Contacts of the strand formed by residues 626 - 633 (chain D) in PDB entry 4OIN
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 SER 626 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006C HIS* 5.6 0.3 - - - -
1007C ALA* 3.8 0.2 - - - -
1008C ARG* 2.9 28.7 + - - +
1028C GLY 5.0 1.6 - - - +
1029C GLY* 3.7 1.4 - - - -
1030C GLN* 2.9 32.0 + - - +
623D VAL* 3.0 13.9 + - - -
624D ASP 3.8 4.0 - - - -
625D TYR* 1.3 77.3 - - - +
627D GLY* 1.3 58.6 + - - +
652D LEU* 3.4 5.6 - - - -
747D VAL 3.1 7.0 - - - -
748D HIS* 3.4 33.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 627 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006C HIS* 3.2 14.4 - - - -
1007C ALA* 3.8 5.6 - - - -
1030C GLN* 3.2 16.0 - - - +
626D SER* 1.3 75.1 - - - +
628D ARG* 1.3 59.9 + - - -
648D MET* 4.0 9.6 - - - -
652D LEU* 3.8 2.5 - - - +
746D ALA* 3.1 5.9 - - - -
747D VAL 2.8 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 628 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004C LYS 3.5 7.8 - - - +
1006C HIS* 2.8 35.0 + - + +
1030C GLN* 2.3 45.8 + - - +
627D GLY* 1.3 75.3 - - - +
629D SER* 1.3 63.4 + - - +
648D MET* 3.6 6.3 - - - +
705D ALA* 5.8 1.8 - - - +
744D GLN* 3.6 44.3 + - - +
745D MET* 3.1 13.6 - - - +
746D ALA* 4.0 12.5 - - - +
747D VAL 4.6 0.2 - - - +
16G C 3.4 33.5 + - - +
17G G 3.7 35.1 + - - -
18G A 5.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 629 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001C VAL* 3.3 9.2 - - - +
1004C LYS 4.4 7.0 - - - -
1005C MET* 3.6 7.8 - - - +
628D ARG* 1.3 77.4 - - - +
630D VAL* 1.3 74.5 + - - +
631D ILE* 4.2 1.4 - - - +
648D MET* 3.8 16.6 - - - -
724D GLN 2.7 27.5 + - - -
726D ILE* 4.0 8.8 - - - +
744D GLN* 3.2 10.1 - - - +
745D MET* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 630 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836C GLY* 3.5 24.2 - - - +
848C VAL* 3.7 17.9 - - + -
999C HIS 6.3 0.4 - - - -
1000C MET 5.1 0.2 - - - -
1001C VAL* 3.7 34.8 - - + +
1004C LYS* 4.1 24.5 - - + +
629D SER* 1.3 81.2 + - - +
631D ILE* 1.3 69.1 + - - +
725D SER* 3.6 5.0 - - - +
726D ILE* 2.9 25.6 + - - +
742D GLY* 4.7 5.4 - - - +
743D ASP 3.6 11.4 - - - +
744D GLN* 4.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 631 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848C VAL* 3.6 19.2 - - - +
629D SER 4.2 0.7 - - - +
630D VAL* 1.3 78.7 - - - +
632D VAL* 1.3 62.1 + - - +
726D ILE* 3.3 15.9 - - + +
728D LEU* 4.3 9.9 - - + -
738D ALA* 3.9 22.4 - - + -
739D ASP 3.6 10.5 - - - +
740D PHE* 3.6 22.8 - - + +
743D ASP* 3.1 37.9 + - + +
745D MET* 3.7 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 632 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835C VAL* 3.6 15.0 - - + -
848C VAL* 3.5 18.6 - - + -
849C VAL 3.5 24.5 - - - +
850C ALA* 3.5 25.4 - - + +
631D ILE* 1.3 73.6 - - - +
633D VAL* 1.3 75.3 + - - +
725D SER* 3.9 14.1 - - - +
726D ILE 2.9 9.8 + - - +
727D GLN* 3.2 17.5 - - + +
728D LEU 2.9 24.3 + - - -
740D PHE* 3.3 8.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 633 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681C GLY 3.4 22.2 - - - +
682C TYR* 3.2 34.5 - - + +
684C PHE* 3.8 26.5 - - + +
687C ALA* 3.9 3.8 - - + -
850C ALA* 3.7 12.1 - - + +
632D VAL* 1.3 85.3 - - - +
634D GLY* 1.3 61.9 + - - +
635D PRO* 3.2 10.4 - - + +
636D GLN* 4.8 0.5 - - - +
727D GLN* 4.6 3.8 - - - +
730D PRO* 3.9 13.2 - - + -
740D PHE* 3.3 29.1 - - + -
----------------------------------------------------------
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