 3.1 37.8 + - + +
1462A PHE* 3.6 25.8 - - + -
1463A ASP 3.7 4.0 + - - -
1464A ASP* 2.7 38.1 + - - +
1465A GLU 4.6 0.6 - - - -
1466A SER 4.3 2.4 - - - +
1467A GLY* 3.8 18.0 - - - +
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Residues in contact with GLU1311 (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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1309A SER* 2.7 30.9 + - - -
1310A LYS* 1.3 75.4 + - - +
1312A GLU* 1.3 71.4 + - - +
1315A ASN* 2.3 38.2 + - - +
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Residues in contact with GLU1312 (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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1307A ASP 4.2 4.0 - - - +
1308A VAL* 3.2 14.6 - - + -
1309A SER* 2.4 43.9 + - - +
1311A GLU* 1.3 100.5 - - - +
1313A LEU* 1.3 67.7 + - - +
1314A GLN 3.4 1.1 - - - -
1315A ASN* 3.5 4.5 + - - +
1316A VAL* 3.1 25.6 + - - +
1498A ILE* 3.3 22.1 - - + +
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Residues in contact with LEU1313 (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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1263A LEU* 4.9 11.4 - - + -
1266A VAL* 4.3 24.7 - - + -
1296A PHE* 4.3 18.6 - - + -
1302A TYR* 4.6 18.2 - - + -
1308A VAL* 4.6 18.6 - - + -
1309A SER 2.9 21.4 + - - +
1310A LYS* 4.7 1.3 - - + -
1312A GLU* 1.3 79.7 - - + +
1314A GLN* 1.3 58.5 + - - +
1316A VAL* 3.2 8.8 - - - +
1317A ILE* 3.1 35.5 + - + +
1462A PHE* 4.0 29.6 - - + -
1498A ILE* 4.1 5.6 - - + -
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Residues in contact with GLN1314 (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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1310A LYS* 3.1 21.5 + - + +
1313A LEU* 1.3 77.0 - - - +
1315A ASN* 1.3 56.9 + - - +
1317A ILE* 3.3 5.1 - - - +
1318A SER* 2.7 46.5 + - - +
1446A ARG* 3.1 33.1 - - - +
1450A ILE* 5.5 0.8 - - - +
1460A TYR* 2.4 39.5 + - - -
1462A PHE* 3.2 34.5 - - + -
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Residues in contact with ASN1315 (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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1310A LYS 4.3 0.6 + - - -
1311A GLU* 2.3 32.9 + - - +
1312A GLU* 3.5 5.2 + - - +
1313A LEU 3.4 0.4 - - - -
1314A GLN* 1.3 83.0 - - - +
1316A VAL* 1.3 57.2 + - - +
1318A SER* 3.5 5.9 + - - -
1319A ASN* 2.9 43.7 + - - +
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Residues in contact with VAL1316 (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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1263A LEU* 4.1 17.9 - - + -
1312A GLU 3.1 16.2 + - - +
1313A LEU* 3.2 13.9 - - - +
1315A ASN* 1.3 76.8 - - - +
1317A ILE* 1.3 62.7 + - - +
1320A GLN* 3.0 38.3 + - + +
1321A PHE* 3.0 9.8 + - - +
1496A SER* 3.7 14.4 - - - +
1497A ILE 3.2 30.5 - - - +
1498A ILE* 3.7 22.0 - - + +
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Residues in contact with ILE1317 (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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1263A LEU* 5.1 13.5 - - + -
1294A MET* 5.9 2.9 - - + -
1296A PHE* 4.0 27.1 - - + -
1313A LEU* 3.1 23.3 + - + +
1314A GLN* 3.3 24.2 - - - +
1316A VAL* 1.3 79.7 - - + +
1318A SER* 1.3 58.6 + - - +
1321A PHE* 3.7 31.7 - - + +
1322A ILE* 3.3 21.7 - - - +
1460A TYR* 3.4 21.0 + - + +
1470A CYS* 4.1 17.5 - - - -
1472A PHE* 5.1 7.0 - - + -
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Residues in contact with SER1318 (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* 2.7 34.6 + - - +
1315A ASN* 3.2 13.9 + - - -
1317A ILE* 1.3 80.9 - - - +
1319A ASN* 1.3 68.9 + - - +
1320A GLN 3.8 0.2 - - - -
1322A ILE* 4.2 17.4 - - - +
1450A ILE* 3.7 31.7 - - - +
1454A HIS* 4.2 10.9 - - - -
1460A TYR* 4.5 4.0 - - - -
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Residues in contact with ASN1319 (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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1315A ASN* 2.9 32.5 + - - +
1318A SER* 1.3 90.7 + - - +
1320A GLN* 1.3 71.4 + - + +
1323A HIS* 3.2 22.7 - - - +
1450A ILE* 5.9 1.6 - - - +
1453A HIS* 5.7 9.9 + - - -
1454A HIS* 5.8 0.7 - - - -
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Residues in contact with GLN1320 (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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1316A VAL* 3.0 29.0 + - + +
1319A ASN* 1.3 92.1 + - + +
1321A PHE* 1.3 62.1 + - - +
1322A ILE 3.4 1.1 - - - -
1323A HIS* 3.8 6.3 + - - +
1324A LEU* 2.9 48.9 + - + +
1496A SER* 3.8 16.1 - - - +
1497A ILE* 4.8 10.0 - - + +
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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