Contacts of the helix formed by residues 1185 - 1189 (chain C) in PDB entry 6RIN
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 PRO1185 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C ASP* 4.3 4.3 - - - +
15C PHE 3.8 20.6 - - - +
16C GLY* 4.8 7.4 - - - -
657C THR* 5.2 7.2 - - + -
658C GLN* 4.9 13.7 - - + +
702C THR 4.2 12.1 - - - +
703C GLY* 6.4 0.4 - - - -
1156C ARG* 4.2 20.4 - - - +
1183C ALA* 5.4 0.2 - - + -
1184C THR* 1.3 101.4 - - + +
1186C VAL* 1.3 70.5 + - + +
1187C PHE 3.7 0.9 - - - +
1188C ASP* 3.8 21.9 + - + +
1189C GLY* 3.8 1.5 + - - -
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Residues in contact with VAL1186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657C THR* 5.4 0.6 - - - +
658C GLN* 5.2 16.4 - - + +
661C VAL* 4.9 8.3 - - + -
666C SER* 3.6 39.3 - - - +
668C ILE 5.1 6.1 - - - +
669C PRO* 6.4 0.4 - - - -
670C PHE* 5.2 2.0 - - - +
671C LEU* 3.8 33.3 + - + +
672C GLU* 3.6 19.4 + - - +
702C THR* 5.3 2.7 - - + +
704C MET* 6.1 1.1 - - + -
1184C THR* 4.4 3.5 - - - +
1185C PRO* 1.3 78.1 - - + +
1187C PHE* 1.3 88.0 + - + +
1188C ASP 3.3 2.1 + - - -
1189C GLY* 4.2 3.5 + - - -
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Residues in contact with PHE1187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620C ASN* 4.8 14.4 + - - +
657C THR* 3.3 37.6 + - - +
658C GLN* 5.5 0.4 - - - -
660C VAL* 3.7 25.4 - - + -
661C VAL* 4.1 9.2 - - + -
671C LEU* 4.6 4.9 - - + -
672C GLU* 4.0 24.2 - - + -
1186C VAL* 1.3 98.0 - - + +
1188C ASP* 1.3 59.7 + - - +
1189C GLY 3.7 1.3 - - - -
767D LEU 3.8 23.4 - - - +
769D VAL* 4.3 17.0 - - + -
772D TYR* 3.9 41.5 - + + -
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Residues in contact with ASP1188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLY* 3.2 13.2 - - - -
17C LYS* 2.7 39.1 + - - +
18C ARG* 3.4 36.5 + - + +
620C ASN* 5.3 3.5 - - - +
657C THR* 4.5 15.7 - - + -
1185C PRO* 3.8 14.7 + - + +
1186C VAL 3.3 1.2 - - - -
1187C PHE* 1.3 80.7 - - - +
1189C GLY* 1.3 66.6 + - - +
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Residues in contact with GLY1189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PHE* 5.1 2.7 - - - -
17C LYS* 4.5 6.4 + - - -
670C PHE* 5.0 1.8 - - - -
672C GLU* 5.0 9.4 + - - -
1184C THR* 3.4 26.2 - - - -
1185C PRO* 3.8 2.8 + - - -
1186C VAL 4.2 3.1 + - - -
1187C PHE 3.7 1.4 - - - -
1188C ASP* 1.3 83.4 - - - +
1190C ALA* 1.3 69.1 + - - +
1191C LYS* 3.6 11.6 + - - +
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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