Contacts of the strand formed by residues 1164 - 1167 (chain D) in PDB entry 5UH8
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 ARG1164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1160D GLN 5.5 1.2 + - - -
1162D LEU* 3.1 6.5 - - - +
1163D ARG* 1.3 89.2 - - + +
1165D VAL* 1.3 66.6 + - - +
1180D LEU* 3.5 24.9 + - + -
1181D ILE* 3.4 19.9 - - - +
1182D ASP* 3.8 11.6 - - + +
1206D VAL* 3.2 25.4 + - + +
1208D MET* 3.6 41.2 - - + +
1213D ALA* 3.9 11.9 + - - +
1216D ALA* 2.3 49.7 + - - +
1217D THR* 3.9 7.1 - - - +
1218D ASP 4.8 1.0 - - - +
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Residues in contact with VAL1165 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1162D LEU 5.2 0.4 - - - +
1164D ARG* 1.3 78.8 - - - +
1166D THR* 1.3 67.3 + - - +
1167D ILE* 4.7 1.0 - - - +
1179D SER 3.5 0.2 - - - +
1180D LEU* 3.5 4.0 - - - -
1181D ILE* 3.0 33.2 + - + +
1183D ARG* 3.8 25.8 - - + +
1186D PHE* 4.0 36.8 - - + -
1203D GLY* 4.8 2.7 - - - -
1204D ARG 3.5 11.2 - - - +
1205D PRO* 3.7 22.9 - - + -
1206D VAL* 4.3 2.0 - - - +
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Residues in contact with THR1166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1165D VAL* 1.3 76.8 - - - +
1167D ILE* 1.3 72.0 + - - +
1168D ILE* 3.9 14.1 - - + -
1178D GLY* 4.2 5.2 - - - -
1179D SER 3.3 14.5 + - - -
1180D LEU* 3.7 11.8 - - - +
1202D ALA 3.8 0.2 - - - +
1203D GLY* 3.4 7.8 - - - -
1204D ARG* 2.9 55.8 + - + +
1206D VAL* 3.6 22.9 - - + +
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Residues in contact with ILE1167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1165D VAL 4.7 2.5 - - - +
1166D THR* 1.3 86.0 + - - +
1168D ILE* 1.3 64.8 + - - +
1169D ASP 3.4 27.6 - - - +
1175D PHE* 4.1 24.9 - - + +
1176D LEU 3.7 18.2 - - - +
1177D PRO* 3.9 11.4 - - + +
1178D GLY* 3.0 20.2 + - - +
1179D SER 3.1 15.6 + - - +
1181D ILE* 4.0 15.0 - - + -
1186D PHE* 3.8 31.4 - - + -
1201D ALA* 4.2 5.6 - - + -
1202D ALA 3.6 2.0 - - - +
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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