Contacts of the helix formed by residues 640 - 654 (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 HIS 640 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485A TYR* 5.7 2.0 + - - -
607A ALA* 4.3 15.6 - - + +
608A TYR* 3.5 33.5 - + + -
611A THR* 3.1 28.1 + - - -
633A ALA* 4.8 3.4 - - + +
634A ILE* 4.5 1.9 - - - +
637A ASN* 3.5 30.6 + - + +
638A PRO 3.4 3.4 - - - -
639A ARG* 1.3 72.4 - - - +
641A TYR* 1.3 65.7 + + - +
642A ASN* 3.2 28.5 + - + -
643A ALA* 3.4 16.0 + - + +
644A TRP* 3.9 9.9 - - - -
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Residues in contact with TYR 641 (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* 3.1 38.8 - + - -
516A PHE* 5.0 3.6 - - - -
517A GLU* 2.6 32.3 + - - -
639A ARG 3.1 7.5 + - - +
640A HIS* 1.3 73.5 - + - +
642A ASN* 1.3 107.8 + - - +
643A ALA 3.1 1.2 + - - -
644A TRP* 3.3 23.2 + - - +
645A TYR* 3.4 12.5 + - + +
667A ALA* 4.1 11.4 - - + +
670A ILE* 4.1 20.4 - - + -
671A ASN* 3.8 6.5 - - + -
674A SER* 3.9 26.2 - - - +
677A LEU* 4.8 11.4 - - - +
678A LEU* 3.8 18.4 - - + -
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Residues in contact with ASN 642 (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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516A PHE* 5.8 5.9 - - - -
608A TYR* 4.2 17.2 + - - -
611A THR* 3.5 21.4 - - + +
615A HIS* 4.2 6.3 + - + -
640A HIS* 3.2 21.3 + - - +
641A TYR* 1.3 116.2 + - - +
643A ALA* 1.3 57.3 + - - +
646A GLY* 3.0 23.4 + - - -
677A LEU* 6.1 1.0 - - - +
678A LEU* 3.4 24.8 - - + +
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Residues in contact with ALA 643 (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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611A THR* 4.0 6.1 + - - +
630A PHE* 3.5 34.6 - - + +
633A ALA* 3.5 32.5 - - + -
634A ILE* 3.8 11.4 - - + +
640A HIS* 3.4 6.8 + - + +
641A TYR 3.2 1.0 - - - -
642A ASN* 1.3 76.3 - - - +
644A TRP* 1.3 66.1 + - - +
646A GLY 3.3 0.2 + - - -
647A LEU* 3.0 20.4 + - - +
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Residues in contact with TRP 644 (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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634A ILE* 3.4 44.0 - - + +
638A PRO* 2.9 31.1 + - + -
639A ARG* 4.9 1.1 - - - +
640A HIS 3.9 12.1 - - - -
641A TYR* 3.3 11.3 + - - +
643A ALA* 1.3 76.6 - - - +
645A TYR* 1.3 57.9 + - - +
647A LEU* 3.1 9.1 + - - +
648A GLY 2.9 23.4 + - - -
663A HIS* 3.7 35.7 - + - +
666A LYS* 4.5 24.4 + - + -
667A ALA* 3.5 26.7 - - + -
670A ILE* 5.8 1.5 - - + +
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Residues in contact with TYR 645 (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 3.4 10.3 + - - +
643A ALA 3.3 0.4 - - - -
644A TRP* 1.3 79.9 - - - +
646A GLY* 1.3 51.9 + - - +
648A GLY 3.1 1.2 + - - -
649A MET* 2.6 40.0 + - + +
664A PHE* 3.6 38.1 - + + -
667A ALA* 4.0 12.3 - - + +
668A LEU* 6.3 1.8 - - + -
674A SER* 4.3 15.7 - - - -
675A SER* 3.8 28.9 + - - -
678A LEU* 3.9 36.6 - - + -
679A CYS* 4.7 2.5 - - - -
713A PHE* 5.6 0.8 - + - -
714A HIS* 2.4 56.0 + + - +
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Residues in contact with GLY 646 (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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615A HIS* 4.9 0.7 - - - -
618A VAL* 5.6 1.7 - - - +
630A PHE* 3.7 30.0 - - - -
642A ASN 3.0 17.6 + - - -
643A ALA 3.3 2.0 + - - -
644A TRP 3.3 0.4 - - - -
645A TYR* 1.3 75.5 - - - +
647A LEU* 1.3 62.9 + - - +
649A MET* 3.5 8.2 + - - +
650A ILE* 3.4 17.2 + - - +
678A LEU* 4.0 8.2 - - - +
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Residues in contact with LEU 647 (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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627A LEU* 5.9 3.8 - - - +
630A PHE* 3.8 16.5 - - + -
634A ILE* 6.4 1.1 - - + -
643A ALA 3.0 13.3 + - - +
644A TRP* 3.4 9.6 - - - +
646A GLY* 1.3 75.8 - - - +
648A GLY* 1.3 63.6 + - - +
650A ILE* 3.1 8.6 + - - +
651A TYR* 3.0 34.4 + - + -
663A HIS* 3.9 17.3 - - + -
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Residues in contact with GLY 648 (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 2.9 13.0 + - - -
645A TYR 3.4 3.6 - - - -
647A LEU* 1.3 77.5 - - - +
649A MET* 1.3 55.4 + - - +
651A TYR* 3.8 10.5 - - - -
652A TYR* 3.0 22.7 + - - +
660A ALA* 3.5 7.3 - - - +
663A HIS* 4.0 12.0 - - - +
664A PHE* 3.2 28.1 - - - -
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Residues in contact with MET 649 (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* 2.6 31.7 + - + +
646A GLY* 3.7 9.9 - - - +
647A LEU 3.1 0.2 - - - -
648A GLY* 1.3 74.1 - - - +
650A ILE* 1.3 59.2 + - - +
652A TYR* 3.4 6.5 + - - +
653A LYS* 2.8 28.9 + - - +
664A PHE* 3.6 7.4 - - - -
678A LEU* 6.2 0.4 - - + -
714A HIS* 4.9 10.9 + - + +
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Residues in contact with ILE 650 (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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618A VAL* 5.5 11.0 - - + -
623A LEU* 5.5 14.4 - - + +
626A ALA* 6.1 2.5 - - + -
630A PHE* 5.8 2.2 - - + -
646A GLY 3.4 8.9 + - - +
647A LEU* 3.1 8.4 + - - +
649A MET* 1.3 76.1 - - - +
651A TYR* 1.3 63.9 + - - +
653A LYS* 3.8 10.1 - - - +
654A GLN* 3.3 19.9 + - - +
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Residues in contact with TYR 651 (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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627A LEU* 6.1 1.5 - - + +
647A LEU* 3.0 33.5 + - + +
648A GLY* 3.7 5.6 - - - +
650A ILE* 1.3 76.8 - - - +
652A TYR* 1.3 53.4 + - - +
654A GLN* 3.0 5.9 + - + +
655A GLU 2.6 30.8 + - - -
656A LYS* 2.8 39.1 + - + +
659A LEU* 5.0 7.4 - - + -
660A ALA* 3.7 11.4 - - + -
663A HIS* 3.4 39.3 + + - -
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Residues in contact with TYR 652 (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 3.0 15.6 + - - +
649A MET* 3.5 6.7 - - - +
651A TYR* 1.3 79.5 - - - +
653A LYS* 1.3 62.3 + - + +
655A GLU* 2.9 22.4 + - - +
656A LYS 4.6 1.8 - - - +
657A PHE* 5.5 3.8 - - + +
660A ALA* 3.9 7.9 - - + +
664A PHE* 4.3 9.0 - + + -
701A ALA* 5.1 15.3 - - + +
711A CYS* 3.5 39.0 - - + -
712A LYS* 5.7 0.2 - - - -
714A HIS* 3.8 27.6 - + - -
715A ARG* 3.2 24.9 - - + +
718A VAL* 5.6 0.7 - - - +
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Residues in contact with LYS 653 (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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649A MET 2.8 17.2 + - - +
650A ILE* 3.9 11.7 - - - +
651A TYR 3.2 0.4 - - - -
652A TYR* 1.3 83.7 - - + +
654A GLN* 1.3 59.7 + - - +
655A GLU* 4.9 1.4 - - - +
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Residues in contact with GLN 654 (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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650A ILE 3.3 14.6 + - - +
651A TYR* 3.0 8.5 + - + +
653A LYS* 1.3 76.8 - - - +
655A GLU* 1.3 69.4 + - - +
656A LYS* 3.3 5.0 + - + +
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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