Contacts of the helix formed by residues 676 - 697 (chain A) in PDB entry 6AH0
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 ARG 676 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675A GLN* 1.3 76.1 - - - +
677A VAL* 1.3 62.9 + - - +
678A GLU 3.6 0.9 - - - -
679A SER* 4.1 3.5 - - - +
680A HIS* 3.0 20.4 + - - -
40O LYS* 5.6 10.0 - - - +
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Residues in contact with VAL 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A GLN* 3.3 5.7 + - - +
676A ARG* 1.3 78.1 - - - +
678A GLU* 1.3 59.5 + - - +
680A HIS* 3.2 1.7 + - - -
681A PHE* 2.9 26.0 + - - -
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Residues in contact with GLU 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A GLN 4.6 2.2 + - - -
676A ARG 3.6 0.2 - - - -
677A VAL* 1.3 75.3 - - - +
679A SER* 1.3 62.1 + - - +
681A PHE* 3.3 2.8 + - - +
682A ASP* 3.3 17.7 + - - -
746A LYS* 6.1 1.2 - - - -
749A TRP* 5.4 15.7 - - - +
750A TRP* 5.7 1.3 - - - +
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Residues in contact with SER 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A GLN 5.1 1.8 + - - -
676A ARG* 3.8 6.1 + - - +
677A VAL 3.2 0.4 - - - -
678A GLU* 1.3 75.2 - - - +
680A HIS* 1.3 64.7 + - - +
682A ASP* 3.4 2.9 + - - -
683A LEU* 3.0 19.2 + - - -
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Residues in contact with HIS 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A ARG 3.0 18.5 + - - -
677A VAL 3.6 0.9 - - - -
679A SER* 1.3 76.0 - - - +
681A PHE* 1.3 62.2 + - - +
683A LEU* 3.2 2.6 + - - +
684A GLU* 3.0 20.3 + - - -
39O MET 5.9 3.8 - - - -
40O LYS* 6.1 3.8 - - - +
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Residues in contact with PHE 681 (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 VAL 2.9 14.3 + - - -
678A GLU* 3.8 3.8 - - - +
679A SER 3.2 0.6 - - - -
680A HIS* 1.3 76.9 - - - +
682A ASP* 1.3 55.9 + - - +
684A GLU* 3.3 1.4 + - - -
685A LEU* 2.9 25.6 + - - -
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Residues in contact with ASP 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A GLU 3.3 12.0 + - - -
679A SER* 3.9 2.2 - - - +
681A PHE* 1.3 75.0 - - - +
683A LEU* 1.3 62.1 - - - +
685A LEU* 3.2 2.6 + - - +
686A ARG* 3.0 21.5 + - - -
746A LYS* 6.0 6.2 - - - +
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Residues in contact with LEU 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A SER 3.0 14.1 + - - -
680A HIS* 3.2 4.4 + - - +
682A ASP* 1.3 77.1 - - - +
684A GLU* 1.3 61.4 + - - +
686A ARG* 3.5 1.2 + - - -
687A ALA* 3.2 17.0 + - - -
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Residues in contact with GLU 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A HIS 3.0 13.5 + - - -
681A PHE 3.8 2.2 - - - -
683A LEU* 1.3 76.4 - - - +
685A LEU* 1.3 56.3 + - - +
687A ALA* 3.2 3.0 + - - +
688A ALA* 2.9 26.2 + - - -
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Residues in contact with LEU 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A PHE 2.9 15.1 + - - -
682A ASP* 3.2 4.2 + - - +
684A GLU* 1.3 76.3 - - - +
686A ARG* 1.3 61.1 + - - +
688A ALA* 3.2 3.0 + - - +
689A VAL* 3.2 18.7 + - - -
138N ILE* 6.5 0.7 - - - +
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Residues in contact with ARG 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A ASP 3.0 15.0 + - - -
683A LEU 4.0 1.8 - - - -
685A LEU* 1.3 77.8 - - - +
687A ALA* 1.3 60.3 + - - +
689A VAL* 3.4 2.5 + - - +
690A MET* 3.0 19.4 + - - -
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Residues in contact with ALA 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A LEU 3.2 11.1 + - - -
684A GLU* 3.2 7.7 + - - +
686A ARG* 1.3 76.3 - - - +
688A ALA* 1.3 62.2 + - - +
690A MET* 3.2 2.8 + - - +
691A HIS* 3.0 20.4 + - - -
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Residues in contact with ALA 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A GLU 2.9 14.0 + - - -
685A LEU* 3.2 4.6 + - - +
687A ALA* 1.3 76.8 - - - +
689A VAL* 1.3 57.5 + - - +
691A HIS* 3.3 1.8 + - - +
692A ASP* 2.8 25.6 + - - -
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Residues in contact with VAL 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A LEU 3.2 11.7 + - - -
686A ARG* 3.8 2.7 - - - +
688A ALA* 1.3 75.6 - - - +
690A MET* 1.3 52.3 + - - +
692A ASP* 4.3 1.8 - - - +
693A ILE* 2.3 39.3 + - - +
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Residues in contact with MET 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A ARG 3.0 14.5 + - - -
687A ALA* 3.2 4.7 + - - +
689A VAL* 1.3 77.6 - - - +
691A HIS* 1.3 60.4 + - - +
693A ILE* 4.3 1.3 - - - +
694A LEU* 3.7 12.8 + - - -
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Residues in contact with HIS 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A ALA 3.0 14.1 + - - -
688A ALA 3.8 2.2 - - - -
690A MET* 1.3 77.2 - - - +
692A ASP* 1.3 63.0 + - - +
694A LEU* 3.8 1.6 + - - -
695A ASP* 3.8 12.3 + - - -
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Residues in contact with ASP 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A ALA 2.8 15.1 + - - -
689A VAL* 3.2 4.0 - - - +
691A HIS* 1.3 75.6 - - - +
693A ILE* 1.3 52.2 + - - +
695A ASP* 3.3 3.3 + - - +
696A MET* 2.5 35.5 + - - -
146N LYS* 6.0 4.3 - - - +
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Residues in contact with ILE 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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689A VAL 2.3 25.2 + - - -
690A MET* 4.3 1.8 - - - +
691A HIS 3.4 0.4 - - - -
692A ASP* 1.3 65.9 - - - +
694A LEU* 1.3 65.8 + - - +
696A MET* 4.2 2.2 - - - +
697A MET 3.0 28.5 + - - +
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Residues in contact with LEU 694 (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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690A MET 3.7 11.7 + - - -
691A HIS 3.8 2.4 + - - -
692A ASP 3.4 0.6 - - - -
693A ILE* 1.3 76.3 - - - +
695A ASP* 1.3 60.5 + - - +
697A MET* 3.8 11.0 + - - +
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Residues in contact with ASP 695 (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 HIS 3.8 8.1 + - - -
692A ASP* 3.3 5.7 + - - +
693A ILE 3.2 0.4 - - - -
694A LEU* 1.3 77.3 - - - +
696A MET* 1.3 59.8 + - - +
697A MET* 3.6 0.3 + - - -
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Residues in contact with MET 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A ASP 2.5 21.9 + - - -
693A ILE* 3.2 3.1 + - - +
695A ASP* 1.3 75.2 - - - +
697A MET* 1.3 55.9 + - - +
146N LYS* 4.6 15.3 - - - +
149N LEU* 3.9 4.5 - - - +
150N ALA* 3.2 33.0 + - - +
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Residues in contact with MET 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 ILE* 3.0 18.0 + - - +
694A LEU* 3.8 9.6 - - - +
695A ASP 3.5 3.5 - - - -
696A MET* 1.3 78.7 - - - +
698A PRO* 1.3 65.8 - - - +
699A GLU* 3.2 3.4 + - - -
149N LEU 5.4 1.8 - - - -
150N ALA 5.4 0.4 - - - -
152N VAL* 5.0 9.2 - - - +
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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