Contacts of the strand formed by residues 1164 - 1173 (chain A) in PDB entry 2NZ6
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 ILE1164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1124A TRP* 4.1 19.7 - - + +
1125A ARG* 4.5 12.1 - - + +
1128A TRP* 3.4 46.0 - - + -
1159A GLN 3.9 0.2 - - - +
1160A ASP* 3.4 3.1 - - - +
1161A TYR* 2.8 40.6 + - - +
1162A GLY 3.3 1.4 - - - -
1163A ASP* 1.3 87.0 - - + +
1165A THR* 1.3 68.2 + - - +
1166A VAL* 4.1 8.9 + - + -
1184A VAL* 3.3 29.4 - - + -
1185A LYS 3.5 2.9 - - - +
1186A ASN* 3.9 13.2 - - + +
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Residues in contact with THR1165 (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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1158A ALA* 3.7 27.4 - - + -
1159A GLN 3.5 4.5 - - - +
1160A ASP* 2.7 24.8 + - - +
1164A ILE* 1.3 71.7 - - - +
1166A VAL* 1.3 65.1 + - - +
1167A ALA* 5.1 1.8 - - + +
1183A THR* 3.6 1.7 + - - +
1184A VAL* 3.6 3.8 - - - -
1185A LYS* 2.9 51.0 + - + +
1187A ILE* 4.3 12.5 - - - +
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Residues in contact with VAL1166 (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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1124A TRP* 3.8 36.8 - - + -
1154A PRO* 3.2 25.8 - - + +
1158A ALA* 3.2 4.3 - - - -
1159A GLN 2.9 33.6 + - - -
1161A TYR* 3.7 29.6 - - + -
1164A ILE* 4.2 9.0 - - + -
1165A THR* 1.3 77.7 - - - +
1167A ALA* 1.3 61.5 + - - +
1182A PHE* 3.8 19.5 - - + -
1183A THR 3.5 10.1 - - - +
1184A VAL* 4.8 2.5 - - + -
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Residues in contact with ALA1167 (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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1154A PRO* 4.3 1.6 - - - -
1158A ALA* 4.1 19.7 - - + +
1165A THR* 4.3 2.0 - - + -
1166A VAL* 1.3 76.8 - - - +
1168A MET* 1.3 64.9 + - - +
1169A THR* 3.7 3.7 + - + +
1182A PHE* 3.1 7.4 - - - -
1183A THR* 2.9 45.2 + - - +
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Residues in contact with MET1168 (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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1153A TRP* 3.6 11.0 - - + +
1154A PRO* 3.4 29.3 - - - +
1155A SER* 4.0 29.9 - - - +
1157A GLN 5.6 1.8 + - - -
1167A ALA* 1.3 75.4 - - - +
1169A THR* 1.3 64.0 + - - +
1170A SER 3.7 10.3 - - - +
1171A GLU* 4.1 25.8 - - - +
1180A ARG* 3.5 33.4 - - + -
1181A ASP 3.5 11.9 - - - +
1182A PHE* 3.5 10.6 - - + -
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Residues in contact with THR1169 (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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1167A ALA* 4.0 7.4 - - + +
1168A MET* 1.3 78.0 - - - +
1170A SER* 1.3 59.7 + - - +
1181A ASP* 2.7 34.6 + - - +
1182A PHE* 3.8 2.4 + - - -
1183A THR* 3.9 28.0 - - + +
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Residues in contact with SER1170 (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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1168A MET* 3.7 10.0 - - - +
1169A THR* 1.3 82.0 + - - +
1171A GLU* 1.3 62.5 + - - +
1172A ILE* 3.9 20.8 - - - +
1179A ILE 4.4 0.8 + - - -
1180A ARG* 3.3 4.1 - - - -
1181A ASP* 2.8 46.0 + - - +
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Residues in contact with GLU1171 (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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1153A TRP* 4.8 1.2 + - - -
1155A SER* 5.5 4.6 - - - -
1168A MET* 4.1 21.3 - - - +
1170A SER* 1.3 76.3 + - - +
1172A ILE* 1.3 68.9 + - - +
1173A VAL* 4.1 15.9 + - + +
1178A THR* 4.1 15.0 - - + -
1179A ILE 3.5 3.8 - - - -
1180A ARG* 2.9 32.8 + - + +
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Residues in contact with ILE1172 (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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1170A SER* 3.9 16.8 - - - +
1171A GLU* 1.3 79.0 - - - +
1173A VAL* 1.3 65.7 + - - +
1174A LEU* 3.7 22.8 + - + +
1177A TRP 4.1 0.3 - - - +
1178A THR* 3.3 4.7 - - - -
1179A ILE* 2.8 57.3 + - + +
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Residues in contact with VAL1173 (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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1171A GLU* 4.0 17.6 + - + +
1172A ILE* 1.3 76.2 - - - +
1174A LEU* 1.3 77.3 + - - +
1178A THR* 3.8 25.1 - - + +
1180A ARG* 5.7 1.1 - - - +
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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