Contacts of the strand formed by residues 1164 - 1170 (chain A) in PDB entry 3PT6
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 SER1164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1141A LYS* 3.3 19.1 + - - +
1142A LEU 3.5 2.9 - - - -
1144A THR* 3.0 28.9 - - - +
1158A PHE* 3.2 28.4 + - - +
1159A HIS* 3.2 34.3 + - - -
1162A GLY* 5.2 0.2 - - - -
1163A ILE* 1.3 87.5 + - - +
1165A GLU* 1.3 58.5 + - - +
1166A THR* 4.2 1.2 + - - -
1222A MET* 5.2 1.1 - - - -
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Residues in contact with GLU1165 (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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1141A LYS* 4.0 21.4 - - + +
1142A LEU 3.1 8.2 + - - +
1143A ARG* 3.6 9.9 + - - +
1144A THR 3.2 15.0 + - - -
1159A HIS* 4.3 2.0 - - - -
1164A SER* 1.3 73.1 - - - +
1166A THR* 1.3 66.3 + - - +
1167A LEU* 3.2 43.3 + - + +
1210B LEU 4.4 5.4 - - - +
1211B GLY* 3.6 25.1 - - - +
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Residues in contact with THR1166 (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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1144A THR* 3.5 20.1 - - - +
1146A ASP* 4.0 12.1 - - + +
1155A SER* 3.0 22.5 + - - +
1159A HIS* 2.9 30.5 - - - -
1164A SER* 4.2 1.4 + - - -
1165A GLU* 1.3 70.7 - - - +
1167A LEU* 1.3 62.4 + - - +
1168A TRP 3.4 24.2 - - - +
1180A PHE* 4.1 13.5 - - + -
1184A ASN* 5.5 0.2 - - - +
1186A GLY 4.3 1.2 - - - -
1187A THR* 3.0 26.9 + - - +
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Residues in contact with LEU1167 (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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1143A ARG* 3.7 33.7 - - + -
1144A THR 3.1 5.5 + - - -
1165A GLU* 3.4 42.4 - - + +
1166A THR* 1.3 76.3 - - - +
1168A TRP* 1.3 94.8 + - + +
1186A GLY* 4.2 14.2 - - - +
1187A THR* 3.4 6.3 - - - +
1188A THR* 2.9 26.0 + - - -
1211B GLY 4.7 5.6 - - - +
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Residues in contact with TRP1168 (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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1143A ARG* 3.9 20.0 - - + -
1144A THR 3.4 17.0 - - - -
1145A LEU* 3.4 23.1 - - + -
1146A ASP 3.0 22.3 + - - -
1166A THR* 3.4 6.9 - - - +
1167A LEU* 1.3 116.8 + - + +
1169A ALA* 1.3 60.2 - - - +
1187A THR* 3.4 3.6 + - - -
1188A THR* 3.4 11.0 + - - -
1190A PHE* 4.0 18.2 - + + -
1213A ARG* 4.1 19.6 + - - +
1215A PRO* 3.3 33.9 - - + +
1219A ASP* 3.6 43.7 - - + -
1220A VAL* 4.3 8.3 - - + -
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Residues in contact with ALA1169 (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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1145A LEU* 4.5 0.2 - - - -
1146A ASP* 3.2 9.2 - - + +
1149A SER* 3.7 14.8 - - - +
1168A TRP* 1.3 75.8 - - - +
1170A ILE* 1.3 66.0 + - - +
1171A GLU 4.2 0.4 - - - -
1180A PHE* 3.6 35.7 - - + -
1187A THR* 3.7 0.2 + - - -
1188A THR 3.1 6.5 + - - +
1189A VAL* 3.3 12.1 - - + +
1190A PHE* 2.8 27.2 + - - -
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Residues in contact with ILE1170 (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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1145A LEU* 4.2 15.3 - - + -
1146A ASP 3.0 7.3 + - - -
1147A VAL* 4.4 13.7 - - + -
1148A PHE* 2.8 28.8 + - - -
1149A SER 3.0 6.5 + - - -
1169A ALA* 1.3 79.2 - - - +
1171A GLU* 1.3 63.2 + - - +
1190A PHE* 3.6 10.8 - - + +
1192A GLU 3.7 20.2 - - - +
1194A CYS* 4.2 14.1 - - + -
1197A LEU* 3.2 32.5 - - + -
1215A PRO* 6.4 0.9 - - + -
1257A TYR* 3.5 32.1 - - + +
1603A SAH 4.1 9.6 - - + -
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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