Contacts of the strand formed by residues 631 - 637 (chain A) in PDB entry 2O8B
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 ARG 631 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A LEU* 3.7 37.5 - - + +
629A GLN* 3.9 4.0 - - + +
630A GLY* 1.3 75.6 - - - +
632A ILE* 1.3 62.8 + - - +
633A ILE* 3.8 25.9 - - + +
657A PHE 3.4 5.4 - - - +
658A GLU* 4.2 16.3 + - + -
701A GLU* 3.5 32.1 + - + +
702A VAL* 3.9 0.7 - - - -
703A SER* 2.6 38.1 + - - -
777A PHE* 4.1 1.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
631A ARG* 1.3 78.4 - - - +
633A ILE* 1.3 61.6 + - - +
634A LEU* 4.0 26.5 - - + -
655A VAL* 3.6 7.4 - - + +
656A TYR* 3.7 1.0 - - - -
657A PHE* 3.1 49.7 + - + +
682A THR* 5.4 0.9 - - + -
686A VAL* 4.3 22.0 - - + -
701A GLU 3.3 7.0 - - - +
702A VAL* 4.6 2.2 - - + -
703A SER* 4.0 13.0 - - - +
705A VAL* 4.2 16.4 - - + -
744A LEU* 5.5 2.5 - - + -
777A PHE* 4.0 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 633 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A ARG* 3.8 23.8 - - + +
632A ILE* 1.3 76.1 - - - +
634A LEU* 1.3 66.2 + - - +
635A LYS* 4.2 11.8 + - + +
655A VAL 3.6 7.4 - - - +
656A TYR* 4.6 25.6 - - + -
657A PHE 4.8 3.8 - - - +
658A GLU* 4.5 10.1 - - + +
699A SER* 4.6 4.7 + - - +
700A ALA* 3.6 2.9 - - - -
701A GLU* 2.8 62.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 634 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A ILE* 4.0 13.9 - - + -
633A ILE* 1.3 82.1 - - - +
635A LYS* 1.3 61.1 + - - +
637A SER* 4.2 10.3 - - - -
653A ASN 4.1 0.7 - - - +
654A ASP* 3.4 6.1 - - - +
655A VAL* 2.9 68.4 + - + +
682A THR* 4.4 11.0 - - + +
685A ILE* 3.8 35.4 - - + -
686A VAL* 5.2 0.4 - - + -
697A CYS* 4.3 3.4 - - - -
699A SER 3.9 3.6 - - - -
700A ALA* 4.3 9.6 - - + -
701A GLU 3.9 3.1 - - - +
702A VAL* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 635 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A ILE* 4.1 11.3 - - + -
634A LEU* 1.3 73.3 - - - +
636A ALA* 1.3 68.9 + - + +
654A ASP* 3.5 24.4 + - - +
697A CYS* 3.4 4.3 - - - +
698A GLU* 3.1 31.2 + - + +
699A SER* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A LYS* 1.3 77.0 - - + +
637A SER* 1.3 62.8 + - - +
638A ARG* 3.8 11.4 + - - +
652A PRO* 4.0 22.2 - - + -
653A ASN 3.4 4.7 + - - +
654A ASP* 2.9 15.5 + - - -
696A PRO 3.6 1.7 - - - +
697A CYS* 3.4 13.3 - - - -
698A GLU* 3.8 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 637 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A LEU* 4.2 11.9 - - - -
635A LYS 3.4 0.2 - - - -
636A ALA* 1.3 70.2 - - - +
638A ARG* 1.3 70.6 + - - +
650A PHE* 4.0 1.0 - - - -
652A PRO* 3.4 2.6 - - - +
653A ASN 2.6 45.3 + - - -
655A VAL* 3.9 12.0 - - - +
681A GLN* 3.0 21.9 + - - -
685A ILE* 3.7 21.3 - - - -
697A CYS* 3.7 14.1 - - - -
----------------------------------------------------------
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