Contacts of the helix formed by residues 1314 - 1323 (chain r) in PDB entry 6FF7
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 ASN1314 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1312r LEU* 3.0 12.4 - - + +
1313r ARG* 1.3 76.2 - - - +
1315r SER* 1.3 64.0 + - - +
1316r ALA* 4.6 3.4 - - + +
1317r PHE* 3.6 21.7 - - + +
1318r GLU* 3.1 19.9 + - - +
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Residues in contact with SER1315 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313r ARG 3.5 5.7 + - - -
1314r ASN* 1.3 67.0 - - - +
1316r ALA* 1.3 65.5 + - - +
1317r PHE 3.1 1.6 - - - -
1318r GLU* 3.0 10.5 + - - +
1319r SER* 3.0 23.7 + - - -
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Residues in contact with ALA1316 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1314r ASN* 3.4 3.3 - - + +
1315r SER* 1.3 78.7 - - - +
1317r PHE* 1.3 60.6 + - - +
1319r SER* 3.9 14.4 - - - -
1320r LEU* 4.4 4.5 + - - +
1400r ARG* 5.6 5.5 - - - +
1401r LEU* 6.1 2.3 - - + +
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Residues in contact with PHE1317 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1312r LEU* 4.8 11.4 - - + -
1314r ASN* 3.4 22.6 + - + +
1315r SER 3.1 0.6 - - - -
1316r ALA* 1.3 76.1 - - - +
1318r GLU* 1.3 66.6 + - - +
1319r SER 3.0 2.5 + - - -
1320r LEU* 3.2 17.1 + - - +
1321r TYR* 4.2 4.5 + - - +
1365r LEU* 5.6 10.5 - - + -
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Residues in contact with GLU1318 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309r VAL* 4.3 25.3 - - + +
1310r SER* 5.6 2.0 - - - -
1312r LEU* 5.2 3.5 - - + +
1314r ASN 3.1 10.9 + - - +
1315r SER* 3.0 13.4 + - - +
1317r PHE* 1.3 79.1 - - - +
1319r SER* 1.3 62.0 + - - +
1321r TYR* 3.1 5.2 + - - +
1322r GLN* 3.0 30.4 + - + +
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Residues in contact with SER1319 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1315r SER 3.0 14.1 + - - -
1316r ALA* 3.9 11.9 - - - -
1317r PHE 3.0 0.6 + - - -
1318r GLU* 1.3 76.8 - - - +
1320r LEU* 1.3 57.4 + - - +
1321r TYR 3.2 4.4 + - - -
1322r GLN* 4.4 6.1 + - - +
1323r ASP* 4.7 9.9 + - - +
1400r ARG* 6.4 2.0 - - - -
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Residues in contact with LEU1320 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1316r ALA 4.4 3.8 + - - +
1317r PHE* 3.2 10.7 + - - +
1318r GLU 3.2 0.2 + - - -
1319r SER* 1.3 75.3 - - - +
1321r TYR* 1.3 57.6 + - - +
1324r LYS* 5.2 4.1 - - - +
1396r LYS* 4.6 25.4 - - + +
1400r ARG* 5.3 9.2 - - + -
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Residues in contact with TYR1321 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309r VAL* 4.6 13.5 - - + -
1317r PHE 4.8 3.4 - - - +
1318r GLU* 3.1 7.1 + - - +
1319r SER 3.2 0.6 - - - -
1320r LEU* 1.3 82.1 - - - +
1322r GLN* 1.3 56.4 + - - +
1323r ASP 3.2 2.2 - - - -
1324r LYS* 2.7 31.0 + - - +
1325r PHE 3.2 15.3 + - - +
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Residues in contact with GLN1322 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309r VAL* 4.5 13.4 - - + +
1318r GLU* 3.0 21.2 + - + +
1319r SER* 4.4 3.8 + - - +
1321r TYR* 1.3 76.6 - - - +
1323r ASP* 1.3 58.1 + - - +
1324r LYS 3.2 1.3 + - - -
1325r PHE 3.9 16.8 + - - +
1326r PRO* 4.7 3.2 - - - +
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Residues in contact with ASP1323 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1319r SER 4.7 9.7 + - - +
1321r TYR 3.0 1.2 + - - -
1322r GLN* 1.3 76.5 - - - +
1324r LYS* 1.3 59.2 + - - +
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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