Contacts of the helix formed by residues 694 - 709 (chain W) in PDB entry 5O9G
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 SER 694 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619W SER* 4.6 5.4 - - - -
622W GLN* 3.7 6.0 + - - -
660W ASN 3.1 26.2 + - - -
661W HIS* 3.8 4.6 + - - -
662W PRO* 3.4 17.5 - - - +
691W ILE 3.1 17.6 + - - +
692W MET 3.3 2.1 - - - -
693W SER* 1.3 83.4 + - - +
695W GLY* 1.3 64.7 + - - +
696W LYS* 4.2 7.9 - - - -
697W MET* 3.4 19.0 + - - +
698W VAL* 3.7 6.3 + - - +
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Residues in contact with GLY 695 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616W VAL* 3.7 21.7 - - - +
617W GLU 4.6 7.9 + - - -
618W LEU 6.1 0.2 - - - -
619W SER* 5.5 3.2 + - - +
694W SER* 1.3 72.2 - - - +
696W LYS* 1.3 59.4 + - - +
698W VAL* 3.4 6.3 + - - +
699W LEU* 2.9 36.7 + - - +
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Residues in contact with LYS 696 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616W VAL* 3.7 19.0 - - + +
660W ASN* 3.5 35.2 - - + +
694W SER* 3.3 5.9 - - - -
695W GLY* 1.3 76.8 - - - +
697W MET* 1.3 55.6 + - + +
699W LEU* 4.7 2.9 - - - -
700W LEU* 2.6 42.1 + - - +
723W MET* 6.4 1.1 - - + -
789W PHE* 2.8 36.1 + - + +
790W ASP* 4.2 3.0 - - - +
819W LEU* 3.4 46.1 + - + +
821W SER* 3.1 24.8 + - - -
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Residues in contact with MET 697 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661W HIS* 4.7 9.9 - - + +
690W LEU* 4.2 16.2 - - + +
691W ILE* 3.3 27.5 - - + +
694W SER* 3.4 15.2 + - - +
695W GLY 3.2 0.6 - - - -
696W LYS* 1.3 81.5 - - + +
698W VAL* 1.3 59.8 + - - +
700W LEU* 3.9 10.2 - - + +
701W ASP* 2.9 30.5 + - - +
723W MET* 3.9 25.8 - - - -
726W ILE* 5.9 2.2 - - + -
727W LEU* 4.0 16.2 - - + -
730W TYR* 3.8 44.7 + - + -
789W PHE* 5.3 1.3 - - - -
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Residues in contact with VAL 698 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691W ILE* 3.3 37.5 - - + +
692W MET* 4.1 12.8 - - + -
694W SER 3.8 6.5 - - - +
695W GLY* 3.4 7.9 + - - +
697W MET* 1.3 75.5 - - - +
699W LEU* 1.3 64.9 + - + +
701W ASP* 3.3 2.4 + - - +
702W GLN* 2.9 32.6 + - + +
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Residues in contact with LEU 699 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614W LEU* 3.7 36.6 - - + -
616W VAL* 3.8 25.4 - - + -
695W GLY* 2.9 19.1 + - - +
696W LYS* 4.6 2.2 - - - +
698W VAL* 1.3 80.6 - - + +
700W LEU* 1.3 58.7 + - - +
702W GLN* 3.9 19.7 - - - +
703W LEU* 2.9 37.8 + - + +
819W LEU* 5.5 2.5 - - + -
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Residues in contact with LEU 700 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696W LYS 2.6 23.5 + - - +
697W MET* 3.9 11.9 - - + +
698W VAL 3.3 0.2 - - - -
699W LEU* 1.3 76.9 - - - +
701W ASP* 1.3 57.6 + - - +
703W LEU* 4.3 6.2 - - + +
704W LEU* 2.9 39.2 + - + +
714W VAL* 5.8 2.5 - - + -
716W ILE* 4.8 14.1 - - + -
727W LEU* 4.7 11.9 - - + -
730W TYR* 6.2 2.0 - - + -
731W LEU* 6.2 3.6 - - + -
787W VAL* 3.9 32.5 - - + -
789W PHE* 3.6 31.4 - - + -
819W LEU* 5.0 6.6 - - + +
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Residues in contact with ASP 701 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691W ILE* 3.8 11.8 - - + +
697W MET 2.9 19.2 + - - +
698W VAL 3.7 3.8 - - - +
699W LEU 3.3 0.2 - - - -
700W LEU* 1.3 76.7 - - - +
702W GLN* 1.3 57.5 + - - +
704W LEU* 3.7 12.9 - - - +
705W THR* 2.7 45.7 + - - -
730W TYR* 3.5 27.0 + - + +
734W LYS* 4.9 11.9 - - - +
736W ILE* 6.2 0.2 - - - +
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Residues in contact with GLN 702 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698W VAL* 2.9 20.7 + - + +
699W LEU* 3.9 22.0 - - - +
701W ASP* 1.3 76.9 + - - +
703W LEU* 1.3 66.7 + - + +
705W THR* 3.3 7.4 + - - -
706W ARG* 2.9 27.1 + - + +
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Residues in contact with LEU 703 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612W ARG* 4.0 18.4 - - - +
614W LEU* 4.5 17.9 - - + -
699W LEU* 2.9 24.4 + - + +
700W LEU* 4.3 6.5 - - + +
702W GLN* 1.3 82.2 - - + +
704W LEU* 1.3 58.0 + - - +
706W ARG* 3.3 26.9 + - - +
707W LEU* 2.9 37.1 + - + +
787W VAL* 6.3 2.2 - - + -
817W TYR* 3.8 36.3 - - + -
819W LEU* 5.3 4.3 - - + -
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Residues in contact with LEU 704 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700W LEU* 2.9 28.0 + - + +
701W ASP* 3.7 13.9 - - - +
703W LEU* 1.3 78.1 - - - +
705W THR* 1.3 58.5 + - - +
707W LEU* 3.4 7.0 + - + -
708W LYS* 2.9 45.7 + - + +
714W VAL* 3.7 32.3 - - + -
730W TYR* 6.1 1.3 - - + -
731W LEU* 4.5 12.3 - - + -
736W ILE* 3.7 28.0 - - + -
765W PHE* 4.6 2.9 - - + -
766W VAL* 4.4 11.0 - - + -
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Residues in contact with THR 705 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701W ASP* 2.7 32.4 + - - -
702W GLN* 3.3 6.7 + - - -
704W LEU* 1.3 75.5 - - - +
706W ARG* 1.3 59.3 + - - +
708W LYS* 3.1 9.2 + - + +
709W LYS* 2.9 44.5 + - + +
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Residues in contact with ARG 706 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612W ARG* 5.6 2.6 - - - +
702W GLN* 2.9 18.3 + - + +
703W LEU* 3.3 27.2 + - + +
705W THR* 1.3 76.6 - - - +
707W LEU* 1.3 67.8 + - + +
709W LYS* 3.3 26.7 + - + +
710W ASP* 3.8 13.9 + - - +
817W TYR* 4.6 13.5 + - - -
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Residues in contact with LEU 707 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703W LEU* 2.9 25.0 + - + +
704W LEU* 3.8 10.1 - - + +
706W ARG* 1.3 84.2 - - + +
708W LYS* 1.3 59.4 + - + +
710W ASP* 3.4 2.5 + - - +
711W GLY* 2.9 28.8 + - - -
712W HIS* 3.7 37.4 + - + +
714W VAL* 4.2 17.3 - - + -
785W THR* 3.7 33.9 - - + +
787W VAL* 5.6 1.6 - - + -
815W MET* 6.0 3.8 - - + -
817W TYR* 5.2 17.3 - - + +
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Residues in contact with LYS 708 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704W LEU* 2.9 29.0 + - + +
705W THR* 3.1 10.3 + - + +
707W LEU* 1.3 75.9 - - + +
709W LYS* 1.3 62.5 + - - +
710W ASP 3.1 3.1 + - - -
711W GLY* 4.2 8.8 + - - +
712W HIS 4.7 10.3 + - - +
765W PHE* 3.2 64.0 - - + +
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Residues in contact with LYS 709 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705W THR* 2.9 29.4 + - + +
706W ARG* 3.3 17.4 + - + +
708W LYS* 1.3 76.2 - - - +
710W ASP* 1.3 66.9 + - - +
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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