Contacts of the helix formed by residues 720 - 729 (chain J) in PDB entry 6XAV
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 720 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1223I ARG* 4.1 1.3 - - - +
642J ASP 5.0 1.4 + - - -
643J ASP* 2.9 39.2 + - - +
645J VAL* 5.2 3.0 - - - +
701J LEU* 3.5 20.7 - - + +
704J GLU* 5.0 5.6 - - + +
718J SER* 3.2 13.8 + - - +
719J PHE* 1.3 82.0 - - - +
721J SER* 1.3 76.6 + - - +
722J ILE* 3.1 16.9 + - - +
723J TYR* 3.6 17.0 - - + +
724J MET* 3.2 22.9 + - - +
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Residues in contact with SER 721 (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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1209I GLN* 5.6 0.3 + - - -
1223I ARG* 3.4 18.0 + - - +
637J ALA* 5.4 2.5 - - - +
638J SER* 3.2 29.1 + - - -
639J VAL* 4.4 3.1 - - - -
643J ASP* 3.1 32.0 + - - +
720J ASN* 1.3 81.0 + - - +
722J ILE* 1.3 63.1 + - - -
723J TYR 3.3 0.2 + - - -
724J MET* 3.6 13.0 + - - +
725J MET* 3.4 23.8 + - - +
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Residues in contact with ILE 722 (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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1104I PRO* 4.9 18.5 - - + +
639J VAL* 4.2 25.1 - - + -
643J ASP* 3.4 20.0 - - + +
644J MET* 3.7 28.9 - - + -
701J LEU* 4.2 19.3 - - + -
720J ASN* 3.1 12.3 + - - +
721J SER* 1.3 76.9 - - - +
723J TYR* 1.3 61.8 + - - +
725J MET* 3.7 12.5 + - - +
726J ALA* 3.4 21.3 + - - +
737J ILE* 4.3 21.2 - - + +
740J LEU* 5.0 9.9 - - + -
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Residues in contact with TYR 723 (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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511J TYR* 4.8 1.6 - - - -
698J MET* 4.8 13.0 - - - -
701J LEU* 4.0 25.8 - - + -
702J GLN* 3.2 46.9 + - + +
717J VAL* 3.6 24.8 - - + +
718J SER* 3.8 19.1 - - - -
720J ASN* 3.5 21.7 + - + +
721J SER 3.2 1.0 - - - -
722J ILE* 1.3 81.0 - - - +
724J MET* 1.3 60.1 + - + +
726J ALA* 3.2 4.7 + - + +
727J ASP* 2.7 69.3 + - + +
737J ILE* 5.2 4.7 - - + -
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Residues in contact with MET 724 (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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1223I ARG* 3.3 33.2 - - - +
508J LEU* 4.1 13.9 - - + +
511J TYR* 4.0 17.0 - - + -
512J TYR* 4.9 15.5 - - + -
515J ARG* 3.7 27.1 - - - +
637J ALA* 4.4 20.6 - - + -
718J SER 4.6 2.5 - - - +
719J PHE* 4.2 15.0 - - - +
720J ASN 3.2 17.3 + - - +
721J SER* 3.6 6.3 + - - +
722J ILE 3.5 0.2 - - - -
723J TYR* 1.3 77.7 - - + +
725J MET* 1.3 53.3 + - + +
727J ASP* 4.4 2.9 - - - -
728J SER* 2.6 40.8 + - - -
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Residues in contact with MET 725 (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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1100I PRO* 4.1 12.1 - - + +
1101I LEU* 3.8 38.1 - - + -
1104I PRO* 3.7 28.3 - - + -
508J LEU* 4.5 12.1 - - + -
637J ALA* 4.0 23.6 - - + +
638J SER 4.2 10.5 - - - +
639J VAL* 4.9 3.4 - - + -
721J SER 3.4 18.8 + - - +
722J ILE* 3.9 11.0 - - - +
723J TYR 3.2 0.6 - - - -
724J MET* 1.3 77.0 - - + +
726J ALA* 1.3 61.2 + - - +
728J SER* 3.9 3.1 - - - -
729J GLY* 3.2 2.9 + - - -
730J ALA* 3.0 32.1 + - + +
731J ARG 3.9 15.3 + - - +
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Residues in contact with ALA 726 (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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722J ILE 3.4 7.6 + - - +
723J TYR* 3.2 4.5 + - + +
725J MET* 1.3 76.3 - - - +
727J ASP* 1.3 67.1 + - - +
729J GLY* 3.1 12.6 + - - -
731J ARG 5.1 0.2 + - - -
732J GLY* 4.4 13.8 - - - +
733J SER* 4.3 20.1 - - - +
734J ALA 4.8 0.9 - - - +
737J ILE* 3.7 30.5 - - + -
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Residues in contact with ASP 727 (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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511J TYR* 3.8 21.4 + - - +
597J GLY* 5.5 1.7 - - - -
717J VAL* 4.3 4.0 - - - +
723J TYR* 2.7 60.5 + - + +
724J MET* 4.1 2.2 - - - +
726J ALA* 1.3 74.5 - - - +
728J SER* 1.3 63.0 + - - +
729J GLY 3.2 0.7 + - - -
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Residues in contact with SER 728 (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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507J VAL* 3.8 10.5 - - - +
508J LEU* 3.8 12.0 - - - +
511J TYR* 3.6 39.4 - - - -
597J GLY* 3.8 5.7 - - - -
598J LYS* 3.0 28.5 + - - +
724J MET 2.6 25.2 + - - -
725J MET* 3.5 5.0 + - - -
727J ASP* 1.3 76.2 - - - +
729J GLY* 1.3 60.9 + - - +
730J ALA* 3.3 8.0 + - - +
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Residues in contact with GLY 729 (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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503J SER* 5.5 0.3 - - - -
507J VAL* 4.5 1.1 - - - +
598J LYS* 3.2 38.4 + - - +
725J MET 3.2 1.9 + - - -
726J ALA* 3.1 13.5 + - - -
727J ASP 3.1 5.4 - - - -
728J SER* 1.3 79.7 - - - +
730J ALA* 1.3 66.6 + - - +
731J ARG 3.6 0.9 - - - -
732J GLY 5.1 6.3 - - - -
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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
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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