Contacts of the helix formed by residues 633 - 651 (chain A) in PDB entry 5OQN
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 633 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593A LEU* 4.0 27.2 - - + +
594A THR* 4.8 12.4 - - - +
629A CYS 3.2 5.0 + - - +
630A CYS 3.0 15.0 - - - +
632A LEU* 1.3 77.0 - - - +
634A VAL* 1.3 69.3 + - - +
635A LYS* 2.9 19.9 + - - +
636A LEU* 3.3 23.2 + - + +
637A ALA 3.2 11.3 + - - -
670A HIS* 4.6 0.4 - - - -
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Residues in contact with VAL 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A LEU 4.2 1.8 + - - -
633A ASP* 1.3 73.0 + - - +
635A LYS* 1.3 75.7 + - + +
637A ALA* 2.8 15.9 + - - +
638A ILE* 3.0 26.6 + - + +
670A HIS* 4.0 26.7 - - + +
673A THR* 3.9 23.6 - - - +
674A VAL* 4.3 5.4 - - + -
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Residues in contact with LYS 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A ASP* 2.9 9.9 + - - +
634A VAL* 1.3 84.1 - - + +
636A LEU* 1.3 57.7 + - - +
638A ILE* 3.3 23.8 + - + +
639A ASP* 3.0 56.5 + - - +
678A GLU 5.8 2.8 + - - -
679A GLY* 5.3 5.3 + - - -
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Residues in contact with LEU 636 (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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593A LEU* 3.9 10.5 - - + -
603A MET* 3.5 41.7 - - + -
626A LEU* 4.7 2.5 - - + -
629A CYS* 3.9 24.5 - - + +
630A CYS* 4.1 9.2 - - - +
633A ASP* 3.3 22.7 + - + +
634A VAL 3.1 0.6 - - - -
635A LYS* 1.3 79.5 - - - +
637A ALA* 1.3 61.3 + - - +
639A ASP* 3.5 5.1 + - + +
640A ASN* 2.5 55.7 + - - +
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Residues in contact with ALA 637 (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 CYS* 3.8 30.7 - - + +
633A ASP 3.2 2.4 + - - -
634A VAL* 2.8 12.5 + - - +
636A LEU* 1.3 79.8 - - - +
638A ILE* 1.3 51.4 + - - +
640A ASN 2.9 3.8 + - - -
641A MET* 2.7 38.3 + - - +
666A ILE* 3.8 30.2 - - + +
670A HIS* 4.6 1.1 - - + -
674A VAL* 3.9 8.3 - - + -
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Residues in contact with ILE 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A VAL* 3.0 25.5 + - + +
635A LYS* 3.3 22.4 + - + +
637A ALA* 1.3 74.5 - - - +
639A ASP* 1.3 66.3 + - - +
640A ASN 3.0 1.7 + - - -
641A MET* 3.2 20.4 + - - +
642A TYR* 4.6 1.9 + - - +
673A THR* 3.7 18.6 - - - +
674A VAL* 3.9 19.1 - - + +
679A GLY 3.6 25.3 - - - +
680A LYS* 3.9 30.3 - - + +
681A VAL* 5.1 2.6 - - - +
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Residues in contact with ASP 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A LYS* 3.0 53.9 + - - +
636A LEU* 3.8 4.1 - - + +
638A ILE* 1.3 75.7 - - - +
640A ASN* 1.3 69.2 + - - +
641A MET 3.7 0.2 - - - -
642A TYR* 5.1 3.2 + - - +
643A ILE* 4.7 3.6 + - - +
679A GLY 5.5 1.2 - - - +
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Residues in contact with ASN 640 (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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612A ARG* 6.1 2.0 - - - +
626A LEU* 3.5 35.2 - - + +
630A CYS* 4.3 11.4 - - - -
636A LEU* 2.5 41.6 - - - +
637A ALA 2.9 5.6 + - - +
639A ASP* 1.3 86.3 - - - +
641A MET* 1.3 63.4 + - - +
642A TYR 3.3 2.7 - - - -
643A ILE* 3.0 28.2 - - + +
644A LEU* 3.1 16.2 - - + +
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Residues in contact with MET 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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637A ALA 2.7 21.2 + - - +
638A ILE* 3.2 13.5 + - - +
640A ASN* 1.3 75.5 - - - +
642A TYR* 1.3 65.4 + - - +
644A LEU* 3.5 5.8 + - - +
645A GLY* 3.4 13.7 + - - -
663A ILE* 4.2 15.8 - - + +
666A ILE* 4.1 24.9 - - - -
667A PHE* 4.1 14.1 - - + -
674A VAL* 3.5 36.1 - - + +
675A VAL* 4.5 2.2 - - + -
681A VAL* 3.8 16.8 - - + +
686A LEU* 3.7 35.0 - - + +
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Residues in contact with TYR 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A ILE 4.6 2.1 + - - +
639A ASP 5.1 2.4 + - - +
640A ASN* 3.3 0.4 - - - +
641A MET* 1.3 76.8 - - - +
643A ILE* 1.3 74.3 + - + +
645A GLY* 2.8 15.0 + - - -
646A MET* 3.3 47.8 + - + +
681A VAL* 3.7 27.2 - - + +
686A LEU* 6.4 0.2 - - - -
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Residues in contact with ILE 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 VAL* 4.7 20.6 - - + -
612A ARG* 5.4 13.9 - - - +
626A LEU* 5.1 4.7 - - + -
639A ASP 4.7 2.9 + - - +
640A ASN* 3.0 47.3 - - + +
642A TYR* 1.3 86.6 - - + +
644A LEU* 1.3 66.3 + - + +
646A MET* 3.3 17.4 + - + +
647A CYS* 3.5 20.0 + - - -
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Residues in contact with LEU 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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623A VAL* 3.4 32.8 - - + -
626A LEU* 4.7 11.7 - - + -
630A CYS* 5.4 2.2 - - - -
640A ASN* 3.1 26.4 + - + +
641A MET* 3.7 9.0 - - - +
642A TYR 3.1 0.6 - - - -
643A ILE* 1.3 81.6 - - + +
645A GLY* 1.3 62.9 + - - +
647A CYS* 3.0 18.4 + - + +
648A VAL* 3.1 17.8 + - - +
659A ALA* 4.5 4.7 - - + +
662A VAL* 4.1 17.3 - - + -
663A ILE* 4.0 19.5 - - + -
666A ILE* 3.8 29.2 - - + -
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Residues in contact with GLY 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 MET 3.4 7.0 + - - -
642A TYR* 2.8 11.1 + - - -
644A LEU* 1.3 79.5 - - - +
646A MET* 1.3 60.7 + - - +
648A VAL* 3.6 2.5 + - - +
649A SER* 2.7 28.4 + - - -
663A ILE* 4.4 9.1 - - - +
686A LEU* 5.0 3.6 - - - -
689A ILE* 3.4 24.5 - - - +
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Residues in contact with MET 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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642A TYR* 3.3 49.3 + - + +
643A ILE* 3.3 12.8 + - + +
644A LEU 3.1 0.8 - - - -
645A GLY* 1.3 77.5 - - - +
647A CYS* 1.3 61.5 + - - +
649A SER* 4.4 5.2 - - - -
650A LYS* 2.9 74.0 + - + +
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Residues in contact with CYS 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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611A VAL* 5.7 4.9 - - - -
619A ARG* 3.7 27.6 - - - +
623A VAL* 5.5 6.3 - - + -
643A ILE* 3.5 23.5 + - - -
644A LEU* 3.0 10.5 + - - +
646A MET* 1.3 76.7 - - - +
648A VAL* 1.3 59.5 + - - +
651A GLY* 2.9 31.3 + - - +
655A LEU* 4.1 23.1 - - + -
656A LYS* 3.9 8.7 - - - -
659A ALA* 4.2 8.1 - - + -
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Residues in contact with VAL 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 LEU 3.1 17.3 + - - +
645A GLY 3.9 2.7 - - - +
647A CYS* 1.3 76.7 - - - +
649A SER* 1.3 58.4 + - - +
656A LYS* 2.8 33.9 - - + +
659A ALA* 3.5 20.6 - - + -
660A LEU* 3.8 21.3 - - + +
663A ILE* 3.8 20.2 - - + -
689A ILE* 3.5 27.9 - - + +
692A LYS* 6.0 1.2 - - - +
693A VAL* 3.7 21.0 - - + +
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Residues in contact with SER 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 GLY 2.7 21.4 + - - -
646A MET* 3.3 9.0 + - - -
647A CYS 3.2 0.4 - - - -
648A VAL* 1.3 81.3 - - - +
650A LYS* 1.3 70.3 + - - +
651A GLY 3.6 0.4 - - - -
656A LYS* 4.4 8.6 + - - +
689A ILE* 3.8 18.9 - - - +
692A LYS* 6.0 6.5 - - - +
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Residues in contact with LYS 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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646A MET* 2.9 49.0 + - + +
649A SER* 1.3 83.6 - - - +
651A GLY* 1.3 65.6 + - - +
652A ASN 3.8 0.7 + - - -
656A LYS* 4.9 0.4 - - - -
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Residues in contact with GLY 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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619A ARG* 5.6 1.6 - - - -
646A MET 4.0 0.4 + - - -
647A CYS* 2.9 25.3 + - - +
649A SER 3.6 0.2 - - - -
650A LYS* 1.3 80.9 - - - +
652A ASN* 1.3 62.2 + - - +
655A LEU* 4.4 15.5 - - - -
656A LYS* 2.5 35.7 + - - +
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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