Contacts of the strand formed by residues 291 - 296 (chain D) in PDB entry 3EI4
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 VAL 291 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D THR* 2.5 35.7 + - - +
261D ALA* 3.5 27.4 - - + -
262D SER 3.1 16.7 + - - +
263D VAL* 5.0 0.2 - - - -
265D GLN 4.4 2.0 - - - -
266D THR 4.1 5.8 - - - +
267D VAL* 3.8 10.1 - - + -
287D HIS* 3.4 44.6 - - + +
289D HIS 4.1 0.9 - - - +
290D PRO* 1.3 77.3 - - - +
292D ASN* 1.3 57.9 + - - +
293D ALA 3.7 17.5 - - - +
305D THR* 4.6 2.7 - - + -
306D THR 3.8 7.0 - - - +
307D ASP* 4.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D THR* 3.5 22.6 - - - +
247D HIS* 4.0 0.3 - - - +
290D PRO* 3.8 1.1 + - - +
291D VAL* 1.3 75.4 - - - +
293D ALA* 1.3 63.8 + - + +
306D THR 2.8 13.3 + - - +
307D ASP 3.3 18.3 + - - -
308D GLN* 3.5 35.3 + - - +
331D HIS* 4.7 2.8 - - - -
332D ARG 4.9 4.4 + - - -
339D PRO* 3.9 25.9 - - + +
340D ILE* 3.5 28.8 + - - +
341D LYS* 3.5 16.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D HIS* 3.2 28.0 - - + +
291D VAL* 3.5 7.7 - - - +
292D ASN* 1.3 83.6 - - - +
294D ALA* 1.3 62.1 + - - +
295D CYS* 5.3 2.0 - - - +
304D LEU 3.5 2.3 - - - +
305D THR* 3.5 0.7 - - - -
306D THR* 2.8 38.4 + - - +
341D LYS* 3.6 26.5 - - + -
342D ALA 5.2 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D HIS* 3.5 22.3 + - - +
249D ALA* 3.8 7.3 - - - +
259D ALA* 4.7 5.6 - - + +
261D ALA* 3.7 19.7 - - + +
267D VAL* 3.8 23.1 - - + -
293D ALA* 1.3 77.0 - - - +
295D CYS* 1.3 61.5 + - - +
303D LEU* 3.9 14.0 - - + +
304D LEU 3.2 5.8 - - - -
305D THR* 3.8 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D HIS* 3.8 22.0 - - + +
249D ALA* 4.4 5.8 - - + -
293D ALA* 5.8 2.0 - - - -
294D ALA* 1.3 77.4 - - - +
296D PHE* 1.3 61.2 + - - +
303D LEU* 3.7 6.0 - - - +
304D LEU* 2.9 31.2 + - - -
342D ALA 3.8 22.4 - - - -
343D ALA* 4.4 9.0 - - - -
344D TRP* 2.9 25.3 + - - -
399D GLU* 5.7 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ALA* 3.4 24.9 - - + +
250D LEU 3.9 2.2 - - - -
251D ASN* 3.2 52.3 - - - +
252D PRO* 3.7 18.6 - - + +
257D PHE* 3.6 21.3 - + - -
258D LEU 4.7 0.2 - - - -
259D ALA* 3.6 17.5 - - + -
269D ILE* 5.5 2.2 - - + -
295D CYS* 1.3 76.5 - - - +
297D SER* 1.3 64.3 + - - +
298D PRO* 3.9 1.2 - - - +
300D GLY* 3.8 4.7 - - - -
302D ARG 3.6 13.0 - - - -
303D LEU* 3.5 18.2 - - + -
320D TRP* 3.7 22.4 - + - -
344D TRP* 3.0 12.7 - - - +
----------------------------------------------------------
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