Contacts of the helix formed by residues 427 - 436 (chain B) in PDB entry 2XGZ
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 GLY 427 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B VAL* 3.2 19.0 - - - +
174B THR* 3.2 23.5 - - - -
176B ALA 4.7 1.3 - - - -
425B PHE* 3.3 25.9 - - - -
426B ALA* 1.3 75.6 - - - +
428B GLU* 1.3 63.3 + - - -
429B ASN 3.1 1.4 + - - -
430B PHE* 3.3 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B THR* 3.5 18.2 + - - +
426B ALA 3.3 0.2 + - - -
427B GLY* 1.3 70.8 - - - -
429B ASN* 1.3 65.2 + - - +
430B PHE* 3.3 17.2 + - - -
431B HIS* 5.0 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B ALA* 2.9 16.3 + - - +
428B GLU* 1.3 84.0 - - - +
430B PHE* 1.3 63.8 + - - +
431B HIS 3.2 4.0 + - - -
432B HIS* 3.3 14.9 + - + +
433B GLY* 3.3 10.9 + - - -
436B LEU* 3.9 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B VAL* 3.9 8.7 - - + -
150B PHE* 3.9 15.3 - + - -
174B THR* 3.7 21.1 - - + -
292B VAL* 3.8 37.7 - - + -
316B GLN* 3.8 26.0 - - + -
392B THR 3.0 22.7 - - - +
393B GLY* 3.5 21.5 - - - +
394B GLN* 3.6 21.7 + - + +
426B ALA* 3.8 6.9 + - - -
427B GLY 3.3 19.7 + - - +
428B GLU* 3.3 12.7 - - - -
429B ASN* 1.3 77.3 - - - +
431B HIS* 1.3 82.5 + - + +
433B GLY 3.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B GLN* 2.7 30.1 + - + +
340B ASP* 3.2 51.9 + - - +
363B PHE* 5.7 0.2 - - - -
366B GLY 4.1 4.6 + - - -
368B GLY* 3.3 33.7 + - - -
392B THR 4.5 1.2 - - - +
394B GLN* 3.8 7.7 + - - +
428B GLU 5.0 0.9 + - - +
429B ASN 3.2 1.2 + - - -
430B PHE* 1.3 93.0 - - + +
432B HIS* 1.3 98.3 + + - +
433B GLY 3.7 1.4 + - - -
434B ASP* 4.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B GLY* 3.2 32.9 + - - -
367B TRP 4.7 2.0 - - - -
429B ASN* 3.3 11.0 + - + +
431B HIS* 1.3 104.2 - + - +
433B GLY* 1.3 64.8 + - - +
434B ASP* 3.1 14.8 - - - +
435B LYS* 3.0 23.0 + - + -
436B LEU* 3.2 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL* 3.8 11.3 - - - +
391B ARG* 3.0 23.3 + - - +
392B THR 3.4 19.0 + - - -
393B GLY* 4.1 6.3 - - - -
426B ALA* 5.0 0.2 - - - -
429B ASN 3.3 8.9 + - - -
430B PHE 3.3 9.2 + - - -
431B HIS 3.4 1.2 + - - -
432B HIS* 1.3 76.1 - - - +
434B ASP* 1.3 61.4 + - - +
435B LYS 3.3 0.5 + - - -
436B LEU* 3.4 13.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LYS* 5.1 4.3 + - - +
363B PHE* 3.3 60.4 - - + +
367B TRP 4.6 1.4 - - - +
390B LEU 4.5 1.3 - - - +
391B ARG* 2.8 36.8 + - + +
392B THR 4.2 1.2 + - - -
431B HIS 4.5 1.9 - - - +
432B HIS* 3.6 20.8 - - - +
433B GLY* 1.3 76.8 + - - +
435B LYS* 1.3 66.3 + - - +
436B LEU 3.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ARG* 4.0 0.2 - - - -
432B HIS* 3.0 22.2 + - + +
434B ASP* 1.3 84.2 - - - +
436B LEU* 1.3 66.4 + - - +
437B LEU* 3.2 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL* 4.2 15.3 - - + -
391B ARG* 2.6 31.1 + - - +
424B VAL* 4.2 18.2 - - + -
425B PHE 4.4 1.3 - - - +
426B ALA* 3.9 30.1 - - + +
429B ASN* 3.9 34.1 - - + +
432B HIS 3.2 9.4 + - - +
433B GLY* 3.4 16.0 + - - +
435B LYS* 1.3 77.3 - - - +
437B LEU* 1.3 82.9 + - - +
----------------------------------------------------------
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