Contacts of the helix formed by residues 697 - 711 (chain A) in PDB entry 3OPY
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 697 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A VAL 3.3 10.1 + - - -
607A GLY* 4.7 4.8 - - - -
696A GLY* 1.3 71.9 - - - +
698A PHE* 1.3 61.2 + - - -
699A GLU* 3.2 2.9 - - - -
700A ALA* 3.2 2.4 + - - +
701A PHE* 3.0 23.6 + - - +
723A CYS* 4.5 0.2 - - - -
726A ALA 3.2 9.8 + - - -
727A THR* 4.0 9.4 - - - -
732A VAL* 3.4 20.1 - - - +
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Residues in contact with PHE 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670A ARG* 5.9 0.4 - - - +
697A GLY* 1.3 72.9 - - - -
699A GLU* 1.4 53.2 + - - +
701A PHE* 3.3 30.0 + + - +
702A THR* 2.8 50.5 + - - -
731A ASN* 3.4 32.4 + - - +
732A VAL* 3.7 4.1 - - - +
733A PRO* 3.8 16.2 - - + -
954A TRP* 5.4 5.4 - + - -
957A GLU* 4.6 4.5 - - + -
958A THR 4.5 7.6 - - - -
961A LYS* 3.6 70.7 - - + +
962A TRP* 3.9 6.3 - - + -
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Residues in contact with GLU 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A VAL* 3.6 18.1 - - + +
607A GLY* 4.8 4.4 - - - -
670A ARG* 2.7 63.5 + - + +
672A LEU* 3.4 18.2 - - + +
697A GLY* 3.2 1.2 - - - -
698A PHE* 1.4 78.8 + - - +
700A ALA* 1.3 54.1 + - - +
702A THR* 3.9 6.0 + - - -
703A ALA* 2.7 34.8 + - - +
961A LYS* 2.7 26.4 + - - +
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Residues in contact with ALA 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A VAL* 3.6 9.7 + - - +
694A ILE* 3.6 29.0 - - + +
696A GLY* 3.5 32.3 - - - +
697A GLY 3.2 10.5 + - - +
699A GLU* 1.3 73.1 - - - +
701A PHE* 1.3 65.4 + - - +
703A ALA* 3.9 1.8 - - - +
704A LEU* 3.1 23.9 + - - +
723A CYS* 3.8 12.1 - - - -
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Residues in contact with PHE 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A GLY 3.0 12.2 + - - +
698A PHE* 3.3 36.3 - + - +
699A GLU 3.2 0.2 - - - -
700A ALA* 1.3 78.5 - - - +
702A THR* 1.4 62.9 + - - +
704A LEU* 3.4 5.6 + - - +
705A TYR* 3.2 19.9 + - - +
723A CYS* 3.8 7.8 - - - -
732A VAL* 3.8 13.2 - - + -
733A PRO* 3.7 32.1 - - + -
937A VAL* 3.9 17.3 - - + -
950A VAL* 3.9 13.3 - - + +
953A LEU* 3.8 38.8 - - + -
954A TRP* 3.4 31.4 - + - -
957A GLU* 4.4 3.6 - - + -
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Residues in contact with THR 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A LEU* 3.6 27.1 - - + -
698A PHE* 2.8 44.1 + - - -
699A GLU* 3.3 12.5 + - - -
701A PHE* 1.4 72.2 - - - +
703A ALA* 1.4 55.8 + - - +
705A TYR* 3.2 8.6 + - - +
706A GLU* 2.9 39.6 + - + +
954A TRP* 4.5 18.0 + - + +
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Residues in contact with ALA 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A VAL* 4.7 1.8 - - + -
638A PHE* 3.7 19.3 - - + -
672A LEU* 4.0 3.8 - - + +
673A PRO* 3.6 30.5 - - + -
694A ILE* 4.3 9.0 - - + -
699A GLU 2.7 21.2 + - - +
700A ALA* 3.9 6.7 - - - +
701A PHE 3.4 0.2 - - - -
702A THR* 1.4 67.3 - - - +
704A LEU* 1.4 56.7 + - - +
706A GLU* 3.1 2.3 + - - +
707A LEU* 2.8 38.6 + - - +
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Residues in contact with LEU 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694A ILE* 3.7 13.6 - - + +
700A ALA 3.1 14.2 + - - +
701A PHE 3.5 10.5 - - - +
703A ALA* 1.4 74.3 - - - +
705A TYR* 1.3 56.9 + - - +
707A LEU* 3.9 1.4 - - - +
708A ASP* 2.9 30.7 + - - +
721A MET* 3.5 39.3 - - + +
722A CYS 4.1 0.9 - - - -
723A CYS* 4.0 17.0 - - + +
935A SER* 4.1 7.6 - - - +
936A VAL 3.4 30.7 - - - +
937A VAL* 4.2 4.5 - - + -
950A VAL* 3.3 31.6 - - + -
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Residues in contact with TYR 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701A PHE 3.2 6.1 + - - +
702A THR* 3.2 11.1 + - + +
704A LEU* 1.3 78.9 - - - +
706A GLU* 1.3 61.2 + - + +
708A ASP* 3.2 5.1 + - - +
709A ALA* 2.9 46.4 + - + +
950A VAL* 4.0 22.4 - - + +
951A LYS* 4.6 16.8 - - + -
954A TRP* 3.5 81.6 - + + -
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Residues in contact with GLU 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A LEU* 3.7 9.2 - - - +
673A PRO* 3.3 13.2 - - + +
674A SER* 2.5 44.6 + - - -
677A MET* 3.6 13.2 - - + +
702A THR* 2.9 36.2 + - + +
703A ALA 3.5 6.7 - - - +
705A TYR* 1.3 82.7 - - + +
707A LEU* 1.4 55.7 + - - +
709A ALA* 3.3 7.3 + - - +
710A ALA* 2.9 27.9 + - - +
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Residues in contact with LEU 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A PHE* 3.7 19.5 - - + -
673A PRO* 3.8 24.5 - - + -
677A MET* 4.0 5.2 - - - -
680A VAL* 4.1 5.2 - - + -
684A PHE* 4.7 1.3 - - + -
692A LEU* 3.7 29.6 - - + -
694A ILE* 4.2 7.2 - - + -
703A ALA 2.8 21.5 + - - +
704A LEU 4.0 2.7 - - - +
706A GLU* 1.4 69.1 - - - +
708A ASP* 1.3 66.6 + - - +
710A ALA* 3.1 12.7 + - - +
711A ARG* 3.3 9.2 + - - +
717A PHE* 3.7 45.0 - - + +
721A MET* 3.7 19.5 - - + -
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Residues in contact with ASP 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A LEU 2.9 19.8 + - - +
705A TYR* 3.4 7.0 - - - +
707A LEU* 1.3 75.2 - - - +
709A ALA* 1.3 62.2 + - - +
711A ARG* 3.2 41.3 + - - +
721A MET* 4.8 0.8 - - - -
930A ILE* 5.7 0.2 - - - +
932A ASP* 3.9 13.2 - - - +
935A SER* 3.2 36.1 + - - +
950A VAL* 4.0 9.6 - - + +
951A LYS* 3.3 34.9 - - - +
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Residues in contact with ALA 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A TYR* 2.9 32.7 + - + +
706A GLU* 3.6 7.9 - - - +
708A ASP* 1.3 78.8 + - - +
710A ALA* 1.4 60.6 + - - +
711A ARG 3.3 1.0 + - - -
712A ALA* 3.8 9.4 + - - +
713A GLN* 3.6 14.5 - - - +
951A LYS* 5.4 8.3 - - - +
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Residues in contact with ALA 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A MET* 3.9 15.5 - - + -
706A GLU 2.9 17.3 + - - +
707A LEU 3.1 7.7 + - - +
709A ALA* 1.4 72.8 - - - +
711A ARG* 1.4 52.2 + - - +
712A ALA 3.1 3.6 - - - -
713A GLN* 3.0 18.8 + - - +
714A TYR* 2.7 45.0 + - + -
717A PHE* 3.6 18.4 - - + -
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Residues in contact with ARG 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707A LEU 3.3 6.9 + - - +
708A ASP* 3.2 29.3 + - - +
709A ALA 3.2 0.8 - - - -
710A ALA* 1.4 74.0 - - - +
712A ALA* 1.3 61.0 + - - +
714A TYR 3.7 20.1 - - - +
715A PRO* 3.8 6.9 - - - +
717A PHE* 3.4 27.5 + - - +
718A ASN* 3.5 21.8 + - + +
719A ILE 2.8 26.6 + - - -
721A MET* 4.7 1.0 - - - -
930A ILE* 3.6 32.2 - - + +
931A ASP 2.6 32.1 + - - -
934A THR* 2.8 22.2 + - - -
935A SER* 3.1 27.4 + - - +
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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