Contacts of the strand formed by residues 1159 - 1164 (chain F) in PDB entry 6X34
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 THR1159 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1153F ILE* 3.8 1.0 - - - +
1154F ASP* 3.0 30.1 + - - +
1157F GLU* 3.2 15.2 - - - -
1158F ASN* 1.3 78.3 - - - +
1160F ILE* 1.3 67.9 + - - +
1161F ILE* 4.3 14.7 - - - +
1177F THR* 3.6 25.4 - - - -
1179F PHE 4.3 1.6 - - - -
1182F ILE* 3.9 0.6 - - - +
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Residues in contact with ILE1160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104F TRP* 4.0 22.7 - - + +
1122F TYR* 3.6 38.4 - - + -
1152F MET 4.0 3.1 - - - +
1153F ILE* 3.7 24.0 - - + +
1159F THR* 1.3 78.0 - - - +
1161F ILE* 1.3 66.2 + - - +
1162F PHE* 3.6 34.8 - - + -
1176F GLU 4.3 0.9 - - - +
1177F THR* 4.0 5.2 + - - -
1178F ALA* 3.1 31.2 + - + +
1179F PHE* 4.2 15.8 + - + +
1182F ILE* 4.0 9.0 - - + -
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Residues in contact with ILE1161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151F CYS* 3.9 0.3 - - - -
1152F MET* 2.9 47.4 + - + +
1154F ASP* 5.0 9.6 - - + -
1159F THR* 4.3 16.4 - - - +
1160F ILE* 1.3 85.2 - - - +
1162F PHE* 1.3 71.2 + - - +
1163F THR* 4.0 6.1 + - - +
1168F VAL* 4.8 21.8 - - + -
1176F GLU* 4.1 17.9 - - + +
1177F THR* 5.8 0.2 - - - -
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Residues in contact with PHE1162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102F VAL* 4.6 0.7 - - + -
1103F GLY* 3.8 26.0 - - - -
1104F TRP* 5.2 0.9 - + - -
1122F TYR* 5.9 3.6 - - + -
1123F VAL* 4.9 7.4 - - - -
1124F PHE* 3.8 43.5 - + + -
1131F ARG* 6.0 3.1 - - + -
1150F GLY 3.6 2.7 - - - +
1151F CYS* 3.6 22.0 - - + -
1160F ILE* 3.6 25.1 - - + -
1161F ILE* 1.3 80.6 - - - +
1163F THR* 1.3 61.5 + - - +
1164F LEU* 4.2 14.6 - - + -
1167F GLU 4.3 0.3 - - - +
1168F VAL* 4.5 0.7 - - - -
1169F LEU* 3.8 27.3 + - + +
1178F ALA* 3.6 31.6 - - + +
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Residues in contact with THR1163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089F TYR* 4.3 21.6 - - + +
1149F VAL* 3.4 2.3 - - - +
1150F GLY* 2.5 55.7 + - - +
1151F CYS* 4.5 1.7 + - - -
1152F MET* 5.0 2.9 + - - +
1161F ILE* 4.4 9.4 + - - +
1162F PHE* 1.3 71.7 - - - +
1164F LEU* 1.3 64.8 + - - +
1166F GLY* 3.7 15.3 - - - +
1167F GLU 3.7 25.4 - - - +
1168F VAL* 5.3 1.6 - - + +
1213F PHE 5.5 1.8 - - - +
1216F ILE* 5.9 2.2 - - + -
1217F CYS* 6.0 4.7 - - + +
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Residues in contact with LEU1164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124F PHE* 4.0 24.0 - - + -
1140F GLY* 5.8 3.1 - - - -
1141F ARG 5.3 4.9 - - - +
1142F PRO 5.7 0.7 - - - +
1143F TRP* 3.4 35.4 - - + +
1147F ASP* 6.4 1.1 - - + -
1149F VAL* 4.2 14.6 - - + +
1162F PHE* 4.2 12.1 - - + -
1163F THR* 1.3 76.7 - - - +
1165F ASN* 1.3 78.3 + - - +
1167F GLU* 2.9 29.4 + - - +
1168F VAL 5.9 0.2 - - - -
1169F LEU* 4.1 24.5 - - + -
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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