Contacts of the strand formed by residues 1112 - 1115 (chain D) in PDB entry 1AWV
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 PHE1112 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1008D PHE* 3.5 29.8 - + - -
1036D PHE* 3.8 9.0 - + + -
1048D TYR* 3.7 21.1 - + - -
1053D PHE* 4.0 27.8 - + - -
1063D GLN* 3.4 3.3 - - - +
1064D GLY 2.9 29.9 + - - +
1065D GLY* 3.4 27.6 - - - -
1098D LEU* 3.9 15.3 - - + -
1099D SER 3.5 8.1 - - - +
1100D MET* 4.1 11.2 - - - -
1101D ALA* 3.5 11.0 - - - +
1110D SER 3.5 13.2 - - - -
1111D GLN* 1.3 76.6 - - - +
1113D PHE* 1.3 69.7 + - - +
1114D ILE* 4.2 8.1 - - + -
1129D PHE* 4.2 7.6 - - + -
1158D ILE* 4.4 4.0 - - + -
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Residues in contact with PHE1113 (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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1060D PHE* 5.7 0.2 - + - -
1061D MET* 3.8 31.0 - - + -
1062D CYS 3.2 12.8 - - - +
1063D GLN* 4.0 4.7 - - + -
1092D HIS* 3.7 3.4 - + - -
1098D LEU* 3.7 3.1 - - - +
1099D SER* 2.9 57.9 + - - +
1100D MET 3.2 23.8 - - - -
1101D ALA* 3.7 17.0 - - + -
1112D PHE* 1.3 79.3 - - - +
1114D ILE* 1.3 62.4 + - - +
1115D CYS* 3.6 28.7 - - - -
1122D LEU* 3.6 28.9 - - + -
1126D HIS* 4.0 7.4 - + - -
104J PRO* 3.9 14.8 - - + -
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Residues in contact with ILE1114 (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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1008D PHE* 5.0 0.9 - - + -
1020D VAL* 5.1 2.0 - - + -
1022D PHE* 3.8 23.8 - - + -
1053D PHE* 4.0 28.0 - - + -
1061D MET* 3.3 3.2 - - - +
1062D CYS* 2.8 33.5 + - + +
1096D GLY* 3.9 9.9 - - - +
1097D ILE 3.5 3.6 - - - -
1098D LEU* 3.9 16.6 - - + +
1112D PHE* 4.2 7.6 - - + -
1113D PHE* 1.3 74.1 - - - +
1115D CYS* 1.3 69.0 + - - +
1116D THR* 4.1 3.3 - - - +
1132D VAL* 3.8 24.7 - - + -
1136D MET* 5.1 0.2 - - + -
1139D VAL* 4.2 28.0 - - + -
1142D MET* 5.2 2.5 - - + -
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Residues in contact with CYS1115 (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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1060D PHE 4.0 5.6 - - - +
1061D MET* 4.1 1.6 - - - -
1092D HIS* 3.9 8.3 - - - -
1094D GLY 3.8 1.3 - - - +
1096D GLY* 2.6 30.5 + - - -
1097D ILE* 2.6 40.5 + - + +
1113D PHE* 3.6 28.5 - - - -
1114D ILE* 1.3 72.8 - - - +
1116D THR* 1.3 58.9 + - - +
1117D ALA 3.4 17.3 - - - +
1119D THR* 3.7 20.9 - - + -
1136D MET* 3.9 2.8 - - - +
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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