Contacts of the strand formed by residues 631 - 637 (chain B) in PDB entry 3U11
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 LYS 631 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B ARG* 6.4 0.4 - - - -
614B GLU* 3.3 28.1 + - - -
630B LYS* 1.3 83.1 - - + +
632B MET* 1.3 60.8 + - - +
633B TYR* 3.6 31.0 + - + +
659B GLY 3.7 1.2 - - - +
663B LEU* 3.6 8.4 - - - +
669B ARG* 2.9 32.4 + - - +
683B SER* 4.0 18.6 - - - -
684B LEU 3.4 7.6 - - - +
685B SER* 4.4 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 632 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B LYS* 1.3 74.0 - - - +
633B TYR* 1.3 60.6 + - - +
634B PHE* 3.5 25.1 - - + -
657B TYR* 3.4 37.0 - - + -
658B PHE 3.6 10.3 - - - +
659B GLY 4.1 0.9 - - - -
660B GLU* 3.8 19.5 - - + +
663B LEU* 3.4 11.4 - - + +
682B TYR 4.6 0.2 - - - -
683B SER* 3.0 9.4 - - - -
684B LEU* 2.5 64.1 + - + +
689B PHE* 4.0 18.8 - - - -
703B PHE* 3.7 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 633 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B GLU* 3.9 20.6 + - - -
616B PHE* 4.1 7.0 - + - -
622B ILE* 3.5 31.4 + - + +
623B ILE* 4.1 12.5 - - + +
631B LYS* 3.6 38.7 + - + +
632B MET* 1.3 78.5 - - - +
634B PHE* 1.3 65.4 + - - +
657B TYR* 3.1 7.8 - - - +
658B PHE* 2.9 77.7 + + + +
669B ARG* 4.5 2.8 + - - -
681B LEU* 3.9 23.3 - - + -
682B TYR 3.6 2.9 - - - -
683B SER* 4.0 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 634 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B LEU* 4.4 17.7 - - + -
593B MET* 3.8 17.9 - - + -
595B LEU* 4.3 8.3 - - + -
596B PHE* 4.2 18.2 - + - -
607B MET* 3.9 20.0 - - + -
611B LEU* 4.1 17.3 - - + -
632B MET* 3.5 26.2 - - + -
633B TYR* 1.3 75.6 - - - +
635B ILE* 1.3 63.5 + - - +
636B GLN 3.3 0.9 + - - -
656B SER 3.7 2.5 - - - -
657B TYR* 3.7 24.7 - + + -
681B LEU* 3.2 7.3 - - - -
682B TYR* 2.8 50.2 + - + +
684B LEU* 4.0 23.3 - - + -
703B PHE* 4.9 2.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 635 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B LEU* 3.4 9.3 - - - +
634B PHE* 1.3 70.5 - - - +
636B GLN* 1.3 63.3 + - - +
637B HIS 3.7 16.2 - - - +
638B GLY 3.5 15.3 - - - +
640B VAL* 4.7 6.7 - - + -
652B LEU* 3.9 25.8 - - + +
653B ALA 3.1 34.5 - - - +
654B ASP 3.7 0.7 - - - +
655B GLY* 3.1 20.1 + - - -
656B SER 2.9 17.2 + - - +
658B PHE* 3.6 36.1 - - + -
679B CYS* 5.7 0.2 - - - -
681B LEU* 3.7 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 636 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B ASN 3.3 23.8 + - - -
586B CSO 4.1 10.3 - - - -
588B LYS* 3.8 37.1 - - + +
589B LEU* 4.0 16.4 - - + +
592B SER* 5.7 0.2 + - - -
613B PHE* 4.4 8.7 - - - -
634B PHE 3.3 4.2 + - - -
635B ILE* 1.3 74.6 - - - +
637B HIS* 1.3 64.9 + - + +
654B ASP* 3.7 16.3 - - - +
655B GLY 4.8 0.2 + - - -
680B ARG* 2.8 28.6 + - + +
682B TYR* 3.2 38.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 637 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A THR* 6.4 0.7 - - + -
645A LYS* 6.5 0.4 - - - -
714A ILE 3.3 18.5 + - - -
715A GLY 3.8 1.7 + - - -
716A LYS* 3.2 44.5 - - + +
588B LYS* 4.1 19.0 + - - +
635B ILE* 3.4 7.8 - - - +
636B GLN* 1.3 84.9 - - + +
638B GLY* 1.3 77.1 + - - +
654B ASP* 3.7 7.7 + - - -
678B TYR* 4.3 9.4 - - + -
679B CYS* 3.3 2.6 - - - -
680B ARG* 2.7 56.0 + - + +
----------------------------------------------------------
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