Contacts of the helix formed by residues 656 - 671 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651B TYR* 2.8 20.1 + - + +
654B GLN* 3.1 10.7 - - + +
655B GLU* 1.3 74.9 - - - +
657B PHE* 1.3 62.8 - - - +
658B SER* 3.2 3.8 - - - -
659B LEU* 3.0 15.9 + - + +
660B ALA 3.0 17.7 + - - -
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Residues in contact with PHE 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651B TYR 5.0 0.2 - - - -
652B TYR* 5.6 2.2 - - - +
655B GLU* 3.3 8.2 + - - +
656B LYS* 1.3 73.2 - - - +
658B SER* 1.3 65.3 + - - +
659B LEU 3.2 0.2 - - - -
660B ALA* 3.8 5.2 - - - -
661B GLU* 2.9 23.2 + - - +
704B ILE* 4.6 18.6 - - + -
708B ASN* 4.7 5.6 - - + +
711B CYS* 3.1 33.7 - - + -
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Residues in contact with SER 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B LYS 3.2 1.3 - - - -
657B PHE* 1.3 79.4 - - - +
659B LEU* 1.3 62.3 + - - +
661B GLU* 3.8 11.5 - - - +
662B MET* 3.8 7.8 + - - +
708B ASN* 5.6 2.7 - - - +
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Residues in contact with LEU 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B TYR* 4.4 11.0 - - + -
656B LYS* 3.0 16.9 + - + +
658B SER* 1.3 78.2 - - - +
660B ALA* 1.3 67.5 + - - +
662B MET* 2.9 20.1 + - - +
663B HIS* 3.2 12.1 + - - +
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Residues in contact with ALA 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B GLY* 3.7 23.8 - - - +
651B TYR* 3.9 7.8 - - + +
652B TYR* 3.9 12.3 - - - +
656B LYS 3.0 12.2 + - - +
657B PHE* 3.4 11.6 + - - +
659B LEU* 1.3 78.0 - - - +
661B GLU* 1.3 51.3 + - - +
663B HIS* 3.3 3.8 + - - +
664B PHE* 2.8 54.0 + - + -
711B CYS* 4.0 3.4 - - - -
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Residues in contact with GLU 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B PHE 2.9 18.8 + - - +
658B SER* 3.8 7.4 - - - +
660B ALA* 1.3 74.3 - - - +
662B MET* 1.3 64.7 + - - +
663B HIS 3.0 0.5 + - - -
664B PHE* 3.0 4.2 + - - +
665B GLN* 2.9 25.3 + - - +
708B ASN* 5.0 11.2 - - + -
709B PRO* 6.1 0.9 - - + -
710B LEU* 4.3 17.2 - - + +
711B CYS* 3.7 11.6 - - - -
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Residues in contact with MET 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B TRP* 5.2 2.3 - - - -
658B SER 3.8 8.0 + - - +
659B LEU* 2.9 14.4 + - - +
661B GLU* 1.3 76.0 - - - +
663B HIS* 1.3 59.9 + - - +
665B GLN* 3.7 7.8 - - - +
666B LYS* 3.5 18.4 + - - +
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Residues in contact with HIS 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B TRP* 3.5 41.4 - - + +
647B LEU* 4.9 3.8 - - + -
648B GLY* 4.0 13.5 - - - +
651B TYR* 6.1 0.7 - - + -
659B LEU 3.2 9.6 + - - +
660B ALA* 3.5 9.2 - - - +
661B GLU 3.0 0.2 - - - -
662B MET* 1.3 74.6 - - - +
664B PHE* 1.3 66.0 + - - +
665B GLN 3.2 1.3 - - - -
666B LYS* 3.0 15.2 + - - +
667B ALA* 3.1 9.9 + - - +
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Residues in contact with PHE 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B TYR* 3.8 17.0 - - + -
648B GLY* 3.3 36.3 - - - -
649B MET* 3.6 9.9 - - + -
652B TYR* 4.3 7.9 - - + -
660B ALA* 2.8 41.2 + - + +
661B GLU 3.6 4.0 - - - +
663B HIS* 1.3 71.9 - - - +
665B GLN* 1.3 56.9 + - - +
667B ALA* 3.3 4.5 + - + +
668B LEU* 2.8 52.0 + - + +
675B SER* 6.2 0.2 - - - -
710B LEU* 4.0 24.7 - - + -
711B CYS* 4.4 7.6 - - - -
714B HIS* 4.1 26.0 - - + -
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Residues in contact with GLN 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661B GLU 2.9 15.8 + - - +
662B MET* 3.7 9.9 - - - +
664B PHE* 1.3 76.0 - - - +
666B LYS* 1.3 54.1 + - - +
668B LEU* 3.4 7.2 - - - +
669B ASP* 2.5 69.6 + - - +
710B LEU* 5.1 6.3 - - + +
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Residues in contact with LYS 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644B TRP* 3.6 41.0 - - + -
662B MET 3.5 7.9 + - - +
663B HIS 3.0 9.9 + - - +
665B GLN* 1.3 79.6 - - - +
667B ALA* 1.3 62.7 + - - +
669B ASP* 3.6 10.3 + - - +
670B ILE* 3.4 18.9 + - - +
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Residues in contact with ALA 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641B TYR* 3.5 25.7 - - + +
644B TRP* 3.7 6.0 - - + +
645B TYR* 3.5 41.1 - - + +
663B HIS 3.1 6.9 + - - +
664B PHE* 3.8 7.4 - - + +
666B LYS* 1.3 75.5 - - - +
668B LEU* 1.3 61.8 + - + +
670B ILE 3.1 3.6 + - - -
671B ASN 2.9 27.9 + - - +
674B SER* 4.1 4.7 - - - +
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Residues in contact with LEU 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B PHE* 2.8 39.6 + - + +
665B GLN* 3.9 7.9 - - - +
667B ALA* 1.3 75.3 - - + +
669B ASP* 1.3 64.4 + - - +
671B ASN 3.3 5.6 - - - +
672B PRO* 3.0 50.5 - - + +
674B SER* 4.2 8.7 - - - +
675B SER* 4.1 20.4 - - - +
710B LEU* 5.1 8.7 - - + +
713B PHE* 6.2 3.4 - - + -
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Residues in contact with ASP 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B GLN* 2.5 57.7 + - - +
666B LYS* 3.8 9.8 - - - +
667B ALA 3.2 0.2 - - - -
668B LEU* 1.3 74.7 - - - +
670B ILE* 1.3 62.9 + - - +
672B PRO* 5.3 1.0 - - - +
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Residues in contact with ILE 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483B CYS 4.9 0.2 - - - +
484B SER* 4.4 4.7 - - - +
485B TYR* 3.1 26.5 - - + +
639B ARG* 4.1 25.4 - - + +
640B HIS 5.2 0.2 - - - -
641B TYR* 4.2 13.2 - - + +
644B TRP* 6.4 0.2 - - + -
666B LYS 3.4 9.0 + - - +
667B ALA 3.1 9.0 + - - +
669B ASP* 1.3 81.7 - - - +
671B ASN* 1.3 60.0 + - + +
672B PRO* 4.3 2.2 - - - +
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Residues in contact with ASN 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485B TYR* 3.4 36.1 - - + +
517B GLU* 5.3 9.6 + - - +
641B TYR* 3.9 27.1 - - + -
667B ALA 2.9 10.2 + - - +
668B LEU* 3.3 6.5 - - - -
670B ILE* 1.3 78.0 - - - +
672B PRO* 1.3 71.7 - - - +
673B GLN* 3.6 11.7 + - - +
674B SER* 2.3 56.5 + - - +
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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