Contacts of the helix formed by residues 695 - 711 (chain A) in PDB entry 2QR8
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 ALA 695 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A LEU* 5.4 0.2 - - - -
614A GLY 4.9 3.7 + - - +
693A GLN* 3.7 29.8 + - + +
694A ASP* 1.3 76.3 - - - +
696A PRO* 1.3 69.9 - - - +
697A HIS 3.1 3.1 - - - -
698A LEU* 2.9 28.9 + - + -
699A VAL* 3.0 15.4 + - + +
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Residues in contact with PRO 696 (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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503A ASP* 3.8 16.8 - - - +
506A LEU* 4.0 33.4 - - + +
507A ARG* 3.6 44.4 - - + +
694A ASP* 3.5 17.9 - - - +
695A ALA* 1.3 89.0 - - - +
697A HIS* 1.3 57.3 + - + +
699A VAL* 3.3 3.6 + - - +
700A LYS* 3.0 26.5 + - - +
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Residues in contact with HIS 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A ARG* 4.4 10.3 - - - +
622A PRO* 5.7 0.2 - - - +
695A ALA 3.1 1.4 - - - -
696A PRO* 1.3 80.1 - - + +
698A LEU* 1.3 65.7 + - - +
700A LYS* 3.3 24.9 + - + +
701A GLY* 3.3 17.4 + - - -
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Residues in contact with LEU 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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620A ASN 3.5 24.2 - - - +
621A GLY* 4.0 11.3 - - - -
622A PRO* 4.0 11.0 - - + -
693A GLN* 4.0 23.3 - - - +
695A ALA* 2.9 18.8 + - + +
697A HIS* 1.3 81.4 - - - +
699A VAL* 1.3 57.7 + - + +
701A GLY* 3.2 3.3 + - - -
702A ALA* 2.9 26.6 + - - +
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Residues in contact with VAL 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A LEU* 4.4 4.0 - - + -
506A LEU* 3.8 17.5 - - + -
610A THR* 3.6 23.6 - - + -
614A GLY 3.3 27.6 - - - +
615A TYR* 3.9 13.5 - - + -
616A THR* 3.7 10.8 - - - +
693A GLN* 6.0 1.1 - - - +
695A ALA* 3.0 14.3 + - + +
696A PRO 3.3 7.4 + - - +
698A LEU* 1.3 78.6 - - + +
700A LYS* 1.3 57.1 + - - +
702A ALA* 3.7 6.2 - - - -
703A MET* 2.8 37.6 + - + +
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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
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500A GLU* 3.4 26.8 + - - +
503A ASP* 3.7 30.1 + - - +
507A ARG* 6.1 0.9 - - - +
696A PRO 3.0 11.5 + - - +
697A HIS* 3.3 27.8 + - + +
699A VAL* 1.3 77.1 - - - +
701A GLY* 1.3 62.4 + - - +
703A MET* 3.8 5.2 - - - +
704A ALA* 3.1 22.9 + - + +
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Residues in contact with GLY 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A PRO* 3.5 30.0 - - - +
697A HIS* 3.3 6.4 + - - -
698A LEU 3.2 6.4 + - - -
700A LYS* 1.3 79.6 - - - +
702A ALA* 1.3 56.5 + - - +
704A ALA* 3.4 6.8 + - - +
705A ALA* 2.9 29.3 + - - +
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Residues in contact with ALA 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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616A THR* 4.1 11.2 - - - +
619A ALA* 3.6 20.1 - - + +
620A ASN 3.9 1.8 - - - -
621A GLY* 3.6 33.9 - - - +
698A LEU 2.9 15.1 + - - +
699A VAL* 3.7 6.3 - - - +
701A GLY* 1.3 72.8 - - - +
703A MET* 1.3 55.9 + - - +
705A ALA* 3.3 2.0 + - - +
706A THR* 2.8 37.4 + - - -
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Residues in contact with MET 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A LEU* 3.6 25.6 - - + -
541A LYS* 5.6 0.2 - - + -
542A PRO* 3.8 30.1 - - + -
543A SER* 5.8 0.9 - - - +
606A VAL* 3.6 26.0 - - + +
610A THR* 3.5 25.8 - - + +
616A THR* 3.5 17.0 + - - +
699A VAL* 2.8 24.1 + - + +
700A LYS* 3.8 6.5 - - - +
702A ALA* 1.3 72.5 - - - +
704A ALA* 1.3 61.9 + - - +
706A THR* 3.2 5.6 + - - -
707A TYR* 3.1 41.0 + - + -
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Residues in contact with ALA 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A LYS* 3.1 19.2 + - + +
701A GLY* 3.4 8.0 + - - +
703A MET* 1.3 75.2 - - - +
705A ALA* 1.3 58.0 + - - +
707A TYR* 3.9 3.1 - - - +
708A SER* 2.9 31.2 + - - -
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Residues in contact with ALA 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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621A GLY 3.9 15.3 - - - +
622A PRO* 4.2 12.3 - - + +
624A ASP 4.6 4.0 - - - +
626A PRO* 5.5 0.5 - - - +
629A ILE* 3.6 19.1 - - + +
701A GLY 2.9 17.6 + - - +
702A ALA 3.6 5.4 - - - +
704A ALA* 1.3 73.2 - - - +
706A THR* 1.3 60.6 + - - +
708A SER* 3.4 6.3 + - - -
709A ALA* 2.9 30.0 + - - +
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Residues in contact with THR 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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602A TRP* 4.3 13.2 - - + -
606A VAL* 5.6 6.1 - - + -
616A THR* 4.1 8.6 - - + +
618A PHE* 4.8 8.4 - - + -
619A ALA* 3.4 16.1 + - - +
629A ILE* 4.0 20.2 - - + +
633A ILE* 4.6 2.2 - - + -
702A ALA 2.8 18.6 + - - -
703A MET* 3.4 11.7 - - - -
705A ALA* 1.3 77.8 - - - +
707A TYR* 1.3 70.8 + - + +
709A ALA* 3.1 5.9 + - - +
710A LEU* 3.1 37.1 + - + +
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Residues in contact with TYR 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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539A ASP* 5.3 3.1 - - - -
540A LEU 5.1 1.8 - - - -
541A LYS* 3.6 50.7 - - + +
542A PRO* 4.0 12.9 - - + +
602A TRP* 4.1 17.4 - + - -
603A SER* 2.8 39.2 + - - -
606A VAL* 4.2 7.5 - - + +
703A MET* 3.1 33.2 + - + +
704A ALA* 4.4 3.6 - - - +
706A THR* 1.3 83.7 - - + +
708A SER* 1.3 65.6 + - - +
710A LEU* 4.2 10.5 - - + -
711A ASN* 3.0 48.8 + - - +
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Residues in contact with SER 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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626A PRO* 6.2 1.0 - - - +
704A ALA 2.9 21.2 + - - -
705A ALA* 3.5 8.5 - - - -
707A TYR* 1.3 78.0 - - - +
709A ALA* 1.3 63.5 + - - +
711A ASN* 3.4 8.8 + - - -
712A ARG* 3.6 13.5 + - - +
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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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626A PRO* 3.8 43.1 - - + +
629A ILE* 4.0 13.7 - - + -
630A LEU* 3.9 8.6 - - + +
705A ALA 2.9 14.2 + - - +
706A THR 3.3 9.4 - - - +
708A SER* 1.3 78.6 - - - +
710A LEU* 1.3 57.8 + - - +
712A ARG* 3.0 31.7 + - - +
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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
----------------------------------------------------------
602A TRP* 3.5 35.7 - - + -
630A LEU* 4.1 10.3 - - + -
633A ILE* 3.8 28.7 - - + -
706A THR* 3.1 26.8 + - + +
707A TYR* 3.4 15.9 + - + +
709A ALA* 1.3 74.7 - - - +
711A ASN* 1.3 70.3 + - - +
712A ARG* 3.5 18.1 + - - +
713A ASN* 4.7 1.6 + - - +
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Residues in contact with ASN 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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539A ASP* 4.3 15.4 + - - -
541A LYS* 4.6 5.7 - - - +
707A TYR* 3.0 38.3 + - - +
708A SER* 3.4 4.0 + - - +
709A ALA 3.3 0.6 - - - -
710A LEU* 1.3 86.5 - - - +
712A ARG* 1.3 63.7 + - - +
713A ASN 3.2 3.4 - - - -
714A GLN* 3.0 29.0 + - + +
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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