Contacts of the strand formed by residues 1177 - 1180 (chain O) in PDB entry 5Z3U
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 THR1177 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1099O LEU* 5.4 3.3 - - + +
1104O HIS* 4.7 4.2 + - - +
1105O ARG 3.2 11.0 + - - +
1106O VAL* 3.3 22.3 - - + +
1107O LEU* 3.2 18.9 + - - +
1175O ALA* 4.8 1.4 - - - +
1176O ASP* 1.3 94.4 + - - +
1178O VAL* 1.3 65.3 + - - +
1179O ILE* 4.2 19.7 - - + -
1207O ARG* 3.0 26.3 + - + +
1208O ILE* 5.2 0.7 - - - -
1209O LEU* 5.7 2.0 - - + +
1289O ARG* 4.7 2.6 + - - -
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Residues in contact with VAL1178 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107O LEU* 3.7 20.4 - - + -
1109O PHE* 3.8 25.6 - - + -
1172O LEU* 6.2 0.9 - - + -
1175O ALA* 6.4 0.4 - - + -
1176O ASP 3.9 0.4 - - - +
1177O THR* 1.3 80.2 - - - +
1179O ILE* 1.3 66.9 + - - +
1180O ILE* 4.0 18.2 - - + -
1193O ALA 4.5 9.2 - - - +
1194O GLN* 4.7 5.2 - - - +
1197O ALA* 3.5 33.4 - - + +
1207O ARG 3.2 5.9 + - - -
1208O ILE* 3.4 37.0 - - + +
1209O LEU 3.5 2.9 + - - -
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Residues in contact with ILE1179 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092O LEU* 5.4 3.1 - - + -
1095O ILE* 3.9 27.8 - - + -
1099O LEU* 5.2 2.0 - - + -
1106O VAL* 3.8 23.3 - - + -
1107O LEU 2.7 21.7 + - - +
1108O ILE* 3.3 8.8 - - + +
1109O PHE* 3.3 22.5 + - - -
1177O THR* 4.2 11.0 - - + -
1178O VAL* 1.3 79.6 - - - +
1180O ILE* 1.3 63.8 + - - +
1181O PHE* 3.4 30.5 - - + -
1209O LEU* 3.7 13.7 - - + +
1211O LEU* 3.6 21.3 - - + -
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Residues in contact with ILE1180 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109O PHE* 4.6 21.1 - - + +
1163O THR* 5.8 4.3 - - + -
1178O VAL* 4.0 12.8 - - + -
1179O ILE* 1.3 78.1 - - - +
1181O PHE* 1.3 88.7 + - - +
1184O ASP* 4.1 7.9 - - - +
1190O ASP* 4.1 24.2 - - - +
1193O ALA* 5.5 2.7 - - + -
1194O GLN* 3.8 39.5 - - - +
1208O ILE* 4.3 8.1 - - + -
1209O LEU 3.6 4.3 + - - +
1210O ARG* 4.0 17.3 - - + +
1211O LEU 3.5 20.4 + - - -
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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