Contacts of the helix formed by residues 628 - 637 (chain M) in PDB entry 2JA7
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 GLY 628 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588M LEU* 4.9 1.8 - - - -
620M LYS 4.5 3.4 - - - -
621M THR* 4.2 4.0 - - - -
623M GLY 5.1 2.2 - - - -
625M SER* 3.3 24.5 + - - -
626M ASN 2.6 15.5 + - - -
627M GLY* 1.3 73.6 - - - +
629M LEU* 1.3 68.1 - - - -
630M ILE 3.1 2.9 - - - -
631M HIS* 3.3 2.9 + - - -
632M VAL* 3.0 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 629 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582M ILE* 3.9 31.4 - - + -
586M ILE* 4.3 17.5 - - + -
588M LEU* 4.5 10.4 - - + +
607M ILE* 4.2 16.4 - - + -
617M VAL* 6.0 2.0 - - + -
621M THR* 2.9 28.3 + - + +
622M VAL* 4.5 19.0 - - + +
623M GLY 5.4 0.2 + - - -
628M GLY* 1.3 71.7 - - - +
630M ILE* 1.3 59.3 + - - +
632M VAL* 3.2 4.5 + - + +
633M VAL* 2.9 47.5 + - + +
645M LEU* 4.3 13.2 - - + -
649M ILE* 4.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 630 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511M ILE* 3.9 14.1 - - + -
519M PRO* 4.1 11.2 - - + -
521M MET 3.5 11.7 - - - +
522M GLY* 3.8 9.2 - - - -
523M ILE* 5.1 2.2 - - + -
621M THR 4.6 0.4 + - - -
622M VAL* 4.2 15.3 - - + +
623M GLY 4.1 15.2 + - - +
628M GLY* 3.1 0.6 - - - -
629M LEU* 1.3 73.7 - - + +
631M HIS* 1.3 69.0 + - - +
632M VAL 2.8 1.4 + - - -
633M VAL* 3.1 6.5 + - - +
634M THR* 2.8 39.9 + - - +
642M CYS* 3.7 11.9 - - - -
645M LEU* 5.0 10.3 - - + -
646M PHE* 3.1 37.9 - - + -
649M ILE* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 631 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512M VAL* 3.7 19.9 - - + +
517M ASN 3.7 22.5 + - - -
518M LYS* 4.4 0.2 - - - -
519M PRO* 3.4 30.6 - - + +
626M ASN* 2.6 41.1 + - - +
627M GLY* 4.2 5.6 - - - -
628M GLY 3.3 8.6 + - - +
630M ILE* 1.3 79.4 - - - +
632M VAL* 1.3 64.8 + - + +
634M THR* 3.9 1.6 - - - -
635M ARG* 3.3 25.6 + - + +
876M ALA 4.9 1.8 - - - -
878M ILE 3.8 13.7 + - - -
879M GLU* 3.9 25.7 - - + +
962M ARG* 5.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 632 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586M ILE* 4.3 12.1 - - + -
587M HIS 4.5 11.7 - - - +
588M LEU* 4.2 18.4 - - + -
627M GLY* 4.2 7.9 - - - +
628M GLY 3.0 15.5 + - - +
629M LEU* 3.3 7.6 - - + +
630M ILE 2.8 1.2 + - - -
631M HIS* 1.3 73.8 - - + +
633M VAL* 1.3 72.2 + - + +
634M THR 3.0 1.3 - - - -
635M ARG* 2.8 6.6 + - - +
636M GLU* 2.7 36.2 + - + +
879M GLU* 5.9 0.7 - - - +
962M ARG* 3.9 38.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 633 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583M PRO* 4.4 12.3 - - + -
586M ILE* 3.3 28.5 - - + -
629M LEU* 2.9 43.6 + - + +
630M ILE* 3.8 3.1 - - - +
632M VAL* 1.3 74.8 - - - +
634M THR* 1.3 59.3 + - - +
636M GLU* 4.3 0.4 - - - -
637M LYS* 2.7 38.1 + - + -
638M GLY 3.3 2.9 + - - -
641M VAL* 4.6 2.2 - - + +
642M CYS* 3.9 26.5 - - + +
645M LEU* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 634 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508M PRO 5.5 0.2 - - - +
511M ILE* 3.4 26.3 - - + +
512M VAL* 4.3 16.8 - - + +
630M ILE* 2.8 15.7 + - - +
631M HIS 3.9 4.3 - - - -
632M VAL 2.8 3.2 + - - -
633M VAL* 1.3 72.0 - - - +
635M ARG* 1.3 74.8 + - - +
638M GLY* 3.2 35.3 + - - +
639M PRO* 4.6 9.8 - - + +
642M CYS* 2.9 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 635 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512M VAL* 4.5 10.3 - - + +
631M HIS* 3.3 25.6 + - + +
632M VAL 2.8 6.1 + - - +
634M THR* 1.3 89.0 + - + +
636M GLU* 1.3 65.8 + - - +
638M GLY* 4.6 0.5 + - - -
876M ALA* 3.6 31.5 + - - +
877M HIS* 3.5 47.4 + - - +
879M GLU* 4.1 15.7 - - + +
962M ARG* 4.1 15.0 - - - +
1052M GLN* 6.0 1.6 + - - -
1055M ARG* 5.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 636 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585M GLY 5.2 7.6 - - - +
586M ILE* 4.7 7.0 - - + -
632M VAL* 2.7 31.2 + - + +
633M VAL* 3.8 3.1 - - - +
635M ARG* 1.3 77.6 - - - +
637M LYS* 1.3 78.5 + - + +
638M GLY* 4.6 0.2 - - - -
962M ARG* 2.7 33.1 + - - +
966M ASN* 3.0 31.4 + - - -
1052M GLN* 5.7 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 637 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583M PRO* 4.3 17.3 - - + -
584M ASN* 2.9 30.6 + - - +
585M GLY* 4.5 9.9 - - - -
586M ILE* 4.6 9.4 - - + +
633M VAL* 2.7 15.7 + - + +
636M GLU* 1.3 86.1 - - + +
638M GLY* 1.3 55.9 + - - +
641M VAL* 3.5 40.5 - - + +
----------------------------------------------------------
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