Contacts of the strand formed by residues 285 - 296 (chain A) in PDB entry 2EG5
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 PHE 285 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 3.4 42.8 - - + -
213A SER* 3.7 28.5 - - - -
216A LEU* 3.6 24.7 - - + -
222A MET* 3.8 29.6 - - + -
279A VAL* 4.1 21.9 + - + +
280A GLU* 5.6 1.4 - - - -
282A GLU* 5.0 0.9 - - + +
283A GLY* 3.4 1.7 - - - +
284A SER* 1.3 82.7 - - - +
286A GLU* 1.3 60.0 + - - +
287A ILE* 4.1 1.0 + - - +
363A LEU* 3.4 36.3 - - + -
364A ALA 3.5 1.3 - - - -
365A LYS* 3.7 24.7 - - + -
366A LYS* 3.7 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PHE* 1.3 72.7 - - - +
287A ILE* 1.3 68.4 + - - +
288A LEU* 3.4 28.3 + - - +
363A LEU* 3.2 6.0 - - - -
364A ALA* 2.9 45.3 + - - +
366A LYS* 3.8 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LYS* 3.9 34.3 - - + +
279A VAL* 3.6 34.5 - - + -
280A GLU* 4.1 17.0 - - + +
285A PHE 4.8 1.1 - - - +
286A GLU* 1.3 78.8 - - - +
288A LEU* 1.3 64.9 + - - +
289A TYR 3.8 23.3 - - - +
290A LEU* 4.4 9.0 - - + -
361A ILE* 4.0 17.5 - - + -
362A SER 3.6 2.9 - - - -
363A LEU* 3.8 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 4.0 16.8 - - - +
221A ARG* 3.5 38.1 - - - +
286A GLU* 3.4 36.8 - - + +
287A ILE* 1.3 74.5 - - - +
289A TYR* 1.3 59.1 + - + +
362A SER* 2.8 31.1 + - - +
363A LEU 4.6 0.2 - - - -
364A ALA* 3.9 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 3.8 34.6 - - + +
38A GLN* 3.9 23.1 - - - +
287A ILE* 3.6 4.1 - - - +
288A LEU* 1.3 80.0 - - + +
290A LEU* 1.3 68.3 + - - +
291A GLU* 2.6 52.1 + - + +
360A ILE* 4.4 7.6 - - + -
361A ILE* 3.3 8.3 - - - +
362A SER* 2.9 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ALA* 4.9 3.4 - - + +
276A LYS* 4.1 37.7 - - + +
287A ILE* 4.4 9.9 - - + -
289A TYR* 1.3 80.2 - - - +
291A GLU* 1.3 72.9 + - - +
292A THR* 4.9 2.9 - - + -
359A LEU* 3.1 38.6 - - + -
360A ILE 3.3 5.8 - - - +
361A ILE* 4.0 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 3.3 31.6 + - - +
35A VAL* 4.1 10.4 - - - +
289A TYR* 2.6 40.0 + - + +
290A LEU* 1.3 75.4 - - - +
292A THR* 1.3 78.5 + - - +
293A PHE* 4.5 5.2 - - - +
359A LEU* 3.4 3.6 - - - +
360A ILE* 2.9 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A CYS* 4.2 7.9 - - - -
272A ALA* 4.0 26.9 - - + -
290A LEU* 4.9 2.0 - - + -
291A GLU* 1.3 87.9 - - - +
293A PHE* 1.3 64.4 + - - +
357A ASN* 4.0 15.5 + - - +
358A ASN 3.0 15.0 - - - +
359A LEU* 4.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 4.2 12.3 - - + -
31A LYS* 3.7 51.6 - - + +
225A THR* 4.1 11.7 - - + -
291A GLU* 4.5 4.7 - - - +
292A THR* 1.3 80.1 - - - +
294A LYS* 1.3 56.2 + - - +
295A VAL* 3.8 17.0 - - + -
357A ASN* 3.5 5.6 - - - -
358A ASN* 2.8 77.1 + - + -
360A ILE* 3.2 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 5.9 0.9 - - - +
232A GLU* 2.7 42.5 + - - +
293A PHE* 1.3 76.8 - - - +
295A VAL* 1.3 66.8 + - - +
296A LEU* 4.2 11.4 - - + -
352A GLY 4.8 2.6 + - - -
355A PHE* 3.7 40.5 - - + -
356A TYR 3.4 4.7 - - - +
357A ASN* 3.9 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.5 35.7 - - + +
27A LEU* 4.0 28.5 - - + -
28A VAL* 4.3 15.3 - - + +
31A LYS* 5.1 3.4 - - + -
293A PHE* 3.8 17.3 - - + -
294A LYS* 1.3 77.3 - - - +
296A LEU* 1.3 68.3 + - - +
299A ALA* 4.5 3.6 - - + -
355A PHE* 3.2 15.8 - - - +
356A TYR 3.1 17.1 + - - -
358A ASN* 3.8 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 4.2 1.6 - - - -
294A LYS* 4.4 13.2 - - + -
295A VAL* 1.3 78.6 - - - +
297A TYR* 1.3 67.6 + - - +
298A ASP* 3.0 16.0 + - - +
299A ALA* 3.0 26.4 + - + +
349A LEU 5.9 0.2 - - - +
352A GLY* 3.8 34.8 - - - +
354A GLY 3.5 5.6 - - - +
355A PHE* 3.6 22.0 - - + -
----------------------------------------------------------
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