Contacts of the helix formed by residues 630 - 638 (chain A) in PDB entry 6O0Z
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 GLU 630 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A ASP* 2.9 9.8 + - + +
629A ARG* 1.3 79.2 - - - +
631A MET* 1.3 63.8 + - + +
632A ILE 3.2 0.7 - - - -
633A GLU* 3.0 9.8 + - - +
634A GLU* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 631 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A TYR* 3.5 31.2 - - + +
484A LYS* 4.4 26.2 - - + +
485A GLY* 5.0 9.9 - - - +
488A ALA* 4.1 24.9 - - - -
626A PHE* 3.9 28.8 - - + -
628A ASP* 3.7 27.1 - - + -
630A GLU* 1.3 74.2 - - + +
632A ILE* 1.3 62.5 + - + +
634A GLU* 3.3 8.8 + - - +
635A ARG* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A THR* 4.6 12.1 - - + +
623A LEU* 4.5 17.9 - - + +
626A PHE* 3.7 46.0 - - + +
627A GLU* 4.6 1.6 - - - -
628A ASP 4.1 1.1 - - - +
629A ARG* 3.5 32.1 - - + +
630A GLU 3.2 0.2 - - - -
631A MET* 1.3 77.9 - - - +
633A GLU* 1.3 55.6 + - - +
635A ARG* 3.3 4.4 + - - +
636A LEU* 2.9 56.7 + - + +
652A LYS* 4.3 15.7 - - + +
654A ARG 5.9 1.1 - - - +
655A ARG* 5.2 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 633 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A ARG 3.8 14.3 + - - +
630A GLU* 3.0 16.0 + - - +
632A ILE* 1.3 79.8 - - - +
634A GLU* 1.3 55.1 + - - +
636A LEU* 3.8 1.9 - - - -
637A LYS* 2.8 29.9 + - - +
652A LYS* 4.0 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 634 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A GLU 2.9 11.8 + - - +
631A MET* 3.7 11.0 - - - +
632A ILE 3.3 0.2 - - - -
633A GLU* 1.3 77.7 - - - +
635A ARG* 1.3 57.6 + - - +
637A LYS* 3.1 8.1 + - - +
638A THR* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 635 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A GLY* 4.2 26.7 + - - -
486A ALA* 4.6 2.0 - - - +
489A GLN* 4.5 15.7 + - - +
618A ASP* 5.2 4.7 - - - +
619A ILE* 5.3 0.3 - - - +
622A THR* 3.7 33.6 + - + +
625A LEU* 6.4 0.7 - - - -
626A PHE* 3.4 28.5 - - - -
631A MET 2.9 15.8 + - - +
632A ILE 3.3 1.3 + - - +
634A GLU* 1.3 76.5 - - - +
636A LEU* 1.3 60.8 + - - +
638A THR* 3.2 22.4 + - - +
639A TYR* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A ILE* 3.8 39.7 - - + +
622A THR* 4.3 14.1 - - + -
623A LEU* 4.8 4.3 - - + -
632A ILE* 2.9 37.9 + - + +
633A GLU* 4.4 2.7 - - - +
635A ARG* 1.3 77.5 - - - +
637A LYS* 1.3 60.9 + - - +
638A THR 3.1 1.3 - - - -
639A TYR* 2.9 32.0 + - + +
640A ALA* 4.4 0.5 - - - -
648A MET* 4.2 21.1 - - + +
651A LEU* 3.7 24.7 - - + -
652A LYS* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 637 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A GLU 2.8 21.3 + - - +
634A GLU* 3.1 8.5 + - - +
636A LEU* 1.3 73.3 - - - +
638A THR* 1.3 64.0 + - - +
639A TYR 3.2 1.5 + - - -
640A ALA* 3.9 18.3 + - + +
648A MET* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A GLU 2.9 16.6 + - - -
635A ARG* 3.2 20.2 + - - +
637A LYS* 1.3 78.4 - - - +
639A TYR* 1.3 76.2 + - + +
640A ALA 3.8 1.7 + - - -
641A HIS* 4.7 6.8 + - - -
----------------------------------------------------------
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