Contacts of the helix formed by residues 655 - 664 (chain J) 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 ASN 655 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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653J THR* 3.3 2.2 - - - +
654J GLU* 1.3 76.8 - - - +
656J MET* 1.3 59.4 + - - +
657J ALA 2.9 1.1 - - - -
658J ARG* 2.6 23.4 + - - -
659J GLU* 2.8 9.5 + - - -
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Residues in contact with MET 656 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H U 6.1 5.4 - - - -
653J THR* 5.0 3.0 - - - +
655J ASN* 1.3 72.8 - - - +
657J ALA* 1.3 50.9 + - - +
659J GLU* 3.4 6.2 - - - +
660J HIS* 2.5 33.4 + - - -
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Residues in contact with ALA 657 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651J CYS* 5.5 8.6 - - - +
653J THR 4.2 12.2 + - - +
654J GLU* 4.4 5.4 - - - +
655J ASN 2.9 4.2 - - - +
656J MET* 1.3 77.9 - - - +
658J ARG* 1.3 58.8 + - - +
660J HIS* 3.6 2.2 + - - +
661J PHE* 3.3 15.8 + - - -
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Residues in contact with ARG 658 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654J GLU 3.8 8.2 + - - -
655J ASN 2.6 16.1 + - - -
657J ALA* 1.3 70.3 - - - +
659J GLU* 1.3 51.9 + - - +
661J PHE* 3.1 3.9 + - - +
662J LYS* 2.3 35.4 + - - -
667J GLU* 4.5 14.8 - - - +
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Residues in contact with GLU 659 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H U 4.3 14.6 - - - +
8H C 3.8 12.5 + - - +
655J ASN 2.8 11.6 + - - -
656J MET* 3.1 6.9 + - - +
658J ARG* 1.3 76.0 - - - +
660J HIS* 1.3 56.4 + - - +
662J LYS* 3.3 5.1 - - - +
663J LYS 3.0 23.6 + - - -
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Residues in contact with HIS 660 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H C 5.0 3.4 + - - -
656J MET 2.5 20.0 + - - -
657J ALA* 3.8 3.4 - - - +
658J ARG 3.2 0.2 - - - -
659J GLU* 1.3 74.4 - - - +
661J PHE* 1.3 61.6 + - - +
663J LYS* 3.2 10.2 + - - -
664J HIS 3.9 2.4 + - - -
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Residues in contact with PHE 661 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657J ALA 3.3 9.3 + - - -
658J ARG* 3.1 7.2 + - - +
660J HIS* 1.3 74.3 - - - +
662J LYS* 1.3 51.0 + - - +
664J HIS* 2.8 21.9 + - - +
666J ALA* 2.8 34.3 + - - +
667J GLU* 4.2 2.9 - - - +
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Residues in contact with LYS 662 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H C 5.6 1.6 - - - -
658J ARG 2.3 25.4 + - - -
659J GLU* 3.1 8.0 + - - +
660J HIS 3.0 1.0 - - - -
661J PHE* 1.3 70.2 - - - +
663J LYS* 1.3 61.7 + - - +
665J GLY* 3.0 14.6 + - - +
666J ALA 4.6 2.0 - - - +
667J GLU* 4.8 4.5 - - - +
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Residues in contact with LYS 663 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H C 4.1 24.6 - - - -
9H U 5.0 7.5 + - - -
659J GLU 3.0 11.5 + - - -
660J HIS 3.2 5.3 + - - -
661J PHE 3.1 1.0 - - - -
662J LYS* 1.3 77.7 - - - +
664J HIS* 1.3 57.7 + - - +
665J GLY 3.6 0.3 + - - -
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Residues in contact with HIS 664 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642J SER* 5.8 10.1 - - - +
660J HIS 3.9 3.2 + - - -
661J PHE* 2.8 9.5 + - - +
663J LYS* 1.3 77.2 - - - +
665J GLY* 1.3 63.3 + - - +
666J ALA* 3.1 4.8 + - - -
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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