Contacts of the strand formed by residues 1175 - 1178 (chain J) in PDB entry 6PSS
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 LEU1175 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1156J LEU 5.9 1.6 - - - +
1163J VAL* 3.7 26.5 - - + -
1164J SER 3.3 12.8 - - - +
1165J PHE* 3.7 3.1 - - - -
1173J ARG* 5.4 2.7 - - - -
1174J ARG* 1.3 79.6 - - - +
1176J VAL* 1.3 58.6 + - - +
1177J ILE* 3.5 15.8 + - + -
1186J TYR* 2.9 16.0 - - + +
1187J GLU* 3.3 5.3 - - - -
1188J GLU* 3.3 14.3 + - + +
1190J ILE* 3.7 30.5 - - + -
1196J LEU* 4.1 22.2 - - + -
1198J VAL* 4.9 6.3 - - + -
1200J GLU* 5.0 10.8 - - + +
1210J ILE* 5.2 11.0 - - + -
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Residues in contact with VAL1176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1164J SER* 2.5 43.4 + - - +
1165J PHE 3.3 17.5 - - - +
1166J GLY* 4.6 3.6 - - - -
1175J LEU* 1.3 68.5 - - - +
1177J ILE* 1.3 61.3 + - - +
1178J THR* 3.3 9.3 + - - +
1184J ASP* 3.6 37.5 - - + +
1186J TYR 3.3 10.3 - - - +
1187J GLU* 3.7 31.0 - - + +
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Residues in contact with ILE1177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1157J ALA* 3.7 36.1 - - + -
1158J GLU 4.8 1.1 - - - +
1159J ILE* 3.3 39.4 - - + +
1160J SER 4.3 1.6 - - - +
1161J GLY* 3.7 19.5 - - - +
1162J ILE 3.6 3.4 - - - +
1163J VAL* 3.7 21.5 - - + +
1175J LEU* 3.5 16.3 + - + -
1176J VAL* 1.3 72.8 - - - +
1178J THR* 1.3 61.3 + - - +
1179J PRO* 3.4 3.3 - - - +
1184J ASP* 3.2 19.1 - - - +
1186J TYR* 3.7 7.8 + - + +
1204J VAL* 3.9 17.3 - - + -
1210J ILE* 5.4 2.0 - - + -
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Residues in contact with THR1178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1161J GLY* 4.2 0.9 - - - -
1162J ILE* 2.6 46.5 + - + +
1163J VAL 5.7 0.4 - - - -
1164J SER* 5.0 5.6 - - - -
1176J VAL* 3.3 13.2 + - - +
1177J ILE* 1.3 72.4 - - - +
1179J PRO* 1.3 74.9 - - - +
1180J VAL* 3.6 2.0 + - + -
1182J GLY 5.1 0.7 - - - +
1184J ASP* 3.0 26.9 + - - +
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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