Contacts of the strand formed by residues 330 - 333 (chain A) in PDB entry 2JG3
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 HIS 330 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PHE* 3.6 22.9 + + - -
326A TYR* 4.9 7.6 - + - -
328A THR* 2.8 21.1 + - + +
329A PRO* 1.3 73.7 - - - +
331A LEU* 1.3 85.8 + - - +
332A VAL* 3.9 4.6 - - + +
345A TRP* 3.6 17.8 - - - -
346A ASP* 2.9 41.6 + - + +
349A ALA* 5.7 1.6 - - - -
350A TYR 5.6 0.7 - - - -
352A TRP* 5.1 1.3 - + - -
357A HIS* 2.7 41.9 + + + +
358A LEU 3.7 14.4 - - - +
359A LEU* 3.9 16.4 - - + -
360A PRO* 5.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 5.3 0.2 - - + -
264A PHE* 4.1 15.9 - - + -
330A HIS* 1.3 79.7 - - - +
332A VAL* 1.3 73.9 + - - +
333A VAL* 4.2 6.5 - - + -
343A ALA* 3.9 13.0 - - + -
344A ALA 3.6 12.6 - - - +
345A TRP* 3.5 16.7 - - + -
356A PHE 4.0 0.2 - - - +
357A HIS* 3.7 0.2 - - - -
358A LEU* 3.0 54.1 + - + +
366A LEU* 5.7 0.2 - - + -
371A LEU* 3.9 27.1 - - + -
372A VAL* 3.8 24.0 - - + -
375A LEU* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 3.7 19.6 - - + +
303A VAL* 5.9 0.7 - - + -
330A HIS* 3.9 13.0 - - - +
331A LEU* 1.3 75.8 - - - +
333A VAL* 1.3 66.7 + - - +
342A VAL 4.1 0.2 - - - +
343A ALA* 3.3 5.9 - - - +
344A ALA 2.9 36.0 + - - +
346A ASP* 4.2 8.1 - - + -
352A TRP* 4.1 23.8 - - + -
355A GLU* 3.7 22.7 - - + -
356A PHE 3.3 10.3 - - - +
357A HIS* 3.8 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 4.0 3.6 - - - -
331A LEU* 4.2 11.2 - - + -
332A VAL* 1.3 79.7 - - - +
334A ALA* 1.3 65.2 + - - +
341A VAL* 4.5 8.5 - - + -
342A VAL 3.4 9.9 - - - +
343A ALA* 4.1 12.6 - - + -
355A GLU* 3.5 1.7 - - - +
356A PHE* 2.8 37.6 + - + +
358A LEU* 3.9 24.5 - - + -
375A LEU* 4.7 5.6 - - + -
395A LEU* 3.7 29.8 - - + -
400A LEU* 3.9 19.1 - - + -
----------------------------------------------------------
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