Contacts of the helix formed by residues 637 - 641 (chain A) in PDB entry 2XP0
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 TRP 637 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A CYS* 3.1 15.3 - - - -
636A TYR* 1.3 94.7 - + + +
638A GLY* 1.3 63.4 + - - +
639A ARG 3.9 0.2 + - - -
640A ASN* 4.0 6.1 + - - +
641A CYS* 3.8 22.5 + - + -
649A HIS* 5.6 2.5 - + - -
659A GLN* 3.2 38.2 + - - +
559B ILE* 4.2 18.7 + - + +
562B ASN* 3.5 43.2 - - + +
563B TYR* 4.1 18.6 - + + -
566B THR* 3.3 29.1 + - + +
624B GLU 4.0 18.6 - - - -
625B LEU* 4.3 9.9 - - + -
626B PRO* 3.8 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A CYS* 3.0 18.4 + - - +
636A TYR 3.4 0.2 - - - -
637A TRP* 1.3 78.4 - - - +
639A ARG* 1.3 66.3 + - - -
641A CYS* 3.0 20.3 + - - +
655A HIS* 3.4 12.5 - - - -
657A CYS* 3.5 17.9 - - - -
658A GLU 3.8 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ASN* 3.5 22.3 + - - +
611A GLU* 5.3 11.7 + - - +
614A TYR* 3.5 54.6 - - - +
615A GLN* 6.1 2.0 - - - +
618A GLN* 5.3 1.0 + - - -
637A TRP 3.9 0.4 + - - -
638A GLY* 1.3 70.4 - - - -
640A ASN* 1.3 79.4 + - - +
644A GLN* 2.8 18.2 + - - -
655A HIS 3.4 14.3 + - - +
657A CYS 2.9 14.9 + - - +
658A GLU* 3.3 39.2 + - - +
659A GLN 4.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 640 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A TRP* 4.0 5.7 + - - +
638A GLY 3.1 0.8 + - - -
639A ARG* 1.3 97.6 + - - +
641A CYS* 1.3 68.3 + - - +
642A ARG* 3.2 21.8 + - - +
658A GLU* 5.9 0.4 + - - -
659A GLN* 6.4 0.4 - - - +
562B ASN* 4.5 0.3 - - - +
565B ALA* 5.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 641 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A CYS* 3.9 2.7 - - - -
637A TRP* 3.8 14.0 + - + -
638A GLY 3.0 17.3 + - - +
639A ARG 3.3 1.0 - - - -
640A ASN* 1.3 76.3 - - - +
642A ARG* 1.3 61.4 + - - +
643A THR* 3.2 17.7 - - - -
644A GLN* 2.9 27.3 + - - +
645A VAL* 5.8 0.5 - - - +
649A HIS* 3.6 4.9 - - - -
655A HIS* 3.4 8.3 - - + -
995A ZN 2.3 37.2 - - - -
562B ASN* 3.4 22.0 - - - -
----------------------------------------------------------
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