Contacts of the strand formed by residues 329 - 334 (chain B) in PDB entry 3LXA
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 TYR 329 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B GLN* 3.5 20.0 - - - +
254B VAL* 4.3 4.7 - - + -
289B ILE* 4.3 1.8 - - - +
327B GLN 4.2 4.9 - - - -
328B GLY* 1.3 79.1 - - - +
330B GLN* 1.3 74.8 + - - +
331B LEU* 4.3 9.2 - - + -
340B TRP* 3.1 13.8 - - - +
341B GLU* 3.0 73.3 + - + +
343B PRO* 4.3 15.3 - - + -
349B TRP* 3.5 4.9 - - - -
374B LYS* 2.7 32.8 + - + +
804B GLA 3.8 44.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B SER* 3.8 24.0 + - - +
250B GLN* 2.9 37.5 + - - +
329B TYR* 1.3 75.7 - - - +
331B LEU* 1.3 64.4 + - - +
332B ARG* 3.8 11.1 - - - +
333B GLN* 3.6 33.6 + - - +
338B GLU* 3.0 29.3 + - + -
339B VAL 3.6 8.3 - - - +
340B TRP* 3.7 25.7 - - + +
804B GLA 4.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B TYR* 3.6 11.4 + - + -
330B GLN* 1.3 75.0 - - - +
332B ARG* 1.3 69.4 + - + +
339B VAL* 2.6 30.2 + - + +
340B TRP* 4.8 2.0 - - - -
341B GLU* 3.1 31.6 - - - +
367B ILE* 4.8 6.5 - - + -
371B SER* 3.7 24.9 - - - +
372B LEU* 4.2 17.9 - - + -
374B LYS* 6.2 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLN* 3.6 8.2 - - - +
331B LEU* 1.3 89.1 - - + +
333B GLN* 1.3 69.8 + - - +
338B GLU* 3.5 0.7 - - - -
339B VAL* 2.8 43.0 + - + +
365B TYR* 3.7 14.2 + - - +
366B THR 5.4 1.4 + - - -
367B ILE* 3.2 29.3 - - - +
371B SER* 3.3 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLN* 3.6 30.9 + - - +
332B ARG* 1.3 81.9 - - - +
334B GLY* 1.3 63.1 + - - +
337B PHE 3.2 13.2 - - - +
338B GLU* 3.9 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLN* 1.3 83.0 + - - +
335B ASP* 1.3 75.4 + - - +
336B ASN 3.0 3.1 - - - +
337B PHE* 2.9 23.9 + - - +
365B TYR* 5.4 0.9 - - - -
----------------------------------------------------------
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