Contacts of the helix formed by residues 1210 - 1217 (chain D) in PDB entry 6VVT
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 GLY1210 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1036D PHE 3.6 2.5 - - - -
1037D GLU* 3.1 35.0 + - - -
1038D ALA* 3.4 6.6 - - - +
1209D MET* 1.3 78.1 - - - +
1211D ILE* 1.3 61.5 + - - -
1212D THR 3.3 2.5 - - - -
1213D LYS* 3.5 7.0 + - - +
1214D ALA* 2.9 27.1 + - - +
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Residues in contact with ILE1211 (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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872D LEU* 4.5 4.9 - - + -
875D ARG* 4.0 18.4 - - + +
876D LEU* 3.4 30.7 - - + +
879D VAL* 3.7 34.1 - - + +
1036D PHE* 3.1 27.9 + - + +
1037D GLU* 3.5 15.7 + - - +
1158D ILE* 4.2 9.2 - - + +
1162D MET* 3.8 20.9 - - + -
1210D GLY* 1.3 71.6 - - - -
1212D THR* 1.3 58.6 + - - +
1214D ALA* 3.7 1.7 - - - +
1215D SER* 2.7 37.5 + - - -
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Residues in contact with THR1212 (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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875D ARG* 3.1 33.4 + - + +
1037D GLU* 2.8 24.7 + - - -
1211D ILE* 1.3 78.4 - - - +
1213D LYS* 1.3 59.7 + - - +
1215D SER* 2.7 21.1 + - - +
1216D LEU* 3.1 23.1 + - + +
1228D GLN* 3.7 28.3 - - + +
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Residues in contact with LYS1213 (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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1037D GLU* 4.2 0.6 + - - -
1209D MET* 4.6 17.1 - - + +
1210D GLY* 3.5 10.5 + - - +
1211D ILE 3.3 0.4 - - - -
1212D THR* 1.3 81.0 - - - +
1214D ALA* 1.3 62.9 + - - +
1216D LEU* 3.4 11.1 + - - +
1217D ALA* 3.3 20.3 + - - +
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Residues in contact with ALA1214 (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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879D VAL* 4.3 7.2 - - + -
1161D GLN 3.9 17.3 - - - +
1162D MET* 5.1 0.4 - - - -
1165D ARG* 4.8 3.2 + - - +
1209D MET* 3.7 31.5 - - + +
1210D GLY 2.9 19.4 + - - +
1211D ILE* 3.7 6.5 - - - +
1213D LYS* 1.3 76.2 - - - +
1215D SER* 1.3 63.3 - - - +
1217D ALA* 2.9 18.4 + - - +
1218D THR* 3.7 4.0 + - - -
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Residues in contact with SER1215 (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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875D ARG 5.4 0.4 + - - -
878D ASP* 3.6 34.8 - - - +
879D VAL* 4.1 7.7 - - - +
1211D ILE 2.7 19.5 + - - -
1212D THR* 2.7 27.5 + - - +
1214D ALA* 1.3 71.8 - - - +
1216D LEU* 1.3 62.2 + - - +
1217D ALA 3.1 1.2 + - - -
1218D THR* 3.2 27.1 + - - +
1227D PHE* 3.9 18.8 - - - +
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Residues in contact with LEU1216 (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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1212D THR* 3.1 31.0 + - + +
1213D LYS* 3.7 8.5 - - - +
1214D ALA 3.2 0.4 - - - -
1215D SER* 1.3 81.6 + - - +
1217D ALA* 1.3 56.5 + - - +
1218D THR 3.3 3.4 + - - +
1224D ALA* 4.1 34.1 - - + +
1227D PHE* 4.3 7.9 - - + -
1228D GLN* 4.1 33.7 - - + +
1233D VAL* 4.7 10.4 - - + +
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Residues in contact with ALA1217 (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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1165D ARG* 2.3 54.1 + - - +
1209D MET* 5.0 2.9 - - + -
1213D LYS 3.3 10.6 + - - +
1214D ALA* 2.9 13.9 + - - +
1216D LEU* 1.3 75.7 - - - +
1218D THR* 1.3 60.0 + - - +
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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