Contacts of the helix formed by residues 647 - 663 (chain A) in PDB entry 6PUO
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 ASP 647 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A ASP* 4.4 8.5 - - - +
645A SER* 4.2 3.0 + - - -
646A GLN* 1.3 79.7 + - + +
648A CYS* 1.3 63.3 + - - +
649A ILE 3.4 1.8 + - - -
650A ALA* 3.8 7.2 + - + +
651A ALA* 3.4 17.7 + - - +
707A ARG* 3.5 29.0 + - - +
709A SER* 4.0 13.3 - - - -
711A ALA* 4.3 7.2 - - - +
712A TRP* 4.2 18.8 + - - -
1122A LEU* 4.2 11.4 - - + -
1125A GLU* 3.3 12.1 - - - +
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Residues in contact with CYS 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A TRP* 3.3 33.0 + - + +
645A SER* 4.3 7.9 - - - +
646A GLN 3.6 2.8 + - - +
647A ASP* 1.3 73.5 - - - +
649A ILE* 1.3 58.2 + - - -
651A ALA* 3.3 3.3 + - - -
652A ALA* 2.9 27.2 + - - +
689A VAL* 3.8 27.1 - - - -
1125A GLU* 2.8 29.7 + - - -
1126A ILE* 6.1 0.2 - - - -
1129A LYS* 3.6 32.8 - - + -
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Residues in contact with ILE 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A TRP* 5.8 0.2 - - - -
647A ASP 3.4 0.8 - - - -
648A CYS* 1.3 73.1 - - - +
650A ALA* 1.3 65.2 + - - +
652A ALA* 3.3 5.3 + - - +
653A LEU* 3.0 31.7 + - + +
686A ALA* 4.4 16.8 - - + +
689A VAL* 3.8 33.0 - - + -
690A PHE* 4.3 22.7 - - + -
693A CYS* 5.4 1.1 - - + -
704A LEU* 3.8 31.4 - - + -
705A LEU* 6.2 1.3 - - + -
717A CYS* 3.7 20.0 - - - -
729A PHE* 4.7 10.5 - - + -
1125A GLU* 3.6 9.1 + - + +
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Residues in contact with ALA 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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647A ASP* 3.8 13.4 + - + +
649A ILE* 1.3 79.4 - - - +
651A ALA* 1.3 58.3 + - - +
653A LEU* 3.4 3.3 + - - +
654A ALA* 2.9 31.4 + - - +
707A ARG* 6.2 0.4 - - - +
709A SER* 4.7 9.9 - - - +
712A TRP* 4.2 21.4 - - + -
716A THR 6.3 0.4 - - - -
717A CYS* 3.9 21.6 - - + -
720A LEU* 4.0 11.5 - - + +
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Residues in contact with ALA 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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626A LEU* 4.5 7.6 - - + -
642A TRP* 4.2 13.7 - - + +
645A SER* 4.2 10.1 - - - +
647A ASP* 3.4 12.9 + - - +
648A CYS* 3.3 11.4 + - - +
649A ILE 3.2 0.4 - - - -
650A ALA* 1.3 78.3 - - - +
652A ALA* 1.3 57.7 + - - +
654A ALA* 3.4 1.4 + - - +
655A CYS* 3.0 35.1 + - - -
712A TRP* 3.6 26.8 - - + +
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Residues in contact with ALA 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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642A TRP* 4.1 14.6 - - + +
648A CYS 2.9 16.9 + - - +
649A ILE 3.3 0.6 + - - +
651A ALA* 1.3 75.8 - - - +
653A LEU* 1.3 59.1 + - - +
655A CYS* 3.4 2.4 + - - +
656A SER* 3.0 27.7 + - - -
682A TYR* 3.7 40.3 - - + +
685A ARG* 4.8 0.4 - - + -
686A ALA* 3.8 19.5 - - + +
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Residues in contact with LEU 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 ILE* 3.0 17.6 + - + +
650A ALA 3.9 3.8 - - - +
652A ALA* 1.3 78.2 - - - +
654A ALA* 1.3 57.5 + - - +
656A SER* 2.8 20.8 + - - +
657A LYS* 3.0 13.7 + - - +
683A GLU* 5.2 4.5 - - - -
686A ALA* 3.9 19.5 - - + -
717A CYS* 3.5 40.2 - - - +
720A LEU* 4.1 16.1 - - + +
721A ALA* 4.1 17.7 - - + +
724A ALA* 4.9 1.4 - - - +
726A ASP* 3.7 20.6 - - - +
729A PHE* 4.2 25.1 - - + -
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Residues in contact with ALA 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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569A LEU* 4.2 12.7 - - + +
650A ALA 2.9 19.1 + - - +
651A ALA 3.9 1.1 - - - +
653A LEU* 1.3 75.5 - - - +
655A CYS* 1.3 57.4 + - - +
657A LYS* 3.3 7.2 + - - +
658A ILE* 2.9 35.9 + - + +
712A TRP* 3.7 33.9 - - + -
720A LEU* 4.2 14.5 - - + +
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Residues in contact with CYS 655 (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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626A LEU* 4.0 24.7 - - - -
627A ILE* 5.8 3.6 - - - -
630A ILE* 3.7 33.4 - - + -
642A TRP* 6.0 0.2 - - - -
651A ALA 3.0 21.4 + - - +
652A ALA 3.8 4.0 - - - +
654A ALA* 1.3 74.1 - - - +
656A SER* 1.3 64.0 + - - +
658A ILE* 3.8 8.0 - - - +
659A LEU* 3.0 31.6 + - + +
682A TYR* 4.3 19.7 - - + -
712A TRP* 5.2 7.0 - - - -
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Residues in contact with SER 656 (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 ALA 3.0 16.0 + - - -
653A LEU* 2.8 11.0 + - - -
655A CYS* 1.3 77.5 - - - +
657A LYS* 1.3 60.3 + - - +
660A LYS* 2.9 35.0 + - - +
679A ALA* 3.8 31.7 - - - +
682A TYR* 4.7 1.7 - - - +
683A GLU* 4.5 7.6 - - - -
724A ALA* 4.0 3.3 - - - +
726A ASP* 2.9 30.1 + - - -
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Residues in contact with LYS 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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568A LEU 3.6 18.5 + - - -
569A LEU* 3.6 32.3 - - + +
570A GLY* 4.7 3.4 - - - +
572A PHE* 5.8 0.4 - - - -
653A LEU 3.0 12.2 + - - +
654A ALA* 3.6 7.0 - - - +
655A CYS 3.3 0.2 - - - -
656A SER* 1.3 82.1 + - - +
658A ILE* 1.3 58.1 + - - +
660A LYS* 3.8 2.4 - - + +
661A GLU* 3.0 47.3 + - - +
720A LEU* 4.9 9.6 - - + +
723A GLU* 4.3 21.9 + - + +
724A ALA* 3.8 32.1 - - + +
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Residues in contact with ILE 658 (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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565A LEU* 4.4 19.7 - - + -
568A LEU* 4.7 20.6 - - + +
569A LEU* 3.8 28.9 - - + -
627A ILE* 4.9 20.2 - - + -
630A ILE* 4.4 17.9 - - + -
631A VAL* 4.4 14.4 - - + -
654A ALA* 2.9 25.5 + - + +
655A CYS* 3.8 8.1 - - - +
657A LYS* 1.3 76.0 - - - +
659A LEU* 1.3 60.7 + - + +
661A GLU* 3.2 6.0 + - - +
662A LEU* 2.9 31.1 + - + +
712A TRP* 5.5 1.6 - - + -
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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
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630A ILE* 3.8 39.0 - - + +
633A ASN* 5.7 0.4 - - - +
655A CYS 3.0 20.8 + - - +
658A ILE* 1.3 77.5 - - + +
660A LYS* 1.3 58.1 + - - +
662A LEU* 3.8 9.0 - - + +
663A SER* 2.9 32.6 + - - -
675A MET* 4.0 30.2 - - + +
676A LEU* 6.0 0.2 - - - -
678A LEU* 3.7 37.2 - - + +
679A ALA* 3.7 26.7 - - + +
682A TYR* 5.2 2.5 - - + -
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Residues in contact with LYS 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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656A SER* 2.9 22.1 + - - +
657A LYS* 3.9 5.4 - - + +
659A LEU* 1.3 77.5 - - - +
661A GLU* 1.3 61.5 + - - +
663A SER* 3.9 7.1 + - - -
664A LYS* 3.9 21.4 + - - +
676A LEU* 4.5 21.1 - - + -
679A ALA* 4.2 21.1 + - - +
680A GLU* 5.4 4.2 - - - +
683A GLU* 5.0 3.8 + - - -
724A ALA* 3.4 23.5 + - + +
725A LYS* 4.7 8.8 + - + -
726A ASP* 3.3 24.6 + - - +
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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
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567A GLU 5.2 1.8 - - - +
568A LEU* 3.6 42.2 - - + +
657A LYS* 3.0 34.2 + - - +
658A ILE* 3.6 4.7 - - - +
659A LEU 3.2 0.2 - - - -
660A LYS* 1.3 78.8 - - - +
662A LEU* 1.3 61.5 + - - +
663A SER 3.4 0.3 + - - -
664A LYS* 3.3 40.2 + - - +
665A GLU* 4.3 13.3 - - - +
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Residues in contact with LEU 662 (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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531A LEU* 4.1 33.0 - - + +
532A PHE* 5.1 10.1 - - + +
535A LYS* 4.8 7.9 - - + -
568A LEU* 3.7 33.0 - - + -
631A VAL* 4.2 29.4 - - + +
658A ILE* 2.9 18.4 + - + +
659A LEU* 3.3 11.4 + - + +
661A GLU* 1.3 77.1 - - - +
663A SER* 1.3 62.2 + - - +
664A LYS 3.2 1.2 + - - -
665A GLU* 3.6 11.2 + - - +
666A GLU* 4.2 5.4 + - - +
675A MET* 4.0 29.8 - - + +
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Residues in contact with SER 663 (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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659A LEU 2.9 17.1 + - - -
660A LYS* 4.4 6.5 - - - -
661A GLU 3.3 0.8 - - - -
662A LEU* 1.3 76.6 - - - +
664A LYS* 1.3 60.9 + - - +
665A GLU 3.4 0.6 + - - -
666A GLU* 4.4 7.1 + - - -
672A SER* 3.2 42.5 + - - -
675A MET* 4.1 16.8 - - - -
676A LEU* 4.2 18.5 - - - +
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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
------------------------------------------------------------
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