Contacts of the helix formed by residues 718 - 727 (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 GLY 718 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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695G THR* 5.8 0.9 - - - -
696G LEU* 4.3 6.0 - - - +
716G GLY 3.0 4.6 + - - -
717G CYS* 1.3 79.7 - - - +
719G LYS* 1.3 64.0 + - - +
721G SER* 4.0 3.3 - - - -
722G LEU* 3.4 16.6 + - - +
902G MET* 3.2 16.0 - - - +
905G GLY* 4.4 7.4 - - - -
2004G ATP 3.0 27.8 + - - -
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Residues in contact with LYS 719 (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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711G ILE* 3.9 27.7 - - + +
712G VAL* 3.6 7.7 - - - +
713G GLY 3.0 39.1 + - - +
714G GLN 3.6 18.4 + - - -
717G CYS* 3.6 7.3 - - - -
718G GLY* 1.3 77.3 - - - +
720G SER* 1.3 66.1 + - - +
722G LEU* 3.6 2.9 + - - +
723G LEU* 3.1 27.0 + - - +
854G ASP* 5.0 4.9 - - - +
886G VAL* 4.4 16.4 - - + -
887G THR 3.7 14.6 + - - -
888G HIS* 5.0 7.2 + - + -
902G MET* 3.6 8.3 - - + -
1512G ASP* 5.4 3.0 - - - +
2004G ATP 2.9 36.6 + - - +
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Residues in contact with SER 720 (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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719G LYS* 1.3 70.4 - - - +
721G SER* 1.3 59.7 + - - +
723G LEU* 3.1 9.7 + - - +
724G LEU* 2.9 41.6 + - - +
774G GLN* 2.7 14.7 + - - -
853G ASP* 2.8 24.8 + - - -
854G ASP* 4.5 0.2 + - - -
2002G MG 2.0 31.3 - - - -
2004G ATP 2.3 28.8 + - - -
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Residues in contact with SER 721 (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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688G TRP* 3.1 16.3 - - - -
695G THR* 4.2 9.6 - - - -
696G LEU* 4.2 1.8 - - - -
718G GLY 4.1 4.7 - - - -
720G SER* 1.3 74.0 - - - +
722G LEU* 1.3 67.2 + - - +
724G LEU* 3.8 2.8 - - - +
725G ALA* 2.9 24.6 + - - +
730G MET* 3.5 23.3 - - - +
2004G ATP 2.5 48.8 + - - -
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Residues in contact with LEU 722 (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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681G ILE* 5.0 5.8 - - + -
686G PHE* 4.5 5.8 - - + -
696G LEU* 3.4 23.1 - - + +
699G ILE* 3.6 31.2 - - + -
701G ILE* 3.5 32.5 - - + -
711G ILE* 5.9 2.0 - - + -
718G GLY 3.4 14.6 + - - +
719G LYS 4.0 4.9 - - - +
720G SER 3.4 0.2 - - - -
721G SER* 1.3 77.4 - - - +
723G LEU* 1.3 65.4 + - + +
725G ALA* 3.3 1.6 + - + +
726G ALA* 2.9 27.5 + - + +
900G ILE* 5.2 0.9 - - + -
902G MET* 3.6 25.6 - - + -
907G ILE* 4.7 2.7 - - + -
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Residues in contact with LEU 723 (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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711G ILE* 4.4 20.2 - - + -
719G LYS 3.1 18.4 - - - +
720G SER* 3.4 11.7 - - - +
721G SER 3.1 0.6 - - - -
722G LEU* 1.3 81.7 - - + +
724G LEU* 1.3 69.3 + - + +
726G ALA* 2.9 18.1 + - + +
727G LEU* 3.0 20.5 + - - +
851G PHE* 3.2 43.7 - - + -
852G LEU 4.9 0.7 - - - +
853G ASP* 5.0 4.0 - - - -
884G VAL* 4.9 2.5 - - + -
886G VAL* 3.6 30.7 - - + -
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Residues in contact with LEU 724 (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* 5.8 5.2 - - + -
688G TRP* 3.9 28.5 - - + -
720G SER* 2.9 38.5 + - - +
721G SER* 3.9 4.3 - - - +
723G LEU* 1.3 78.6 - - + +
725G ALA* 1.3 59.2 + - - +
727G LEU* 2.9 23.5 + - + +
729G GLU* 3.1 37.7 + - + +
730G MET* 5.5 1.8 - - + +
771G TYR* 3.8 27.6 - - + +
851G PHE* 5.7 0.2 - - + -
853G ASP* 4.7 4.0 - - - +
1211G THR* 5.4 12.8 - - + -
2004G ATP 5.8 0.9 - - - +
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Residues in contact with ALA 725 (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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686G PHE* 3.4 45.2 - - + -
696G LEU* 4.4 0.4 - - + -
721G SER 2.9 18.3 + - - +
722G LEU* 3.4 8.3 - - - +
723G LEU 3.1 0.2 - - - -
724G LEU* 1.3 77.2 - - - +
726G ALA* 1.3 57.7 + - - +
727G LEU 3.0 0.2 - - - -
728G GLY* 2.9 22.5 + - - -
729G GLU 3.8 0.2 + - - -
730G MET* 3.6 22.8 + - + +
737G VAL* 5.9 1.6 - - - +
739G TRP* 5.4 0.5 - - - -
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Residues in contact with ALA 726 (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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679G VAL* 5.0 11.6 - - + +
681G ILE* 4.9 15.9 - - + -
686G PHE* 5.3 2.0 - - - -
722G LEU* 2.9 16.4 + - + +
723G LEU* 2.9 14.6 + - + +
725G ALA* 1.3 74.3 - - - +
727G LEU* 1.3 61.2 + - + +
728G GLY 3.2 1.1 - - - -
737G VAL* 5.2 7.2 - - - -
739G TRP* 3.1 28.9 + - - -
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Residues in contact with LEU 727 (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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723G LEU 3.0 26.6 + - - +
724G LEU* 2.9 14.9 + - + +
726G ALA* 1.3 83.0 - - + +
728G GLY* 1.3 54.7 + - - -
729G GLU* 2.9 30.6 + - + +
739G TRP* 5.0 3.6 - - - -
769G VAL* 5.3 14.4 - - + -
771G TYR* 3.7 32.8 - - + -
851G PHE* 4.6 20.2 - - + -
1211G THR* 5.2 3.6 - - - +
1215G ALA* 3.8 24.9 - - + -
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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