Contacts of the strand formed by residues 334 - 339 (chain A) in PDB entry 3E8R
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 LEU 334 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A CYS* 3.5 20.2 - - - -
226A LYS 3.3 2.4 + - - -
227A LEU* 3.3 19.2 - - + -
228A LEU 2.9 22.9 + - - -
332A VAL* 3.4 9.1 - - - +
333A CYS* 1.3 85.8 - - - +
335A ALA* 1.3 62.3 + - - +
336A HIS* 6.0 0.2 - - + -
363A GLY 3.8 0.4 - - - -
364A VAL* 3.7 26.0 - - + +
381A ASN* 3.5 22.0 - - - +
382A SER* 4.9 0.2 - - - -
407A LEU* 3.9 16.8 - - + -
410A ASN* 3.5 42.2 - - + +
411A PHE* 4.3 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 3.2 21.3 - - + +
321A PHE* 4.0 19.1 - - + -
325A ILE* 4.1 18.4 - - + -
329A ALA* 4.4 9.6 - - + -
332A VAL* 4.7 0.7 - - + -
334A LEU* 1.3 77.7 - - - +
336A HIS* 1.3 62.5 + - - +
381A ASN* 2.9 11.5 + - - +
382A SER* 3.2 24.0 - - - -
383A GLY 3.3 4.3 + - - -
410A ASN* 5.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 5.7 6.7 - - + +
228A LEU 2.8 11.7 + - - +
229A VAL* 3.5 7.0 - - + -
230A VAL* 2.9 26.9 + - - +
255A ILE* 6.1 0.9 - - + -
321A PHE* 3.9 3.6 - - - -
334A LEU* 6.0 0.9 - - + -
335A ALA* 1.3 75.2 + - - +
337A LEU* 1.3 73.7 + - - +
338A PHE* 3.4 35.2 + + + -
383A GLY* 3.4 12.7 + - - -
384A LEU 3.3 24.7 - - - -
385A THR* 2.8 22.1 + - - -
403A THR* 4.2 6.8 - - + +
406A GLU* 3.8 22.2 - - + -
407A LEU* 4.0 24.7 - - + +
410A ASN* 4.6 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A VAL* 3.5 13.7 - - + +
232A ASP* 4.0 15.9 - - + +
298A TYR* 3.9 27.4 - - + -
317A LEU* 4.1 37.7 - - + -
321A PHE* 3.7 33.7 - - + -
336A HIS* 1.3 74.2 - - - +
338A PHE* 1.3 76.5 + - - +
339A THR* 4.5 7.0 - - - -
383A GLY 3.0 7.1 + - - -
384A LEU* 3.2 15.1 - - + +
385A THR 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 3.8 29.6 - - + -
230A VAL 2.7 12.9 + - - +
231A ALA* 3.7 2.6 - - - -
232A ASP* 3.3 24.1 + - - +
235A PHE* 3.4 25.3 - + + +
250A TYR* 5.5 0.2 - + - -
251A LEU* 3.4 27.8 - - + -
254A LEU* 4.1 20.2 - - + -
255A ILE* 4.2 6.5 - - + -
336A HIS* 3.4 29.2 - + + -
337A LEU* 1.3 76.3 - - - +
339A THR* 1.3 62.1 + - - +
385A THR* 3.4 20.0 - - + -
387A THR* 5.2 1.8 - - + -
403A THR* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ASP* 2.5 31.1 + - - -
234A ARG* 3.8 2.8 - - - -
235A PHE* 3.6 13.0 - - - -
317A LEU* 4.5 5.8 - - + -
337A LEU* 4.5 10.1 - - + -
338A PHE* 1.3 74.2 - - - +
340A TYR* 1.3 68.6 + - - +
341A GLN* 2.9 34.7 + - + +
343A PHE* 4.3 8.1 - - + -
384A LEU* 4.7 3.1 - - + -
385A THR 2.9 19.3 + - - +
386A SER* 3.4 11.1 - - - -
387A THR* 3.2 20.6 + - - -
----------------------------------------------------------
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