Contacts of the helix formed by residues 626 - 636 (chain D) in PDB entry 1S0V
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 THR 626 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575D ALA* 3.3 18.2 - - - +
624D GLY* 3.4 15.6 + - - +
625D VAL* 1.3 80.9 - - - +
627D ARG* 1.3 65.3 + - - +
628D SER* 3.0 29.1 + - - -
629D VAL* 3.6 11.5 + - - +
630D THR* 3.3 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 627 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472D LYS* 4.3 6.4 - - - +
569D ASP* 2.8 38.8 + - - +
571D TYR* 3.6 9.4 - - + +
572D GLY* 3.7 22.2 - - - +
575D ALA* 3.6 6.2 - - - +
626D THR* 1.3 76.7 - - - +
628D SER* 1.3 66.2 + - - +
629D VAL 3.2 0.7 - - - -
630D THR* 3.5 8.0 + - - -
631D LYS* 3.0 37.1 + - - +
2003D APC 2.9 42.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 628 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626D THR* 3.0 16.7 + - - -
627D ARG* 1.3 84.6 + - - +
629D VAL* 1.3 62.6 + - - +
631D LYS* 4.3 10.6 - - - +
632D ARG* 5.4 1.4 + - - -
653D ASP* 6.0 0.3 - - - +
654D THR* 4.2 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 629 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D TRP* 5.3 5.6 - - + -
623D TYR* 4.5 19.3 - - + +
624D GLY 4.8 0.9 - - - +
625D VAL* 5.2 7.4 - - + -
626D THR* 3.6 15.5 + - - +
627D ARG 3.2 0.4 - - - -
628D SER* 1.3 82.0 - - - +
630D THR* 1.3 70.6 + - + +
631D LYS 3.3 0.8 + - - -
632D ARG* 4.4 7.1 + - - +
633D SER* 4.7 5.2 + - - -
650D VAL* 3.6 24.3 - - + +
653D ASP* 5.7 1.2 - - - +
654D THR* 3.4 43.5 - - + +
677D MET* 4.9 10.8 - - + -
681D ILE* 4.7 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 630 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571D TYR* 3.3 18.0 + - - -
574D VAL* 3.7 30.3 - - + -
575D ALA* 3.9 4.6 - - - +
578D VAL* 4.1 13.2 - - + -
625D VAL* 6.1 2.0 - - + -
626D THR 3.3 16.2 + - - +
627D ARG 3.5 3.5 + - - -
629D VAL* 1.3 84.5 - - + +
631D LYS* 1.3 65.8 + - - +
633D SER* 3.2 4.9 + - - -
634D VAL* 3.0 22.4 + - - +
677D MET* 6.1 0.4 - - - -
681D ILE* 3.9 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 631 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571D TYR* 3.3 26.0 - - + +
627D ARG* 3.0 23.3 + - - +
628D SER* 4.5 10.5 - - - +
629D VAL 3.3 0.4 - - - -
630D THR* 1.3 76.5 - - - +
632D ARG* 1.3 90.3 + - - +
633D SER 3.0 0.2 + - - -
634D VAL* 3.0 13.5 + - - +
635D MET* 3.1 50.9 + - - +
2003D APC 2.4 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 632 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628D SER 5.4 1.9 + - - -
629D VAL 4.4 5.2 + - - +
630D THR 3.6 0.6 - - - -
631D LYS* 1.3 121.0 - - - +
633D SER* 1.3 63.5 + - - +
635D MET* 3.6 2.1 + - - +
636D THR* 3.2 26.2 + - - +
649D GLN* 3.5 11.0 - - + +
653D ASP* 3.0 38.6 - - + +
2003D APC 2.9 75.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 633 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629D VAL 4.7 3.2 + - - -
630D THR* 3.2 9.1 + - - -
631D LYS 3.0 2.2 + - - -
632D ARG* 1.3 79.0 - - - +
634D VAL* 1.3 60.0 + - - -
636D THR* 3.2 12.1 + - - -
637D LEU* 3.4 6.8 + - - -
646D PHE* 3.4 35.0 + - - +
649D GLN* 2.5 37.4 + - - +
650D VAL* 4.8 0.9 - - - +
681D ILE* 4.1 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 634 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D CYS* 5.3 0.4 - - - -
543D ILE* 4.2 18.3 - - + +
570D ILE* 4.0 26.5 - - + -
571D TYR* 3.0 45.5 - - + -
574D VAL* 5.1 2.9 - - + -
630D THR* 3.0 12.1 + - - +
631D LYS 3.2 3.6 - - - +
633D SER* 1.3 70.6 - - - +
635D MET* 1.3 58.9 + - - +
636D THR 2.9 4.7 - - - -
637D LEU* 2.5 44.8 + - + +
638D ALA 4.2 0.2 + - - -
646D PHE* 5.6 0.4 - - - -
681D ILE* 5.6 1.0 - - + +
685D VAL* 4.8 18.2 - - + -
689D VAL* 6.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 635 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D CYS* 4.1 19.6 - - - -
571D TYR* 3.3 23.1 - - + +
631D LYS* 3.1 47.9 + - - +
632D ARG* 3.7 8.7 - - - +
634D VAL* 1.3 82.8 - - - +
636D THR* 1.3 61.0 + - + +
637D LEU 3.5 1.4 + - - -
638D ALA* 4.1 13.5 + - - +
639D TYR* 4.9 7.4 - - - -
2003D APC 3.3 68.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 636 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632D ARG 3.2 14.9 + - - +
633D SER 3.2 11.4 + - - -
634D VAL 2.9 1.2 - - - -
635D MET* 1.3 78.9 - - + +
637D LEU* 1.3 65.5 + - - +
638D ALA 3.0 2.6 + - - +
639D TYR* 3.5 20.8 + - + -
641D SER* 3.0 23.5 + - - -
649D GLN* 3.4 9.6 + - - +
2003D APC 3.5 45.3 - - + +
10N T 4.2 15.3 + - - +
----------------------------------------------------------
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