Contacts of the helix formed by residues 692 - 713 (chain A) in PDB entry 2YD0
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 MET 692 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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687A MET* 4.0 17.3 - - + +
690A ARG* 3.0 56.7 + - + +
691A ASP* 1.3 78.3 - - - +
693A ASN* 1.3 65.4 + - - +
694A GLU 3.4 3.5 + - - -
695A VAL 3.5 2.8 + - - -
696A GLU* 3.0 24.3 + - - +
922A MET* 3.3 33.2 - - + -
926A PHE* 3.4 43.3 - - + -
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Residues in contact with ASN 693 (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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691A ASP* 4.0 1.0 + - - -
692A MET* 1.3 73.4 - - - +
694A GLU* 1.3 67.8 + - - +
696A GLU* 4.1 19.4 + - - +
697A THR* 3.0 43.0 + - - -
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Residues in contact with GLU 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A MET 3.4 1.2 - - - -
693A ASN* 1.3 82.6 + - - +
695A VAL* 1.3 61.5 + - + +
697A THR* 3.6 3.7 - - - -
698A GLN* 3.0 31.9 + - + +
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Residues in contact with VAL 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A MET* 4.0 15.9 - - + -
692A MET 3.5 3.1 + - - +
693A ASN 3.3 0.2 - - - -
694A GLU* 1.3 77.9 - - + +
696A GLU* 1.3 68.0 + - - +
698A GLN* 3.7 9.6 - - + +
699A PHE* 2.9 22.2 + - - +
926A PHE* 3.8 33.7 - - + -
929A ILE* 4.5 3.1 - - + -
930A ARG* 3.6 44.4 - - + +
933A LEU* 4.0 18.2 - - + -
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Residues in contact with GLU 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A TYR* 4.8 2.0 - - + +
687A MET* 3.8 28.3 - - + +
688A GLU* 3.5 28.5 + - + +
690A ARG 5.4 1.2 - - - +
692A MET 3.0 18.2 + - - +
693A ASN* 4.0 23.5 + - - +
695A VAL* 1.3 75.5 - - - +
697A THR* 1.3 58.5 + - - +
699A PHE* 3.2 2.1 + - - +
700A LYS* 2.6 71.1 + - + +
843A PRO* 5.8 1.4 - - - +
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Residues in contact with THR 697 (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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693A ASN* 3.0 35.3 + - - -
694A GLU* 3.6 4.3 - - - +
696A GLU* 1.3 79.4 - - - +
698A GLN* 1.3 59.1 + - + +
700A LYS* 3.9 8.1 - - - +
701A ALA* 3.0 30.4 + - + +
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Residues in contact with GLN 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A GLU* 3.0 22.2 + - + +
695A VAL* 3.7 10.5 - - + +
697A THR* 1.3 77.5 - - + +
699A PHE* 1.3 58.0 + - - +
701A ALA* 3.4 7.4 + - - +
702A PHE* 3.0 28.8 + - - +
705A ARG* 5.6 0.5 + - - -
930A ARG* 5.3 3.0 + - - +
933A LEU* 4.0 24.7 - - + +
934A GLN* 4.6 18.6 - - - +
937A LYS* 5.0 15.9 + - - +
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Residues in contact with PHE 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A LEU* 5.1 6.7 - - + -
680A LEU* 3.4 41.7 - - + -
683A MET* 3.7 36.6 - - + -
684A TYR* 3.8 24.5 - + + -
687A MET* 4.2 13.7 - - + -
695A VAL 2.9 19.1 + - - +
696A GLU 3.5 4.7 - - - +
698A GLN* 1.3 77.9 - - - +
700A LYS* 1.3 61.6 + - - +
702A PHE* 3.4 14.8 + + - +
703A LEU* 3.2 22.0 + - + +
929A ILE* 3.9 28.5 - - + -
933A LEU* 4.1 15.0 - - + -
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Residues in contact with LYS 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A TYR* 3.2 44.9 - - + -
688A GLU* 2.6 23.1 + - - -
696A GLU* 2.6 52.6 + - + +
697A THR* 3.5 6.7 + - - +
699A PHE* 1.3 75.3 - - - +
701A ALA* 1.3 65.1 + - - +
703A LEU* 3.2 8.2 + - - +
704A ILE* 3.2 27.6 + - - +
738A HIS* 3.8 28.3 + - + +
843A PRO* 5.4 1.2 - - - +
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Residues in contact with ALA 701 (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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697A THR* 3.0 19.7 + - + +
698A GLN* 3.6 7.9 - - - +
699A PHE 3.4 0.2 - - - -
700A LYS* 1.3 76.0 - - - +
702A PHE* 1.3 58.5 + - - +
704A ILE* 3.5 5.7 + - - +
705A ARG* 2.9 44.9 + - - +
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Residues in contact with PHE 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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658A LEU* 5.2 3.1 - - + -
661A SER* 4.8 9.0 - - - -
662A LEU* 4.0 25.4 - - + -
680A LEU* 4.7 18.6 - - + -
698A GLN 3.0 16.4 + - - +
699A PHE* 3.6 19.7 - + - +
700A LYS 3.2 0.2 - - - -
701A ALA* 1.3 77.8 - - - +
703A LEU* 1.3 63.3 + - + +
705A ARG* 3.2 17.5 + - - +
706A LEU* 2.8 52.3 + - + +
932A TRP* 4.0 23.3 - + - -
933A LEU* 3.7 20.6 - - + -
936A GLU* 4.1 19.5 - - - +
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Residues in contact with LEU 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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677A LEU* 4.1 22.7 - - + -
680A LEU* 4.0 34.3 - - + -
681A ILE* 4.3 12.6 - - + -
684A TYR* 3.7 33.2 - - + -
699A PHE* 3.2 13.8 + - + +
700A LYS* 3.2 9.8 + - - +
702A PHE* 1.3 84.0 - - + +
704A ILE* 1.3 62.6 + - + +
706A LEU* 3.2 10.3 + - + +
707A LEU* 3.2 27.6 + - + +
734A LEU* 4.7 13.9 - - + -
738A HIS* 4.9 4.0 - - + +
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Residues in contact with ILE 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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700A LYS 3.2 15.7 + - - +
701A ALA* 3.9 5.6 - - - +
703A LEU* 1.3 77.0 - - + +
705A ARG* 1.3 61.0 + - - +
707A LEU* 3.4 1.3 + - - -
708A ARG* 2.7 33.9 + - + +
711A ILE* 4.0 13.0 - - + +
734A LEU* 4.0 22.7 - - + -
735A ALA* 4.2 14.4 - - - -
738A HIS* 3.9 38.1 - - + +
740A TYR* 4.1 35.9 - - + -
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Residues in contact with ARG 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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698A GLN 5.6 0.6 + - - -
701A ALA* 2.9 36.3 + - - +
702A PHE* 3.5 15.4 - - + +
704A ILE* 1.3 76.9 - - - +
706A LEU* 1.3 64.0 + - - +
708A ARG* 3.2 43.4 + - - +
709A ASP 4.8 0.5 + - - -
936A GLU* 3.1 36.7 + - - -
937A LYS* 3.2 33.2 - - - +
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Residues in contact with LEU 706 (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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661A SER* 3.4 28.0 - - - +
662A LEU* 3.7 23.3 - - + +
664A LEU* 4.1 22.4 - - + +
665A LYS* 3.5 48.6 + - + +
680A LEU* 4.2 14.8 - - + -
702A PHE* 2.8 35.4 + - + +
703A LEU* 3.2 15.0 + - + +
705A ARG* 1.3 77.7 - - - +
707A LEU* 1.3 63.2 + - + +
708A ARG 3.7 0.2 + - - -
709A ASP* 5.0 1.2 + - - +
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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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664A LEU* 4.5 25.6 - - + +
673A VAL* 4.3 22.7 - - + -
677A LEU* 3.7 29.8 - - + -
703A LEU* 3.2 17.7 + - + +
704A ILE 3.5 0.4 - - - -
706A LEU* 1.3 84.0 - - + +
708A ARG* 1.3 65.7 + - - +
709A ASP 3.1 2.9 - - - -
710A LEU* 2.8 26.3 + - + +
711A ILE* 2.9 25.4 + - + +
731A LEU* 3.9 21.3 - - + -
734A LEU* 4.1 9.6 - - + -
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Residues in contact with ARG 708 (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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704A ILE* 2.7 25.2 + - + +
705A ARG* 3.2 42.1 + - - +
706A LEU 3.4 0.2 - - - -
707A LEU* 1.3 72.1 - - - +
709A ASP* 1.3 73.4 + - - +
711A ILE* 3.3 8.7 + - - +
712A ASP* 2.9 35.3 + - - +
740A TYR* 3.4 32.3 - - + +
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Residues in contact with ASP 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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665A LYS 4.7 16.9 - - - +
705A ARG 4.8 1.0 + - - -
706A LEU 5.0 1.0 + - - +
707A LEU 3.1 1.2 - - - -
708A ARG* 1.3 89.5 + - - +
710A LEU* 1.3 63.0 + - - +
712A ASP* 3.3 7.9 + - - +
713A LYS* 3.2 24.7 + - - +
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Residues in contact with LEU 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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665A LYS 5.8 0.8 + - - +
667A GLU 3.5 25.8 - - - +
668A THR* 4.5 15.9 - - + +
673A VAL* 3.6 27.4 - - + -
707A LEU* 2.8 18.2 + - + +
709A ASP* 1.3 77.6 - - - +
711A ILE* 1.3 64.3 + - - +
713A LYS* 3.4 23.9 + - + +
714A GLN* 3.1 41.2 + - - +
727A LEU* 4.7 7.9 - - + -
731A LEU* 3.7 20.4 - - + -
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Residues in contact with ILE 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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704A ILE* 4.0 34.8 - - + +
707A LEU* 2.9 23.5 + - + +
708A ARG* 3.5 8.5 - - - +
710A LEU* 1.3 76.6 - - - +
712A ASP* 1.3 62.2 + - - +
713A LYS 3.1 1.3 + - - -
714A GLN* 3.3 22.7 + - - +
731A LEU* 4.3 27.8 - - + +
732A LEU* 4.6 12.2 - - + +
734A LEU* 5.0 2.9 - - + -
735A ALA* 3.8 32.5 - - + -
740A TYR* 3.9 19.5 - - + -
743A CYS* 5.6 1.6 - - + -
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Residues in contact with ASP 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A ARG* 2.9 30.0 + - - +
709A ASP* 3.3 8.1 + - - +
711A ILE* 1.3 75.9 - - - +
713A LYS* 1.3 58.8 + - - +
714A GLN 3.4 4.3 + - - +
740A TYR* 2.6 42.2 + - - -
742A PRO* 5.4 1.4 - - - +
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Residues in contact with LYS 713 (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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668A THR* 5.9 8.1 - - + -
709A ASP 3.2 16.3 + - - +
710A LEU* 3.6 25.1 - - + +
711A ILE 3.1 0.6 - - - -
712A ASP* 1.3 76.6 - - - +
714A GLN* 1.3 65.3 + - - +
715A THR* 3.8 7.3 + - - +
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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
------------------------------------------------------------
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