Contacts of the strand formed by residues 329 - 334 (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 ALA 329 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B VAL 3.4 7.0 - - - -
242B TYR* 3.7 20.0 - - + -
254B CYS* 5.1 0.7 - - - -
258B LEU* 4.6 3.4 - - + -
294B PHE* 4.0 21.6 - - + -
328B THR* 1.3 78.2 - - - +
330B VAL* 1.3 60.8 + - - +
331B VAL 4.2 0.4 - - - -
342B SER 3.7 2.5 - - - +
343B ASN* 3.6 2.4 - - - +
344B CYS* 2.9 37.7 + - + +
347B SER* 5.3 0.2 - - - -
400B ILE* 4.4 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B GLY* 3.5 1.7 - - - -
241B VAL* 2.9 45.7 + - + +
329B ALA* 1.3 73.6 - - - +
331B VAL* 1.3 63.8 + - - +
341B VAL* 4.1 12.3 - - + -
342B SER 3.6 3.6 - - - +
343B ASN* 3.6 19.3 - - + +
347B SER* 3.4 28.0 - - - +
348B ARG 4.2 2.2 - - - +
349B ALA* 3.9 33.9 - - + +
429B LEU* 3.9 14.5 - - + +
430B ALA 4.6 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B PHE* 4.2 13.5 - - + -
239B PHE 3.1 11.0 - - - +
242B TYR* 4.2 15.5 - - + +
258B LEU* 4.0 17.5 - - + -
290B PHE* 3.4 39.0 - - + -
294B PHE* 3.9 21.1 - - + -
329B ALA 4.7 0.2 - - - -
330B VAL* 1.3 80.2 - - - +
332B ALA* 1.3 63.8 + - - +
333B LEU* 5.0 0.2 - - + -
341B VAL* 3.2 7.9 - - - +
342B SER* 3.0 28.2 + - - -
429B LEU* 4.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B HIS 3.4 2.8 - - - +
238B PHE* 3.7 1.6 - - - -
239B PHE* 2.8 39.7 + - + +
331B VAL* 1.3 76.0 - - - +
333B LEU* 1.3 64.8 + - - +
334B VAL* 3.9 4.0 - - + -
339B ILE* 4.7 1.1 - - + -
340B VAL 3.2 6.3 - - - +
341B VAL* 4.1 14.8 - - + -
427B LEU* 4.1 21.1 - - + -
429B LEU* 4.0 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU* 4.6 13.9 - - + -
215B LEU* 4.4 17.0 - - + -
236B GLY* 5.4 0.9 - - - -
237B HIS 3.5 4.0 - - - +
238B PHE* 3.9 17.3 - - + -
262B LEU* 3.7 29.4 - - + -
266B ILE* 5.3 0.4 - - + -
286B TRP* 3.7 35.9 - - + -
290B PHE* 4.2 17.3 - - + -
331B VAL* 5.0 0.7 - - + -
332B ALA* 1.3 78.3 - - - +
334B VAL* 1.3 63.2 + - - +
338B HIS 3.7 1.4 - - - +
339B ILE* 3.3 5.2 - - - +
340B VAL* 2.8 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B CYS* 5.0 2.9 - - - -
236B GLY* 3.5 2.2 - - - -
237B HIS* 2.9 41.7 + - - +
239B PHE* 3.8 28.0 - - + -
332B ALA* 4.7 1.6 - - + -
333B LEU* 1.3 76.5 - - - +
335B CYS* 1.3 72.9 + - - +
338B HIS 3.8 5.2 - - - +
339B ILE* 4.4 5.4 - - + -
420B ARG* 3.6 18.2 - - - +
427B LEU* 4.0 26.0 - - + -
499B ILE* 4.4 8.1 - - + -
501B LEU* 4.2 14.1 - - + -
----------------------------------------------------------
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