Contacts of the helix formed by residues 1170 - 1181 (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 MET1170 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1167D MET 3.2 9.9 + - - -
1168D PRO 3.0 1.0 - - - -
1169D LYS* 1.3 76.9 - - - +
1171D GLY* 1.3 61.8 + - - +
1172D LYS 3.2 2.9 - - - -
1173D THR* 3.0 17.1 + - - +
1174D ILE* 3.1 12.7 + - - -
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Residues in contact with GLY1171 (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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1158D HIS* 3.2 33.0 - - - +
1161D ILE* 5.2 2.4 - - - -
1162D GLY* 4.2 15.3 - - - -
1167D MET 3.9 1.6 + - - -
1168D PRO 2.9 16.4 + - - -
1169D LYS 3.3 0.2 - - - -
1170D MET* 1.3 77.8 - - - +
1172D LYS* 1.3 61.7 + - - +
1174D ILE* 4.5 0.6 - - - -
1175D HIS* 3.5 11.4 + - - -
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Residues in contact with LYS1172 (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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1158D HIS* 5.0 6.0 - - - +
1168D PRO 4.7 0.6 + - - -
1169D LYS 4.7 2.4 + - - -
1170D MET 3.2 0.6 - - - -
1171D GLY* 1.3 73.4 - - - +
1173D THR* 1.3 65.7 + - - +
1175D HIS* 3.0 13.2 + - - -
1176D LYS* 3.1 9.9 + - - -
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Residues in contact with THR1173 (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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1169D LYS 5.4 0.4 + - - -
1170D MET* 3.0 7.6 + - - +
1172D LYS* 1.3 71.4 - - - +
1174D ILE* 1.3 67.7 + - - +
1176D LYS* 3.0 12.6 + - - +
1177D TYR* 3.3 7.6 + - - -
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Residues in contact with ILE1174 (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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1170D MET 3.1 12.4 + - - -
1171D GLY 4.5 1.1 - - - -
1173D THR* 1.3 73.0 - - - +
1175D HIS* 1.3 64.3 + - - +
1177D TYR* 3.0 14.1 + - - +
1178D VAL* 3.0 10.9 + - - -
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Residues in contact with HIS1175 (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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1158D HIS* 5.8 4.3 - - - +
1171D GLY 3.5 11.0 + - - -
1172D LYS 3.0 9.3 + - - -
1174D ILE* 1.3 74.0 - - - +
1176D LYS* 1.3 66.0 + - - +
1178D VAL* 3.0 11.6 + - - +
1179D HIS* 3.1 9.4 + - - -
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Residues in contact with LYS1176 (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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1172D LYS 3.1 7.4 + - - -
1173D THR* 3.0 9.7 + - - +
1175D HIS* 1.3 76.9 - - - +
1177D TYR* 1.3 57.1 + - - +
1179D HIS* 3.0 2.4 + - - -
1180D LEU* 2.9 24.9 + - - -
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Residues in contact with TYR1177 (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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1173D THR 3.3 7.4 + - - -
1174D ILE 3.0 7.5 + - - -
1176D LYS* 1.3 75.7 - - - +
1178D VAL* 1.3 62.6 + - - +
1180D LEU* 2.9 13.8 + - - +
1181D PHE* 3.0 12.3 + - - -
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Residues in contact with VAL1178 (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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1174D ILE 3.0 13.6 + - - -
1175D HIS* 3.0 5.5 + - - +
1177D TYR* 1.3 77.7 - - - +
1179D HIS* 1.3 59.0 + - - +
1180D LEU 3.7 0.2 + - - -
1181D PHE* 3.7 12.5 + - - +
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Residues in contact with HIS1179 (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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1175D HIS 3.1 7.5 + - - -
1176D LYS 3.0 8.0 + - - -
1178D VAL* 1.3 76.5 - - - +
1180D LEU* 1.3 60.1 + - - +
1181D PHE 3.3 2.5 - - - -
1207D ASP 6.0 0.7 - - - -
1208D PHE* 3.8 6.8 - - - +
1209D GLN* 2.9 28.2 + - - -
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Residues in contact with LEU1180 (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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1176D LYS 2.9 13.0 + - - -
1177D TYR* 2.9 7.2 + - - +
1179D HIS* 1.3 78.0 - - - +
1181D PHE* 1.3 62.8 + - - +
1182D PRO* 3.3 4.0 - - - +
1208D PHE* 5.6 0.3 - - - -
1209D GLN 3.9 16.8 + - - +
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Residues in contact with PHE1181 (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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1177D TYR 3.0 12.5 + - - -
1178D VAL 3.7 11.4 + - - +
1179D HIS 3.3 5.3 - - - +
1180D LEU* 1.3 75.7 - - - +
1182D PRO* 1.3 67.2 - - - +
1183D LYS* 3.3 4.2 + - - -
1208D PHE* 4.5 4.4 - - - -
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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