Contacts of the helix formed by residues 1366 - 1377 (chain A) in PDB entry 6J8H
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 ASN1366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1364A VAL 4.1 2.1 - - - +
1365A PRO* 1.3 77.7 - - - +
1367A ARG* 1.3 67.2 + - - +
1368A SER* 3.2 4.0 - - - +
1369A GLU* 3.1 21.9 + - - +
1370A CYS* 3.0 21.0 + - - +
1382A TRP* 4.3 4.9 - - - -
1422A ASP* 3.5 14.6 - - + +
1423A LYS* 3.8 19.3 - - - +
1424A GLN 3.9 1.3 - - - +
1E NAG 1.5 68.3 + - - +
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Residues in contact with ARG1367 (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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766A HIS* 5.8 5.5 - - - -
1348A TYR* 5.2 4.4 - - - -
1366A ASN* 1.3 72.1 - - - +
1368A SER* 1.3 65.3 + - - +
1370A CYS* 3.1 10.9 + - - +
1371A PHE* 3.2 49.0 + - + -
1382A TRP* 3.3 61.2 - - + +
1422A ASP* 2.9 43.6 + - - +
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Residues in contact with SER1368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1366A ASN* 3.2 6.4 - - - +
1367A ARG* 1.3 85.7 - - - +
1369A GLU* 1.3 62.4 + - - +
1371A PHE* 3.5 12.5 + - - +
1372A ALA* 3.6 9.5 + - - +
1422A ASP* 5.3 1.7 + - - -
1E NAG 4.0 29.2 - - - +
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Residues in contact with GLU1369 (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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1364A VAL* 3.9 21.0 - - - +
1365A PRO* 3.9 9.4 - - + -
1366A ASN* 3.1 20.5 + - - +
1368A SER* 1.3 80.5 + - - +
1370A CYS* 1.3 63.1 + - - +
1372A ALA* 3.3 21.4 + - - +
1373A LEU* 3.5 8.3 + - - +
1E NAG 3.3 39.4 - - - +
2E NAG 4.2 11.6 + - - +
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Residues in contact with CYS1370 (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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1350A CYS* 1.9 43.1 - - - -
1364A VAL* 3.1 17.0 - - + +
1366A ASN 3.0 9.4 + - - +
1367A ARG 3.1 9.4 + - - +
1369A GLU* 1.3 77.9 - - - +
1371A PHE* 1.3 62.4 + - - +
1373A LEU* 3.2 13.9 + - - +
1374A MET* 3.3 20.8 + - - +
1380A VAL* 4.2 0.8 - - - +
1382A TRP* 3.7 32.8 - - + -
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Residues in contact with PHE1371 (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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1367A ARG* 3.2 57.7 + - + +
1368A SER* 3.8 9.6 - - - +
1369A GLU 3.3 0.4 - - - -
1370A CYS* 1.3 75.5 - - - +
1372A ALA* 1.3 66.3 + - - +
1374A MET* 3.1 42.7 + - + +
1375A ASN* 3.2 12.0 + - - +
1382A TRP* 3.9 17.5 - + + -
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Residues in contact with ALA1372 (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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1368A SER 3.6 7.7 + - - +
1369A GLU* 3.3 22.1 + - - +
1370A CYS 3.3 0.6 - - - -
1371A PHE* 1.3 77.6 - - - +
1373A LEU* 1.3 61.9 + - - +
1375A ASN* 3.3 15.8 + - - +
1376A VAL* 3.3 18.2 + - - +
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Residues in contact with LEU1373 (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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1359A PHE* 3.8 37.0 - - + -
1363A GLN* 4.4 13.2 - - - +
1364A VAL* 4.7 13.2 - - + -
1369A GLU 3.5 5.8 + - - +
1370A CYS 3.2 12.7 + - - +
1371A PHE 3.1 0.2 - - - -
1372A ALA* 1.3 80.6 - - - +
1374A MET* 1.3 50.5 + - - +
1376A VAL* 3.2 11.6 + - + +
1377A SER* 2.5 52.8 + - - +
1380A VAL* 3.9 13.5 - - + -
1D NAG 5.6 3.6 - - + -
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Residues in contact with MET1374 (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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1370A CYS* 3.3 12.0 + - - +
1371A PHE* 3.1 51.2 + - + +
1373A LEU* 1.3 78.6 - - - +
1375A ASN* 1.3 63.1 + - - +
1377A SER 2.5 25.8 + - - +
1380A VAL* 2.9 35.9 - - + +
1381A ARG* 4.5 3.4 - - - -
1382A TRP* 3.9 22.7 - - + +
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Residues in contact with ASN1375 (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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1371A PHE 3.2 8.2 + - - +
1372A ALA* 3.6 11.9 - - - +
1373A LEU 3.2 0.2 - - - -
1374A MET* 1.3 80.1 - - - +
1376A VAL* 1.3 66.9 + - - +
2005A NAG 1.5 81.4 + - - +
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Residues in contact with VAL1376 (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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1372A ALA 3.3 16.4 - - - +
1373A LEU* 3.5 17.7 - - + +
1375A ASN* 1.3 89.3 - - - +
1377A SER* 1.3 62.6 + - - +
2005A NAG 5.3 2.5 - - - +
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Residues in contact with SER1377 (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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1373A LEU* 2.5 31.8 + - - +
1374A MET* 2.5 29.9 + - - +
1376A VAL* 1.3 77.5 + - - +
1378A GLN* 1.3 63.1 + - - +
1379A ASN 3.7 1.7 + - - -
1380A VAL* 3.9 10.1 - - - +
1D NAG 3.5 29.0 - - - +
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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