Contacts of the strand formed by residues 259 - 271 (chain A) in PDB entry 3ECP
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 ARG 259 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A SER* 3.7 1.6 - - - -
241A ILE* 2.7 64.1 + - + +
256A ARG* 6.6 0.2 - - - -
257A PRO 3.6 6.3 + - - +
258A ALA* 1.3 76.7 - - - +
260A LYS* 1.3 71.7 + - - +
261A ALA* 4.1 9.4 - - - +
286A GLU* 3.1 39.2 + - - -
289A PRO* 5.2 0.2 - - - +
290A PRO* 3.4 31.1 - - - +
293A GLU* 4.2 22.8 + - - +
294A THR 4.1 11.7 + - - -
296A LEU* 4.5 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLN* 3.8 21.9 - - + +
239A ILE 3.3 11.2 - - - +
240A SER* 4.6 9.0 - - - +
259A ARG* 1.3 86.1 + - - +
261A ALA* 1.3 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLN* 3.4 5.4 - - - +
239A ILE* 2.8 43.8 + - + +
241A ILE* 4.3 7.0 - - + -
259A ARG* 4.1 7.9 + - - +
260A LYS* 1.3 75.3 - - - +
262A SER* 1.3 60.2 + - - +
263A LEU* 5.0 1.3 - - + +
286A GLU* 3.9 26.2 - - + +
296A LEU* 4.1 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TYR 3.8 4.0 - - - -
238A GLN* 4.0 20.8 + - - +
261A ALA* 1.3 75.5 - - - +
263A LEU* 1.3 63.6 + - - +
286A GLU* 3.4 8.6 - - - +
287A ILE* 3.0 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLY* 3.3 4.9 - - - -
237A TYR* 2.8 85.9 + - + +
239A ILE* 4.5 7.6 - - + -
261A ALA* 5.0 2.7 - - + +
262A SER* 1.3 77.4 - - - +
264A SER* 1.3 60.4 + - - +
284A ALA* 4.4 2.7 - - + -
285A GLU* 3.4 9.9 - - - +
286A GLU* 3.4 34.3 - - + +
287A ILE* 3.4 7.8 - - - +
296A LEU* 4.0 17.7 - - + -
2C T 3.5 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLU* 3.1 28.5 - - - -
235A GLY 3.9 4.0 - - - -
236A GLY* 4.5 1.3 - - - -
263A LEU* 1.3 74.3 - - - +
265A LEU* 1.3 61.3 + - - +
266A ARG* 4.5 15.7 + - - +
283A LEU 3.7 1.4 - - - +
284A ALA* 3.5 3.9 - - - -
285A GLU* 2.8 39.1 + - - +
286A GLU 5.3 0.2 - - - -
287A ILE* 3.4 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLU* 3.8 1.6 - - - -
234A LEU* 3.0 29.0 + - + -
235A GLY 2.9 19.2 + - - +
237A TYR* 3.9 14.1 - - + -
263A LEU 4.1 0.2 + - - -
264A SER* 1.3 71.8 - - - +
266A ARG* 1.3 67.1 + - - +
282A VAL* 3.5 29.4 - - + -
283A LEU 3.6 1.8 - - - +
284A ALA* 3.7 24.9 - - + -
309A LEU* 4.0 9.6 - - + -
312A ALA* 3.8 22.9 - - + -
313A LEU* 3.3 38.4 - - + -
316A ILE* 3.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 3.3 29.1 - - - +
229A LYS* 3.8 28.3 + - - +
231A GLN* 2.5 38.2 + - + -
232A PRO* 3.8 9.8 - - - +
233A GLU* 3.6 32.8 + - + +
234A LEU* 4.2 8.7 - - - -
264A SER* 4.5 14.6 + - - +
265A LEU* 1.3 80.5 - - - +
267A SER* 1.3 60.2 + - - +
282A VAL* 3.3 6.0 - - - +
283A LEU* 2.8 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 3.8 5.8 - - - -
231A GLN* 3.2 26.6 - - - +
232A PRO 5.3 0.6 + - - -
234A LEU* 3.3 16.7 - - - +
266A ARG* 1.3 75.5 - - - +
268A GLY* 1.3 59.9 + - - +
281A ALA 3.3 14.1 - - - -
282A VAL* 4.2 7.0 - - - -
306A VAL* 2.7 43.7 + - - +
307A GLU* 4.1 4.3 + - - -
312A ALA* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A HIS* 5.3 2.2 - - - -
228A LEU* 3.8 7.3 - - - +
231A GLN* 4.8 7.9 - - - -
267A SER* 1.3 81.2 - - - +
269A ARG* 1.3 64.6 + - - -
270A ILE* 3.9 4.1 + - - +
280A ASN* 3.4 5.4 - - - +
281A ALA* 3.0 30.6 + - - +
306A VAL* 4.6 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASP* 4.5 0.7 - - - +
227A HIS* 4.0 11.8 - - - -
268A GLY* 1.3 73.1 - - - -
270A ILE* 1.3 68.2 + - - +
271A THR* 6.0 0.2 - - - +
278A THR* 3.3 29.3 + - - +
279A LEU* 3.7 13.2 - - - +
280A ASN* 2.5 48.4 + - - +
303A SER 5.7 0.4 + - - -
306A VAL* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASP* 3.2 11.2 - - - +
224A LEU* 3.9 33.7 - - + -
227A HIS* 3.9 22.2 - - + +
228A LEU* 4.5 11.2 - - + -
268A GLY 4.3 6.5 - - - +
269A ARG* 1.3 80.8 - - - +
271A THR* 1.3 64.1 + - - +
272A LEU* 4.0 9.9 - - + -
277A ILE 4.1 0.2 - - - +
278A THR* 3.3 4.2 - - - -
279A LEU* 2.7 72.3 + - + +
280A ASN 4.2 0.4 - - - +
281A ALA* 4.0 22.7 - - + -
301A LEU* 4.7 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASP* 2.7 19.2 + - - -
218A VAL* 2.9 39.1 + - + -
219A GLU* 5.2 5.5 - - - +
269A ARG* 6.0 0.5 - - - +
270A ILE* 1.3 75.4 - - - +
272A LEU* 1.3 75.4 + - - +
276A ASN* 4.1 24.9 - - - +
277A ILE 3.4 16.6 - - - +
278A THR* 3.5 16.9 - - + +
----------------------------------------------------------
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