Contacts of the helix formed by residues 633 - 652 (chain A) in PDB entry 3OJW
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 ALA 633 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A PRO* 6.1 1.3 - - + +
631A GLY* 3.4 0.4 - - - -
632A ASP* 1.3 88.0 + - - +
634A ARG* 1.3 65.7 + - - +
635A ASN* 4.3 4.0 - - + +
636A MET* 3.2 37.5 + - + +
637A ALA 3.4 4.5 + - - -
676A VAL* 3.7 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 634 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASN* 5.3 1.6 - - - +
177A THR* 3.1 51.9 + - - +
178A TYR* 3.5 33.5 + - + +
632A ASP 3.9 0.6 + - - -
633A ALA* 1.3 70.1 - - - +
635A ASN* 1.3 65.8 + - - +
637A ALA* 3.2 6.6 + - - +
638A LYS* 3.0 25.7 + - - +
676A VAL* 3.9 13.7 - - + +
678A SER* 3.4 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 635 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A ALA* 3.2 4.6 - - + +
634A ARG* 1.3 79.1 - - - +
636A MET* 1.3 60.2 + - - +
638A LYS* 3.4 31.7 - - - +
639A ASP* 2.9 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A VAL* 5.2 0.9 - - - -
533A PRO* 3.7 30.3 - - + -
605A VAL* 4.5 11.9 - - + -
606A GLN* 5.3 3.5 + - - +
629A VAL* 4.0 13.7 - - + -
630A CYS 3.6 26.9 - - - +
631A GLY* 3.8 14.8 - - - +
633A ALA* 3.2 27.2 + - + +
634A ARG 3.1 0.6 - - - -
635A ASN* 1.3 76.6 - - - +
637A ALA* 1.3 73.3 + - + +
639A ASP* 3.2 8.0 + - - +
640A VAL* 2.9 37.6 + - - +
676A VAL* 5.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 637 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A VAL* 4.3 14.5 - - + +
633A ALA 3.4 4.0 + - - +
634A ARG* 3.2 9.9 + - - +
636A MET* 1.3 88.8 - - + +
638A LYS* 1.3 56.3 + - - +
640A VAL* 3.6 1.6 - - - +
641A GLN* 2.9 33.3 + - - +
672A TYR* 4.9 1.0 + - - -
674A LEU* 4.7 12.8 - - + +
676A VAL* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ARG 3.0 13.4 + - - +
635A ASN* 3.4 36.0 - - - +
636A MET 3.1 0.2 - - - -
637A ALA* 1.3 76.7 - - - +
639A ASP* 1.3 75.7 + - - +
641A GLN* 3.2 14.8 + - - +
642A ASN* 2.9 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A GLN* 3.8 31.4 + - + +
635A ASN* 2.9 25.4 + - - +
636A MET* 3.8 6.4 - - - +
638A LYS* 1.3 93.1 + - - +
640A VAL* 1.3 60.8 + - - +
642A ASN* 3.3 10.1 + - - +
643A THR* 2.8 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 640 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A VAL* 3.8 23.8 - - + -
605A VAL* 4.0 11.2 - - + -
606A GLN* 4.4 6.1 - - + +
609A LEU* 3.8 10.5 - - + -
629A VAL* 4.0 14.6 - - + -
636A MET* 2.9 33.5 + - - +
637A ALA* 3.6 5.8 - - - +
639A ASP* 1.3 75.6 - - - +
641A GLN* 1.3 65.2 + - - +
643A THR* 3.1 10.0 + - - -
644A PHE* 3.0 46.9 + - + -
672A TYR* 3.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 641 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A ALA 2.9 18.5 + - - +
638A LYS* 3.5 13.2 - - - +
640A VAL* 1.3 76.9 - - - +
642A ASN* 1.3 62.9 + - - +
644A PHE* 3.1 5.3 + - - +
645A TYR* 2.9 62.0 + - + +
663A VAL* 4.6 6.5 - - + -
664A LYS* 4.8 4.7 - - - +
667A MET* 3.9 26.0 - - - +
672A TYR* 3.5 19.7 + - + +
674A LEU* 6.0 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A LYS* 2.9 44.8 + - - +
639A ASP* 3.7 9.4 + - - +
641A GLN* 1.3 77.0 + - - +
643A THR* 1.3 62.8 + - - +
645A TYR* 3.2 27.8 + - - +
646A ASP* 3.1 30.8 + - - +
656A HIS* 5.8 1.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A GLN* 3.0 41.7 - - - +
609A LEU* 4.0 17.3 - - + -
610A LYS* 4.1 15.3 - - + +
639A ASP 2.8 18.8 + - - -
640A VAL* 3.1 9.4 + - - -
642A ASN* 1.3 77.4 - - - +
644A PHE* 1.3 61.7 + - - +
646A ASP* 3.2 11.2 + - - +
647A ILE* 3.1 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A ILE* 4.5 7.4 - - + -
531A VAL* 4.6 2.0 - - + -
609A LEU* 3.7 25.1 - - + -
616A LEU* 4.6 16.6 - - + -
620A ILE* 3.9 21.8 - - + -
627A ILE* 3.8 35.4 - - + -
640A VAL* 3.0 41.9 + - + -
641A GLN 3.1 6.3 + - - +
643A THR* 1.3 74.2 - - - +
645A TYR* 1.3 66.9 + - - +
647A ILE* 3.8 13.9 - - + +
648A VAL* 3.0 30.6 + - + +
663A VAL* 4.2 13.0 - - + -
672A TYR* 3.4 26.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A GLN* 2.9 45.7 + - + -
642A ASN* 3.2 31.4 + - - +
644A PHE* 1.3 76.4 - - - +
646A ASP* 1.3 58.4 + - - +
648A VAL 3.3 1.2 + - - -
649A ALA* 2.9 26.5 + - - +
656A HIS* 4.1 22.4 - + + +
659A ALA* 3.3 13.5 - - + +
660A VAL* 3.7 40.3 - - + +
663A VAL* 3.4 39.7 - - + -
664A LYS* 3.7 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A LYS* 4.2 25.3 + - - +
642A ASN* 3.1 20.3 + - - +
643A THR* 3.2 9.7 + - - +
645A TYR* 1.3 77.4 - - - +
647A ILE* 1.3 61.8 + - - +
649A ALA* 3.3 7.1 + - - +
650A GLU* 3.0 26.5 + - - +
656A HIS* 4.2 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A LEU* 4.0 23.6 - - + +
610A LYS* 4.1 16.4 - - + +
613A ARG* 3.8 30.1 - - + +
616A LEU* 4.5 9.2 - - + -
617A TRP* 4.3 15.2 - - + +
620A ILE* 6.0 2.2 - - + -
643A THR* 3.1 30.8 + - + +
644A PHE* 3.8 21.5 - - + +
645A TYR 3.3 0.2 - - - -
646A ASP* 1.3 75.4 - - - +
648A VAL* 1.3 64.2 + - + +
650A GLU* 3.4 1.9 + - - -
651A PHE* 3.0 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A TRP* 4.1 20.9 - - + -
620A ILE* 5.7 7.0 - - + -
644A PHE* 3.0 20.7 + - + +
645A TYR 3.7 4.3 - - - +
647A ILE* 1.3 78.0 - - + +
649A ALA* 1.3 57.1 + - - +
652A GLY* 2.9 29.1 + - - -
654A MET* 3.6 33.6 - - + +
659A ALA* 3.8 13.2 - - + +
662A TYR* 3.8 29.2 - - + -
663A VAL* 4.0 9.4 - - + -
666A LEU* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 649 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A TYR 2.9 17.9 + - - +
646A ASP* 3.6 9.2 - - - +
647A ILE 3.3 0.2 - - - -
648A VAL* 1.3 76.5 - - - +
650A GLU* 1.3 58.9 + - - +
653A PRO* 3.4 4.0 - - - +
654A MET* 3.0 42.6 + - - +
656A HIS* 4.5 13.2 - - - +
659A ALA* 3.6 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 650 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A LYS* 4.7 10.0 - - - -
613A ARG* 3.9 21.6 + - - -
646A ASP 3.0 16.5 + - - +
647A ILE* 4.8 1.1 - - - -
649A ALA* 1.3 77.9 - - - +
651A PHE* 1.3 84.3 + - + +
653A PRO* 3.4 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 651 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A ARG* 3.7 29.6 - - + -
614A GLU* 3.6 45.1 - - + -
617A TRP* 3.4 52.9 + + + -
618A LYS* 5.8 2.7 - - + -
647A ILE* 3.0 25.5 + - + +
650A GLU* 1.3 100.2 - - + +
652A GLY* 1.3 70.3 + - - +
653A PRO* 3.3 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 652 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A TRP* 3.9 13.2 - - - -
621A HIS* 5.9 0.2 + - - -
648A VAL 2.9 16.7 + - - -
651A PHE* 1.3 79.3 - - - +
653A PRO* 1.3 71.3 - - - +
654A MET* 3.9 15.5 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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