Contacts of the strand formed by residues 1163 - 1168 (chain A) in PDB entry 3O2X
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 ILE1163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1113A TRP* 4.4 4.5 - - + +
1118A LEU* 4.7 11.2 - - + -
1119A THR 3.0 13.3 + - - +
1120A TYR* 3.1 24.7 - - + +
1121A ARG 3.1 5.5 + - - -
1142A PHE* 3.8 31.0 - - + -
1153A PHE* 4.2 16.6 - - + -
1161A ALA* 4.5 0.9 - - - -
1162A ASP* 1.3 83.4 - - + +
1164A MET* 1.3 61.4 + - - +
1165A ILE* 3.7 18.4 + - + -
1197A GLY* 3.1 31.4 - - - +
1198A ASP* 4.0 1.3 - - - -
1199A ALA 4.8 1.1 - - - +
1224A PHE* 4.7 3.8 - - + -
1227A SER* 4.3 16.6 - - - +
1228A LEU* 4.8 4.5 - - + -
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Residues in contact with MET1164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121A ARG* 3.5 25.6 - - - +
1123A VAL* 4.2 7.0 - - + -
1159A GLY 3.5 20.4 - - - +
1160A ILE* 4.3 12.3 - - + -
1161A ALA* 3.4 40.8 - - - +
1163A ILE* 1.3 70.8 - - - +
1165A ILE* 1.3 62.2 + - - +
1166A SER* 4.1 0.6 + - - -
1198A ASP* 2.9 31.6 + - - +
1199A ALA 3.1 22.7 + - - +
1200A HIS* 4.7 2.1 - - - -
1996A CA 4.1 3.6 - - - -
1169C ILE* 3.6 22.0 - - + -
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Residues in contact with ILE1165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120A TYR* 3.7 31.9 - - + -
1121A ARG 2.9 13.6 + - - +
1122A ILE* 3.8 6.4 - - + -
1123A VAL* 2.8 30.4 + - - +
1124A ASN 4.1 0.7 + - - +
1138A PHE* 3.6 40.2 - - + -
1142A PHE* 4.0 3.8 - - + -
1163A ILE* 4.2 14.6 - - + +
1164A MET* 1.3 75.0 - - - +
1166A SER* 1.3 66.7 + - - +
1167A PHE* 5.2 1.1 - - + -
1199A ALA* 3.4 4.7 - - + -
1201A PHE* 3.7 18.6 - - + -
1224A PHE* 3.7 27.1 - - + -
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Residues in contact with SER1166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123A VAL* 4.1 13.7 - - - -
1124A ASN* 3.6 15.7 - - - +
1164A MET 4.1 0.8 + - - -
1165A ILE* 1.3 77.3 - - - +
1167A PHE* 1.3 68.8 + - - +
1172A HIS* 5.9 0.9 - - - -
1199A ALA 3.1 6.1 + - - +
1200A HIS* 3.3 26.3 + - - +
1201A PHE* 2.9 26.8 + - - -
1169C ILE* 6.4 0.7 - - - -
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Residues in contact with PHE1167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122A ILE* 5.1 0.2 - - + -
1124A ASN* 2.9 36.9 + - - +
1125A TYR* 3.8 2.2 - - - -
1126A THR* 3.6 38.1 - - + -
1134A VAL* 4.4 3.1 - - + -
1138A PHE* 3.9 32.5 - + - -
1165A ILE* 5.2 0.9 - - + -
1166A SER* 1.3 79.5 - - - +
1168A GLY* 1.3 57.6 + - - +
1201A PHE* 3.3 30.1 - + + -
1203A ASP* 3.2 31.4 - - - +
1207A TRP* 4.1 13.9 - + - -
1216A LEU* 4.1 13.5 - - + -
1124C ASN* 3.0 25.6 - - + +
1167C PHE 4.8 1.0 - - - +
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Residues in contact with GLY1168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1166A SER 4.2 0.2 - - - -
1167A PHE* 1.3 74.5 - - - +
1169A ILE* 1.3 64.1 + - - -
1172A HIS* 4.3 17.2 - - - -
1178A PHE* 3.5 8.9 - - - -
1200A HIS* 5.9 0.6 - - - +
1201A PHE 3.0 10.1 + - - +
1202A ASP* 3.4 5.5 - - - -
1203A ASP* 2.9 22.9 + - - +
1123C VAL* 5.5 2.5 - - - -
1124C ASN* 4.9 1.8 - - - -
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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