Contacts of the helix formed by residues 308 - 325 (chain A) in PDB entry 3EQR
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 SER 308 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE* 3.5 19.3 - - - +
282A ASP 3.5 21.5 - - - -
283A HIS* 4.5 11.8 - - - +
300A GLU* 4.6 4.2 + - - +
306A THR* 5.6 0.9 - - - -
307A PHE* 1.3 75.9 - - - +
309A HIS* 1.3 63.8 + - - +
310A ALA* 3.1 20.8 + - - +
311A SER* 2.8 24.9 + - - -
312A ASP* 3.2 11.1 + - - +
372A PRO* 5.1 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLU* 3.5 56.6 + - + +
247A ARG* 3.9 13.4 + - - +
248A PHE 3.1 33.5 + - - -
249A ILE* 3.6 9.7 - - + +
277A LEU* 3.4 23.8 - - + +
282A ASP 4.9 1.0 + - - -
308A SER* 1.3 74.5 - - - +
310A ALA* 1.3 57.5 + - - +
312A ASP* 3.2 12.0 + - - +
313A THR* 3.0 27.5 + - - -
378A PHE* 4.0 4.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A SER* 3.1 10.5 + - - +
309A HIS* 1.3 80.5 - - - +
311A SER* 1.3 56.8 + - - +
313A THR* 3.3 7.9 + - - -
314A TRP 3.1 20.8 + - - -
372A PRO* 3.3 42.4 - - + +
375A ARG* 3.2 17.9 + - + +
376A PRO 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ALA* 3.9 5.4 - - - -
300A GLU* 3.7 15.5 - - - -
301A SER* 3.7 18.8 - - - -
306A THR 4.4 0.2 - - - -
307A PHE* 3.2 17.8 - - - +
308A SER* 2.8 36.2 + - - -
310A ALA* 1.3 73.2 - - - +
312A ASP* 1.3 66.1 + - - +
314A TRP* 3.3 2.9 + - - +
315A MET* 3.0 30.6 + - - +
375A ARG* 3.8 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A MET* 3.5 15.8 - - + +
248A PHE 4.3 1.9 - - - +
249A ILE* 3.4 11.1 - - - +
250A HIS* 2.7 24.7 + - - +
251A ARG* 3.0 28.5 + - - +
252A ASP 4.7 0.2 + - - -
253A LEU* 4.2 5.4 + - + +
308A SER 3.2 14.6 + - - +
309A HIS* 3.3 13.9 + - - +
311A SER* 1.3 78.6 + - - +
313A THR* 1.3 58.0 + - - +
315A MET* 3.1 8.4 + - - +
316A PHE* 2.8 29.6 + - - +
378A PHE* 3.6 18.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLU* 5.5 0.2 + - - -
309A HIS 3.0 12.4 + - - -
310A ALA* 3.3 13.2 + - - -
312A ASP* 1.3 72.5 - - - +
314A TRP* 1.3 65.7 - - - +
316A PHE* 3.2 5.0 + - - +
317A GLY 3.0 18.7 + - - -
367A CYS* 3.4 32.5 - - + +
375A ARG* 3.8 12.3 - - + -
376A PRO* 3.0 30.2 + - + +
377A THR* 4.6 1.0 - - - -
378A PHE* 3.6 20.5 - - - -
381A LEU* 3.9 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA 5.3 1.0 + - - -
296A TRP 3.3 21.0 + - - -
297A CYS 3.2 14.1 + - - -
298A ALA* 3.5 21.8 - - + -
299A PRO* 3.5 26.9 - - + -
310A ALA 3.1 11.2 + - - +
311A SER 3.4 8.7 - - - +
313A THR* 1.3 74.8 - - - +
315A MET* 1.3 63.6 + - - +
317A GLY 3.0 10.2 + - - -
318A VAL* 3.1 21.8 + - + +
331A TRP* 6.1 1.3 - - - -
343A ILE* 3.8 25.1 - - + -
349A ARG* 3.8 29.8 - - - -
367A CYS 3.5 12.1 + - - +
368A TRP* 3.3 50.3 + + + -
369A ALA 3.9 5.4 - - - -
375A ARG* 3.8 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ARG* 3.6 29.4 - - - +
252A ASP* 3.8 11.9 - - - -
253A LEU* 3.8 21.1 - - + +
292A VAL* 3.4 34.1 - - + -
296A TRP* 3.2 36.1 - - + +
297A CYS* 4.8 3.6 - - - -
298A ALA 4.9 1.3 - - - +
301A SER* 5.9 0.2 - - - -
307A PHE* 4.4 12.3 - - + -
311A SER* 3.0 16.8 + - - +
312A ASP* 3.1 10.5 + - - +
314A TRP* 1.3 74.5 - - + +
316A PHE* 1.3 60.4 + - - +
318A VAL* 3.2 5.9 + - - +
319A THR* 2.8 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ALA* 3.6 9.2 - - - -
236A VAL* 3.6 33.0 - - + -
237A ALA* 3.7 16.2 - - + -
253A LEU* 3.8 14.0 - - + +
312A ASP 2.8 12.6 + - - +
313A THR* 3.3 8.7 - - - +
315A MET* 1.3 75.6 - - - +
317A GLY* 1.3 59.1 + - - +
319A THR* 3.1 7.7 + - + -
320A LEU* 2.8 50.6 + - + +
323A MET* 6.4 1.3 - - - -
367A CYS* 4.1 6.1 - - - -
378A PHE* 3.7 20.6 - + + -
381A LEU* 3.9 24.5 - - + -
385A LEU* 3.4 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A THR 3.0 11.5 + - - -
314A TRP 3.0 5.3 + - - -
316A PHE* 1.3 77.1 - - - +
318A VAL* 1.3 56.2 + - - +
320A LEU* 3.3 9.9 + - - +
321A TRP 2.9 23.6 + - - -
364A MET* 4.1 4.1 - - - +
367A CYS* 3.7 19.5 - - - -
368A TRP* 3.4 23.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA 4.0 10.5 - - - +
296A TRP* 3.4 35.9 - - + +
314A TRP* 3.1 32.6 + - + +
315A MET 3.2 6.5 + - - +
317A GLY* 1.3 77.0 - - - +
319A THR* 1.3 55.2 + - - +
321A TRP* 3.2 4.4 + - - +
322A GLU* 3.0 26.4 + - - +
330A PRO* 3.8 26.5 - - + -
331A TRP* 6.0 0.9 - - - +
350A LEU* 4.2 7.9 - - + -
368A TRP* 3.3 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL* 5.4 7.4 - - + -
253A LEU* 3.5 7.3 - - + +
254A ALA* 3.3 25.4 + - - +
255A ALA* 3.6 18.8 - - - +
258A LEU* 3.9 26.0 - - + -
315A MET 2.8 20.8 + - - -
316A PHE* 3.1 13.4 + - + -
318A VAL* 1.3 70.0 - - - +
320A LEU* 1.3 59.5 + - - +
322A GLU* 3.2 11.7 + - - +
323A MET* 2.9 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ALA* 3.4 32.3 - - + -
316A PHE* 2.8 42.4 + - + +
317A GLY* 3.3 9.9 - - - +
319A THR* 1.3 71.7 - - - +
321A TRP* 1.3 63.0 + - - +
323A MET* 3.1 10.4 + - - -
324A PHE* 3.0 44.5 + - + +
360A ILE* 4.8 2.7 - - + +
363A VAL* 4.1 12.6 - - + -
364A MET* 3.8 28.0 - - + +
367A CYS* 5.1 0.4 - - - -
385A LEU* 4.1 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLY 2.9 13.5 + - - +
318A VAL 3.2 9.2 + - - +
320A LEU* 1.3 76.5 - - - +
322A GLU* 1.3 64.7 + - + +
324A PHE 3.5 0.3 + - - -
325A THR* 2.9 44.8 + - + +
328A GLN* 3.6 37.0 - - + -
329A GLU 4.2 3.8 - - - -
330A PRO* 3.5 45.3 - - + -
331A TRP 5.1 0.4 - - - -
350A LEU* 3.6 25.9 - - + +
351A PRO* 2.6 48.3 + - + -
353A PRO* 3.7 16.8 - - + +
361A TYR* 5.2 0.2 - + - -
364A MET* 3.9 13.4 - - - -
368A TRP* 4.0 13.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 4.5 11.4 - - - +
217A LEU* 4.7 1.7 - - - +
218A ARG* 5.2 2.8 + - - -
254A ALA* 4.9 0.2 - - - +
255A ALA* 2.9 38.9 + - + +
256A ARG* 4.6 1.0 + - - +
296A TRP* 2.7 44.2 + - - +
318A VAL 3.0 13.5 + - - +
319A THR* 3.4 12.3 - - - +
321A TRP* 1.3 77.9 - - + +
323A MET* 1.3 62.1 + - - +
325A THR* 3.0 9.3 + - - -
327A GLY* 2.6 34.0 + - - -
328A GLN 4.0 17.4 - - - +
330A PRO* 4.2 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU* 4.8 4.5 - - + -
217A LEU* 4.1 19.6 - - + +
229A LEU* 3.5 52.7 - - + +
232A TYR* 3.6 22.2 - - + -
233A ALA* 3.7 14.4 - - + +
236A VAL* 5.2 2.9 - - - -
255A ALA* 5.0 3.6 - - + -
258A LEU* 4.2 22.4 - - + -
316A PHE* 6.4 1.6 - - - -
319A THR* 2.9 28.8 + - + +
320A LEU* 3.1 16.8 + - - +
322A GLU* 1.3 77.2 - - - +
324A PHE* 1.3 65.4 + - + +
326A TYR* 3.1 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 3.7 32.2 - - + +
229A LEU* 3.6 34.5 - - + -
230A SER* 3.8 12.1 - - - -
233A ALA* 4.7 1.3 - - + -
320A LEU* 3.0 38.1 + - + +
323A MET* 1.3 80.4 - - + +
325A THR* 1.3 57.2 + - - +
326A TYR* 3.2 15.7 + - - -
353A PRO* 3.6 14.8 - - + +
354A GLU 4.3 7.4 - - - +
356A CYS* 4.0 22.3 - - + +
360A ILE* 3.7 43.3 - - + -
364A MET* 4.1 14.1 - - + -
385A LEU* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLN* 4.6 3.8 + - - -
321A TRP* 2.9 51.7 + - + +
322A GLU* 3.0 10.9 + - - -
324A PHE* 1.3 75.4 - - - +
326A TYR* 1.3 71.0 + - - +
327A GLY 3.3 0.2 + - - -
328A GLN* 3.1 51.7 + - - +
353A PRO* 3.7 19.5 - - + -
----------------------------------------------------------
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