Contacts of the helix formed by residues 431 - 436 (chain B) in PDB entry 3UJG
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 SER 431 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ASP* 2.7 27.9 + - - -
241B VAL* 3.9 10.9 - - - +
243B ASP* 3.9 23.6 - - - -
347B SER* 3.9 9.4 - - - -
430B ALA* 1.3 77.3 - - - +
432B ASP* 1.3 65.1 + - - +
433B GLY 3.1 8.5 + - - -
434B LEU* 3.1 14.2 + - - +
435B TRP* 3.3 9.9 + - - -
493B ASN 4.0 1.6 + - - -
495B SER 3.1 19.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A SER* 4.2 8.1 + - - -
243B ASP* 2.9 7.5 + - - +
346B ASP* 3.2 40.3 + - + +
347B SER* 4.6 0.6 - - - +
431B SER* 1.3 66.5 - - - +
433B GLY* 1.3 67.0 + - - +
434B LEU 3.0 2.7 - - - -
435B TRP* 3.7 13.2 - - + +
436B ASP* 2.9 52.7 + - - +
492B ASP* 2.6 11.6 - - - +
512B MG 2.3 27.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
172A GLN* 4.6 1.0 - - - +
431B SER* 3.1 3.9 + - - -
432B ASP* 1.3 84.0 + - - +
434B LEU* 1.3 57.9 + - - +
436B ASP 4.7 0.5 + - - -
437B VAL* 4.4 1.4 - - - +
485B ALA* 4.2 2.8 - - - +
490B SER* 2.7 34.6 + - - -
492B ASP* 3.8 7.8 + - - -
493B ASN 3.3 24.9 + - - -
494B ILE* 4.1 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B ILE* 5.0 1.6 - - + -
430B ALA* 3.9 11.9 - - + -
431B SER* 3.1 10.3 + - - +
432B ASP 3.0 0.2 - - - -
433B GLY* 1.3 76.4 - - - +
435B TRP* 1.3 108.2 + - + +
436B ASP 3.2 1.8 - - - -
437B VAL* 3.2 14.0 + - - +
438B MET* 3.3 35.5 + - + +
443B VAL* 3.7 17.9 - - + -
481B LEU* 4.4 10.3 - - + +
485B ALA* 4.1 16.8 - - + -
494B ILE* 4.6 3.7 - - + +
495B SER 5.2 0.2 - - - +
496B ILE* 3.9 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ASP 4.7 4.3 - - - +
348B ARG* 3.4 66.0 + - + +
350B VAL* 3.4 26.0 - - + -
363B ASP* 5.6 0.4 - - - +
428B ILE* 4.0 22.0 - - + -
430B ALA* 3.0 26.5 + - + -
431B SER 3.3 22.2 - - - -
432B ASP* 3.2 8.3 + - + -
434B LEU* 1.3 97.4 - - + +
436B ASP* 1.3 67.0 + - - +
437B VAL 3.2 1.0 + - - -
438B MET 3.3 22.6 + - - +
440B ASN* 3.6 15.7 - - - -
443B VAL* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A HIS* 3.0 26.4 - - + -
171A SER 6.0 0.2 - - - -
172A GLN* 3.1 45.4 - - + +
173A PRO 5.1 3.3 - - - +
432B ASP* 2.9 43.9 + - - +
433B GLY 4.9 0.4 - - - +
435B TRP* 1.3 80.6 - - - +
437B VAL* 1.3 59.9 + - + +
492B ASP* 4.8 1.6 - - - +
----------------------------------------------------------
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