Contacts of the helix formed by residues 1314 - 1323 (chain D) in PDB entry 6AH0
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1312D LEU* 3.0 12.7 - - - +
1313D ARG* 1.3 75.2 - - - +
1315D SER* 1.3 63.9 + - - +
1316D ALA 3.4 2.9 - - - +
1317D PHE* 3.4 6.2 + - - +
1318D GLU* 3.1 17.8 + - - -
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Residues in contact with SER1315 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1313D ARG 3.5 5.4 + - - -
1314D ASN* 1.3 68.0 - - - +
1316D ALA* 1.3 65.2 + - - +
1317D PHE 3.1 2.0 - - - -
1318D GLU* 3.0 4.3 + - - +
1319D SER* 3.0 21.3 + - - -
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Residues in contact with ALA1316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1314D ASN 3.4 0.4 - - - -
1315D SER* 1.3 75.3 - - - +
1317D PHE* 1.3 60.4 + - - +
1319D SER* 3.9 7.8 + - - +
1320D LEU 4.4 2.3 + - - -
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Residues in contact with PHE1317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1314D ASN* 3.4 9.2 + - - +
1315D SER 3.1 0.6 - - - -
1316D ALA* 1.3 75.6 - - - +
1318D GLU* 1.3 66.6 - - - +
1319D SER 3.0 2.8 + - - -
1320D LEU* 3.2 13.2 + - - -
1321D TYR* 4.2 2.1 + - - -
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Residues in contact with GLU1318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309D VAL* 4.6 16.4 - - - +
1312D LEU 5.9 0.2 - - - -
1314D ASN 3.1 11.9 + - - -
1315D SER* 3.0 9.1 + - - +
1317D PHE* 1.3 73.9 - - - +
1319D SER* 1.3 61.4 + - - +
1321D TYR* 3.1 3.5 + - - +
1322D GLN* 3.0 25.3 + - - -
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Residues in contact with SER1319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1315D SER 3.0 13.3 + - - -
1316D ALA* 3.9 4.7 + - - +
1317D PHE 3.0 1.6 + - - -
1318D GLU* 1.3 76.6 - - - +
1320D LEU* 1.3 56.3 + - - +
1321D TYR 3.2 3.7 + - - -
1322D GLN* 4.4 3.3 + - - +
1323D ASP* 4.7 6.2 + - - -
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Residues in contact with LEU1320 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1316D ALA 4.4 3.0 + - - -
1317D PHE 3.2 10.5 + - - -
1318D GLU 3.2 0.2 + - - -
1319D SER* 1.3 75.2 - - - +
1321D TYR* 1.3 55.5 + - - +
1396D LYS* 6.1 2.5 - - - +
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Residues in contact with TYR1321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1317D PHE 4.2 1.2 + - - -
1318D GLU 3.1 4.5 + - - -
1319D SER 3.2 0.6 - - - -
1320D LEU* 1.3 80.4 - - - +
1322D GLN* 1.3 56.5 + - - +
1323D ASP 3.2 2.9 - - - -
1324D LYS* 2.7 28.8 + - - +
1325D PHE 3.2 14.7 + - - +
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Residues in contact with GLN1322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309D VAL* 6.0 6.3 - - - +
1318D GLU 3.0 14.8 + - - -
1319D SER* 4.4 0.8 + - - +
1321D TYR* 1.3 73.6 - - - +
1323D ASP* 1.3 57.4 + - - +
1324D LYS 3.2 1.4 + - - -
1325D PHE 3.9 16.1 - - - +
1326D PRO* 4.7 3.4 - - - +
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Residues in contact with ASP1323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1319D SER 4.7 7.4 + - - -
1321D TYR 3.0 1.2 + - - -
1322D GLN* 1.3 74.8 - - - +
1324D LYS* 1.3 56.9 + - - +
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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