Contacts of the strand formed by residues 1192 - 1198 (chain A) in PDB entry 6FF7
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 PHE1192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1188A ASN* 5.2 0.4 - - - +
1189A MET* 2.9 25.1 + - - +
1190A CYS 3.6 1.2 + - - -
1191A GLY* 1.3 80.5 - - - +
1193A GLU* 1.3 61.7 + - - +
1194A CYS* 4.2 1.2 + - - +
1230A LEU* 6.5 0.4 - - + -
1231A ARG 3.7 11.7 - - - +
1232A VAL* 4.2 9.2 - - + -
1233A ASP* 4.0 4.9 - - - +
1274A PHE* 6.2 2.5 - - + -
1277A ALA* 4.9 11.9 - - + -
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Residues in contact with GLU1193 (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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1187A PHE 3.6 14.1 - - - +
1188A ASN* 3.7 20.2 - - + +
1192A PHE* 1.3 73.9 - - - +
1194A CYS* 1.3 63.7 + - - +
1230A LEU* 3.5 2.6 - - - +
1231A ARG* 2.8 38.3 + - + +
1232A VAL 5.5 0.2 - - - -
1233A ASP* 4.3 10.3 - - + +
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Residues in contact with CYS1194 (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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1186A LEU* 3.7 1.4 - - - +
1187A PHE 2.9 32.1 + - - +
1192A PHE 4.2 1.7 + - - +
1193A GLU* 1.3 76.5 - - - +
1195A ARG* 1.3 65.7 + - - +
1228A CYS* 5.4 6.7 - - + -
1229A PHE 3.1 15.5 - - - +
1230A LEU* 4.2 8.7 - - + -
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Residues in contact with ARG1195 (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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1184A ASN* 5.8 3.8 - - + -
1185A LEU 3.1 16.2 - - - +
1186A LEU* 3.7 13.7 - - + -
1194A CYS* 1.3 79.9 - - - +
1196A ILE* 1.3 62.1 + - - +
1197A LEU* 4.0 1.1 + - - +
1227A GLN 3.5 1.0 - - - +
1228A CYS* 3.2 7.0 - - - -
1229A PHE* 2.9 38.8 + - + +
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Residues in contact with ILE1196 (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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956A CYS* 6.5 1.3 - - + -
1183A PRO 4.7 0.2 - - - +
1184A ASN* 3.8 4.2 - - - +
1185A LEU* 2.8 46.1 + - + +
1195A ARG* 1.3 73.7 - - - +
1197A LEU* 1.3 60.3 + - - +
1198A PRO 4.1 0.6 - - - -
1226A ALA* 5.2 9.4 - - + -
1227A GLN 3.3 7.4 - - - +
1228A CYS* 4.7 2.5 - - + +
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Residues in contact with LEU1197 (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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1183A PRO 4.7 9.6 - - - +
1184A ASN* 5.3 3.6 - - + +
1195A ARG 4.0 1.0 + - - +
1196A ILE* 1.3 71.7 - - - +
1198A PRO* 1.3 66.2 - - - +
1226A ALA* 4.4 1.6 - - - -
1227A GLN* 2.9 40.3 + - + +
1229A PHE* 6.5 1.6 - - + -
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Residues in contact with PRO1198 (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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1183A PRO 5.0 5.2 - - - +
1196A ILE* 4.1 1.6 - - - -
1197A LEU* 1.3 76.9 - - - +
1199A LYS* 1.3 62.7 + - - +
1200A CYS* 3.3 11.1 + - + +
1201A ARG* 3.9 19.7 + - + +
1202A THR* 4.4 5.0 + - - -
1225A THR 4.9 1.6 - - - +
1226A ALA* 4.0 12.8 - - + -
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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