Contacts of the helix formed by residues 656 - 671 (chain A) in PDB entry 4RG7
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 LYS 656 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651A TYR* 2.8 29.9 + - + +
654A GLN* 3.3 6.9 + - + +
655A GLU* 1.3 74.5 - - - +
657A PHE* 1.3 61.3 + - - +
658A SER 3.8 0.4 - - - -
659A LEU* 4.1 7.5 + - + +
660A ALA* 3.2 25.1 + - - +
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Residues in contact with PHE 657 (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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652A TYR* 5.5 4.5 - - + +
655A GLU* 3.4 9.3 + - - +
656A LYS* 1.3 70.2 - - - +
658A SER* 1.3 59.3 + - - +
659A LEU 3.1 2.2 - - - -
660A ALA* 2.8 9.4 + - - +
661A GLU 2.6 32.6 + - - -
704A ILE* 4.9 17.5 - - + -
708A ASN* 6.4 0.4 - - + -
711A CYS* 3.6 21.7 - - + -
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Residues in contact with SER 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A PHE* 1.3 78.0 + - - +
659A LEU* 1.3 57.8 + - - +
661A GLU* 3.7 16.7 - - - +
662A MET* 3.9 7.4 + - - +
708A ASN* 5.8 4.0 - - - -
711A CYS* 5.4 0.2 - - - -
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Residues in contact with LEU 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A TYR* 5.1 11.2 - - + -
656A LYS* 4.1 9.8 + - + +
657A PHE 3.1 1.2 - - - +
658A SER* 1.3 77.3 + - - +
660A ALA* 1.3 61.0 + - - +
661A GLU 3.1 1.6 - - - -
662A MET* 2.9 15.2 + - - +
663A HIS* 2.6 36.6 + - + -
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Residues in contact with ALA 660 (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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648A GLY* 3.5 25.1 - - - +
651A TYR* 3.7 9.7 - - + +
652A TYR* 3.9 7.2 - - + +
656A LYS 3.2 16.9 + - - +
657A PHE* 2.8 12.7 + - - +
659A LEU* 1.3 78.7 - - - +
661A GLU* 1.3 55.9 + - - +
663A HIS* 3.3 7.7 + - - +
664A PHE* 2.9 43.8 + - + -
711A CYS* 4.8 2.0 - - - -
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Residues in contact with GLU 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A PHE 2.6 17.9 + - - +
658A SER* 3.7 12.8 - - - +
660A ALA* 1.3 74.1 - - - +
662A MET* 1.3 53.1 + - - +
664A PHE* 3.0 7.1 + - - +
665A GLN* 2.7 36.6 + - - +
708A ASN* 4.5 13.5 - - + -
710A LEU* 4.2 7.4 - - + +
711A CYS* 3.7 21.0 - - - -
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Residues in contact with MET 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A SER 3.9 6.9 + - - +
659A LEU* 2.9 14.0 + - - +
661A GLU* 1.3 77.6 - - - +
663A HIS* 1.3 61.2 + - + +
665A GLN* 3.7 6.3 - - - +
666A LYS* 3.0 30.7 + - - +
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Residues in contact with HIS 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A TRP* 3.7 44.5 - + - +
647A LEU* 3.9 23.1 - - + +
648A GLY* 4.0 7.6 - - - -
651A TYR* 3.4 31.2 + + - -
659A LEU* 2.6 34.3 + - + -
660A ALA 3.6 6.3 + - - +
661A GLU 3.2 0.4 - - - -
662A MET* 1.3 78.7 - - + +
664A PHE* 1.3 66.2 + - - +
666A LYS* 3.4 1.0 + - - -
667A ALA* 2.9 26.3 + - - +
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Residues in contact with PHE 664 (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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645A TYR* 3.6 39.1 - + + -
648A GLY* 3.2 42.0 - - - -
649A MET* 3.6 8.3 - - - -
652A TYR* 4.3 7.4 - - + -
660A ALA* 2.9 26.6 + - + +
661A GLU 3.4 4.3 - - - +
663A HIS* 1.3 76.4 - - - +
665A GLN* 1.3 58.2 + - - +
667A ALA* 3.6 4.6 - - - +
668A LEU* 2.9 32.2 + - - +
710A LEU* 3.8 31.0 - - + -
711A CYS* 4.0 20.9 - - - -
714A HIS* 4.1 23.6 - + + -
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Residues in contact with GLN 665 (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 GLU 2.7 20.4 + - - +
662A MET* 3.7 7.9 - - - +
664A PHE* 1.3 72.2 - - - +
666A LYS* 1.3 65.8 + - - +
668A LEU* 3.3 2.3 + - - +
669A ASP* 3.0 32.2 + - - +
710A LEU* 3.5 20.1 - - + +
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Residues in contact with LYS 666 (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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644A TRP* 4.5 29.9 + - + -
662A MET 3.0 17.9 + - - +
663A HIS 3.9 2.7 - - - +
665A GLN* 1.3 75.9 - - - +
667A ALA* 1.3 60.1 - - - +
669A ASP* 3.6 10.3 - - - +
670A ILE* 3.5 16.5 + - - +
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Residues in contact with ALA 667 (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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641A TYR* 4.1 12.3 - - + +
644A TRP* 3.5 26.4 - - + +
645A TYR* 4.0 19.1 - - + +
663A HIS 2.9 18.5 + - - +
664A PHE* 3.6 7.2 - - - +
666A LYS* 1.3 74.4 - - - +
668A LEU* 1.3 50.5 + - - +
669A ASP 3.1 4.5 - - - -
670A ILE* 2.9 9.8 + - - +
671A ASN 2.8 31.6 + - - +
674A SER* 4.6 2.9 - - - +
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Residues in contact with LEU 668 (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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645A TYR* 6.0 2.4 - - + -
664A PHE 2.9 21.4 + - - +
665A GLN* 3.3 4.0 + - - +
667A ALA* 1.3 70.1 - - - +
669A ASP* 1.3 66.7 + - - +
671A ASN 3.2 26.5 - - - +
672A PRO* 3.4 14.7 - - + +
674A SER* 4.4 3.3 - - - +
710A LEU* 5.2 12.8 - - + -
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Residues in contact with ASP 669 (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 GLN* 3.0 24.5 + - - +
666A LYS* 3.6 10.4 - - - +
668A LEU* 1.3 78.1 - - - +
670A ILE* 1.3 64.4 + - - +
672A PRO* 4.8 2.4 - - - +
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Residues in contact with ILE 670 (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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483A CYS 5.2 0.9 - - - +
484A SER* 5.4 1.2 - - - -
485A TYR* 4.2 19.3 + - + +
639A ARG* 4.2 20.9 - - + +
641A TYR* 4.1 17.3 - - + -
644A TRP* 5.8 2.0 - - + -
666A LYS 3.5 8.5 + - - +
667A ALA* 2.9 10.3 + - - +
669A ASP* 1.3 81.9 - - - +
671A ASN* 1.3 60.6 + - - +
672A PRO* 4.1 3.9 - - - +
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Residues in contact with ASN 671 (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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485A TYR* 3.3 34.8 - - + -
641A TYR* 3.8 16.4 - - + -
667A ALA 2.8 9.7 + - - -
668A LEU* 3.2 15.5 - - - +
670A ILE* 1.3 75.3 - - - +
672A PRO* 1.3 63.6 - - - +
673A GLN 5.6 0.2 - - - -
674A SER* 2.3 37.6 + - - +
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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