Contacts of the strand formed by residues 1164 - 1170 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1141B LYS* 3.6 21.8 + - - +
1142B LEU* 3.3 9.2 - - - +
1144B THR* 2.8 33.1 + - - +
1158B PHE* 4.0 16.1 + - - +
1159B HIS* 3.4 27.7 + - - -
1162B GLY 3.5 0.4 - - - -
1163B ILE* 1.3 96.8 - - - +
1165B GLU* 1.3 58.8 + - - +
1166B THR* 4.2 1.0 + - - -
1222B MET* 4.9 0.4 - - - -
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Residues in contact with GLU1165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210A LEU 4.8 4.1 - - - +
1211A GLY* 4.5 20.1 + - - +
1141B LYS* 3.9 25.3 - - + +
1142B LEU 3.0 14.6 + - - +
1143B ARG* 3.7 7.5 - - + +
1144B THR 3.1 17.1 + - - -
1159B HIS* 4.2 4.0 - - - -
1164B SER* 1.3 75.6 - - - +
1166B THR* 1.3 64.8 + - - +
1167B LEU* 3.2 31.4 + - + +
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Residues in contact with THR1166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1144B THR* 3.4 19.9 - - + +
1146B ASP* 4.0 16.8 - - + -
1155B SER* 3.6 10.4 + - - -
1159B HIS* 3.1 27.9 + - - -
1164B SER* 4.2 1.6 + - - -
1165B GLU* 1.3 69.3 - - - +
1167B LEU* 1.3 60.2 + - - +
1168B TRP 2.9 29.6 - - - +
1180B PHE* 4.1 13.7 - - + -
1184B ASN* 5.5 0.4 - - - -
1186B GLY 4.1 3.1 - - - +
1187B THR* 2.8 32.4 + - - +
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Residues in contact with LEU1167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1211A GLY 4.8 8.7 - - - +
1143B ARG* 3.9 23.6 - - + -
1144B THR 3.1 5.3 + - - -
1165B GLU* 3.2 35.2 + - + +
1166B THR* 1.3 74.6 - - - +
1168B TRP* 1.3 107.6 + - + +
1186B GLY 4.2 11.8 - - - +
1187B THR* 3.2 8.8 - - - +
1188B THR* 2.9 25.5 + - - -
1213B ARG* 5.5 2.7 - - - +
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Residues in contact with TRP1168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143B ARG* 4.0 15.5 - - + -
1144B THR 3.4 24.5 + - - +
1145B LEU* 3.7 23.6 - - + -
1146B ASP 3.0 11.3 + - - -
1166B THR* 2.9 20.4 - - - +
1167B LEU* 1.3 120.8 + - + +
1169B ALA* 1.3 63.5 + - - +
1187B THR* 3.3 2.4 + - - -
1188B THR* 3.3 11.8 + - - +
1190B PHE* 4.0 17.0 - + + -
1213B ARG* 3.8 29.4 + - - +
1215B PRO* 3.5 32.2 - - + +
1219B ASP* 3.5 37.9 - - + -
1220B VAL* 4.0 15.7 - - + -
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Residues in contact with ALA1169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145B LEU* 4.3 0.7 - - - -
1146B ASP* 3.2 13.2 - - + +
1149B SER* 4.0 12.6 - - - +
1166B THR* 4.5 0.7 - - + -
1168B TRP* 1.3 78.6 - - - +
1170B ILE* 1.3 60.4 + - - +
1180B PHE* 4.0 28.7 - - + -
1187B THR* 4.4 0.4 - - - +
1188B THR 3.1 5.5 + - - -
1189B VAL* 3.3 15.5 - - + +
1190B PHE* 2.6 34.7 + - - +
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Residues in contact with ILE1170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145B LEU* 4.3 17.3 - - + -
1146B ASP 3.0 6.5 + - - -
1147B VAL* 4.4 14.6 - - + -
1148B PHE* 3.0 26.9 + - - -
1149B SER* 3.2 7.0 + - - -
1169B ALA* 1.3 78.3 - - - +
1171B GLU* 1.3 63.5 + - - +
1190B PHE* 3.2 11.9 - - + +
1192B GLU 3.6 20.0 - - - +
1194B CYS* 4.3 8.5 - - + -
1197B LEU* 3.4 33.2 - - + -
1257B TYR* 3.5 31.9 - - + +
1603B SAH 4.1 11.2 + - + -
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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