Contacts of the helix formed by residues 629 - 638 (chain B) in PDB entry 5XA0
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 629 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B ILE 5.1 1.8 - - - +
588B ASP* 4.3 6.1 - - - -
589B VAL* 3.0 38.8 - - + +
625B ASN* 5.5 0.4 - - + -
627B GLU* 2.6 19.8 + - + +
628B PRO* 1.3 75.7 - - - +
630B PHE* 1.3 62.2 + - + +
631B LEU 3.4 2.7 - - - +
632B ASP* 3.6 2.3 + - - +
633B TYR* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 630 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B ILE* 3.6 34.3 - - + +
588B ASP 5.3 0.9 - - - +
589B VAL* 4.2 3.3 - - - +
592B GLU* 5.3 5.8 - - + +
621B LEU* 4.6 6.2 - - + +
625B ASN* 2.9 24.5 - - + +
629B ARG* 1.3 76.4 - - - +
631B LEU* 1.3 64.5 + - - +
633B TYR* 4.7 3.8 - - - -
634B LEU* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 631 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B VAL* 3.4 45.3 - - + +
625B ASN* 3.1 12.7 + - - +
627B GLU 5.1 1.8 - - - +
628B PRO* 5.7 2.2 - - + -
629B ARG 3.4 0.6 - - - +
630B PHE* 1.3 76.6 - - - +
632B ASP* 1.3 63.1 + - - +
634B LEU* 3.4 5.8 - - - +
635B SER* 3.1 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 632 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B PRO* 4.2 21.5 - - + +
629B ARG 3.6 7.8 + - - +
630B PHE 3.4 0.4 - - - -
631B LEU* 1.3 78.2 - - - +
633B TYR* 1.3 64.4 + - - +
635B SER* 2.8 25.2 + - - -
636B ASP* 3.0 7.2 + - - +
695B GLU* 4.1 26.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
589B VAL* 4.6 7.0 - - + +
592B GLU* 3.1 34.1 - - + -
593B ASP* 6.1 0.2 - - - -
596B THR* 5.7 1.4 - - - -
629B ARG 3.0 19.0 + - - +
630B PHE 4.4 0.4 - - - +
632B ASP* 1.3 74.8 - - - +
634B LEU* 1.3 63.8 + - - +
636B ASP* 2.8 19.9 + - - +
637B LEU* 3.0 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 634 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B GLU* 4.7 2.8 - - - +
618B PHE* 6.1 5.4 - - + -
621B LEU* 6.5 1.3 - - + -
630B PHE 3.0 20.4 + - - +
631B LEU* 3.4 6.7 - - - +
632B ASP 3.2 0.2 - - - -
633B TYR* 1.3 77.6 - - - +
635B SER* 1.3 67.0 + - - +
637B LEU* 3.3 17.2 + - - +
638B CYS* 4.5 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 635 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B LEU 3.1 11.2 + - - -
632B ASP* 2.8 17.3 + - - -
634B LEU* 1.3 78.9 - - - +
636B ASP* 1.3 60.2 + - - -
637B LEU 3.1 0.5 + - - -
638B CYS* 3.8 11.6 + - - +
695B GLU* 6.4 0.2 - - - -
699B PHE* 3.7 30.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 636 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B THR* 5.0 5.5 - - - -
632B ASP 3.0 8.6 + - - +
633B TYR* 2.8 16.5 + - - +
635B SER* 1.3 72.6 - - - +
637B LEU* 1.3 68.8 + - - +
638B CYS 3.1 7.4 + - - +
699B PHE* 6.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 637 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B GLU 5.8 0.7 - - - +
595B ILE* 4.7 11.9 - - + -
596B THR* 4.0 30.4 - - - +
599B LEU* 3.2 20.1 - - + +
633B TYR 3.0 9.5 + - - +
634B LEU* 3.6 14.4 - - - +
635B SER 3.1 1.8 + - - -
636B ASP* 1.3 77.7 - - - +
638B CYS* 1.3 69.8 + - - +
639B VAL* 3.8 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 638 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B LEU* 4.8 2.5 - - - -
634B LEU 4.5 1.0 + - - +
635B SER 3.8 10.1 + - - +
636B ASP 3.1 9.7 + - - +
637B LEU* 1.3 86.8 - - - +
639B VAL* 1.3 61.2 + - - +
640B SER 5.1 0.7 - - - +
643B LYS* 4.6 16.8 - - + -
----------------------------------------------------------
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