Contacts of the helix formed by residues 1209 - 1217 (chain G) in PDB entry 6C3P
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 GLY1209 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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777G TRP* 3.4 30.1 - - - -
1205G GLU 2.9 10.5 + - - -
1206G THR 3.7 3.4 - - - -
1208G GLU* 1.3 79.0 - - - +
1210G LEU* 1.3 59.2 + - - -
1211G THR* 3.4 3.6 - - - -
1212G THR* 2.6 25.1 + - - -
1213G ILE* 3.1 14.1 - - - +
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Residues in contact with LEU1210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399G ILE* 3.6 31.6 - - + +
400G MET* 4.5 17.0 - - + -
402G LEU* 4.3 17.3 - - + +
404G THR* 5.3 3.6 - - - +
407G LEU* 6.0 3.4 - - + -
1206G THR* 3.1 34.0 + - + +
1207G VAL* 3.4 16.3 + - + +
1208G GLU 3.5 0.8 + - - -
1209G GLY* 1.3 74.6 - - - +
1211G THR* 1.3 63.5 + - + +
1213G ILE* 3.3 6.5 + - + +
1214G ARG* 3.0 57.3 + - + +
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Residues in contact with THR1211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404G THR* 4.0 16.8 - - + +
724G LEU* 5.4 11.2 - - + -
727G LEU* 5.2 3.9 - - - +
729G GLU* 4.5 10.7 - - + +
771G TYR* 3.9 21.1 + - - -
773G SER* 5.1 2.6 - - - -
1208G GLU 5.7 0.3 + - - -
1209G GLY* 4.9 1.2 - - - -
1210G LEU* 1.3 79.3 + - + +
1212G THR* 1.3 69.1 + - - +
1214G ARG* 3.3 28.8 + - - +
1215G ALA* 2.9 29.0 + - - +
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Residues in contact with THR1212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771G TYR* 3.4 35.4 - - + +
772G ALA* 5.7 0.2 - - - -
773G SER* 4.7 10.1 - - - +
777G TRP* 3.4 30.0 - - + -
789G PHE* 6.1 0.3 - - - -
1209G GLY* 2.6 23.3 + - - +
1211G THR* 1.3 83.9 + - - +
1213G ILE* 1.3 66.2 + - - +
1215G ALA* 3.0 2.9 + - - +
1216G PHE* 2.9 45.4 + - + -
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Residues in contact with ILE1213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400G MET* 4.2 22.7 - - + -
777G TRP* 4.7 6.7 - - + -
789G PHE* 5.2 4.3 - - + -
1205G GLU* 4.5 2.7 - - + +
1206G THR* 4.1 26.7 - - + +
1209G GLY 3.1 21.7 + - - +
1210G LEU* 3.7 8.1 - - + +
1212G THR* 1.3 85.2 + - - +
1214G ARG* 1.3 63.7 + - - +
1215G ALA 3.2 0.3 + - - -
1216G PHE* 3.2 7.7 + - - +
1217G ARG* 2.9 18.5 + - - -
1218G TYR* 3.8 7.6 + - + +
1219G GLU* 4.4 13.4 + - - +
1222G PHE* 3.4 45.5 - - + -
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Residues in contact with ARG1214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400G MET* 4.6 25.5 + - - +
402G LEU 3.3 17.2 + - - -
404G THR* 2.6 18.5 + - - -
619G ILE* 4.7 17.5 - - - +
729G GLU* 2.4 51.2 + - - +
1210G LEU* 3.0 49.5 + - + +
1211G THR* 3.3 23.1 - - - +
1213G ILE* 1.3 77.0 - - - +
1215G ALA* 1.3 61.7 + - - +
1217G ARG* 3.1 34.1 + - - +
1219G GLU* 5.9 3.1 - - - +
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Residues in contact with ALA1215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727G LEU* 3.8 22.2 - - + -
729G GLU* 5.2 0.4 + - - -
767G GLY 3.9 0.9 - - - +
769G VAL* 3.5 22.9 + - + +
771G TYR* 3.7 28.5 - - + -
1211G THR 2.9 14.8 + - - +
1212G THR 3.0 8.5 + - - +
1214G ARG* 1.3 76.9 - - - +
1216G PHE* 1.3 63.2 + - - +
1217G ARG* 3.0 12.0 + - - +
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Residues in contact with PHE1216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768G PRO* 3.3 10.8 - - - +
769G VAL 4.0 8.1 - - - -
770G ALA* 3.7 11.0 - - + -
771G TYR* 3.5 27.8 - - + -
789G PHE* 3.2 45.1 - + + -
841G ARG* 4.7 17.9 - - + -
845G GLN* 3.3 42.0 - - + -
1212G THR* 2.9 50.1 + - - +
1213G ILE 3.9 2.9 - - - +
1215G ALA* 1.3 71.4 - - + +
1217G ARG* 1.3 62.7 + - - +
1218G TYR* 3.0 30.5 - - + -
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Residues in contact with ARG1217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766G ARG* 5.3 12.9 - - + +
767G GLY 3.9 17.7 - - - +
768G PRO* 4.1 9.9 - - + -
1213G ILE 2.9 8.5 + - - -
1214G ARG* 3.1 24.1 + - - +
1215G ALA 3.0 15.3 + - - +
1216G PHE* 1.3 77.7 - - - +
1218G TYR* 1.3 59.4 + - + +
1219G GLU* 3.3 36.6 + - - +
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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