Contacts of the helix formed by residues 364 - 381 (chain A) in PDB entry 3D7T
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 364 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A VAL* 3.0 25.7 - - - +
362A ALA* 3.9 3.2 + - - +
363A PHE* 1.3 73.3 - - - +
365A THR* 1.3 63.5 + - - +
366A LYS* 3.3 14.3 + - - +
367A SER* 3.0 25.4 + - - -
368A ASP* 3.2 7.3 - - - +
427A ALA* 5.5 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLU* 3.3 46.9 + - + +
309A ASN 5.8 0.5 - - - -
310A PHE 3.6 18.4 + - - -
311A VAL* 3.9 1.7 - - - +
364A SER* 1.3 74.0 - - - +
366A LYS* 1.3 72.6 + - + +
367A SER 3.3 0.9 - - - -
368A ASP* 3.7 10.3 + - - +
369A VAL* 3.3 24.7 + - + +
433A PHE* 4.1 6.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLU* 5.5 0.4 - - - -
364A SER* 3.3 10.4 + - - +
365A THR* 1.3 89.5 - - + +
367A SER* 1.3 59.6 + - - +
368A ASP 3.3 0.2 - - - -
369A VAL* 3.8 4.6 - - + +
370A TRP 3.3 9.9 + - - -
427A ALA* 3.0 47.8 - - + +
428A ALA* 5.0 6.7 + - - +
430A ARG* 2.7 39.4 + - + +
431A PRO 3.1 29.4 + - - +
432A SER* 3.9 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ALA* 4.0 14.5 + - - +
356A GLU* 5.0 4.3 + - - +
357A ALA* 3.8 19.4 + - - +
362A ALA 4.0 1.4 + - - -
363A PHE* 3.5 19.8 - - - -
364A SER* 3.0 34.2 + - - -
366A LYS* 1.3 78.2 - - - +
368A ASP* 1.3 64.0 + - - +
370A TRP* 3.2 7.4 + - - +
371A SER* 3.2 22.3 + - - -
430A ARG* 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A MET* 3.7 25.7 - - + +
310A PHE 4.2 2.1 - - - +
311A VAL* 3.3 28.3 - - - +
312A HIS* 3.5 7.6 + - - +
313A ARG* 3.4 23.9 + - - -
315A LEU* 3.8 5.7 - - + +
364A SER 3.2 15.9 - - - +
365A THR* 3.7 6.8 + - - +
366A LYS 3.3 0.4 - - - -
367A SER* 1.3 77.3 - - - +
369A VAL* 1.3 58.5 + - - +
371A SER* 3.2 10.2 + - - +
372A PHE* 2.8 28.6 + - - +
433A PHE* 3.7 10.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A THR* 3.3 18.9 + - + +
366A LYS* 3.9 7.0 - - + +
367A SER 3.3 0.6 - - - -
368A ASP* 1.3 77.2 - - - +
370A TRP* 1.3 60.1 + - - +
372A PHE* 3.5 4.6 - - - +
373A GLY 3.3 6.8 + - - -
422A CYS* 3.0 31.1 - - + +
430A ARG* 3.7 23.1 - - + -
431A PRO* 3.3 33.2 - - + +
432A SER* 4.3 4.5 - - - -
433A PHE* 3.9 26.2 - - + -
436A LEU* 4.2 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LYS 5.0 1.0 + - - -
352A TRP 3.5 14.3 + - - -
353A THR 3.4 10.9 + - - -
354A ALA* 3.5 24.5 - - + -
355A PRO* 3.8 16.4 - - + -
366A LYS 3.3 2.8 + - - -
367A SER 3.2 10.4 + - - +
368A ASP 3.1 0.2 - - - -
369A VAL* 1.3 76.0 - - - +
371A SER* 1.3 59.1 + - - +
372A PHE 3.0 1.6 - - - -
373A GLY* 3.0 17.7 + - - -
374A ILE* 3.3 20.1 + - + +
387A TYR* 4.2 10.8 + - - -
399A VAL* 3.9 30.5 - - + -
403A TYR 5.3 5.2 - - - -
422A CYS 3.5 8.5 - - - -
423A TRP* 3.2 62.2 + + + -
424A HIS 3.9 6.7 - - - -
425A LEU* 5.2 6.7 - - + -
430A ARG* 3.5 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ARG 5.4 4.6 + - - -
315A LEU* 3.4 40.1 + - - +
352A TRP* 2.9 27.9 + - - +
353A THR* 4.2 5.4 - - - -
354A ALA 4.6 0.2 + - - -
367A SER 3.2 10.5 + - - -
368A ASP* 3.2 9.5 + - - -
370A TRP* 1.3 77.7 - - - +
372A PHE* 1.3 57.2 + - - +
374A ILE* 3.6 4.7 + - - +
375A LEU* 3.1 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A SER* 3.6 12.8 - - - -
298A VAL* 3.2 29.6 - - + -
299A CYS* 3.6 33.4 - - + -
315A LEU* 3.8 18.8 - - + +
368A ASP 2.8 12.2 + - - +
369A VAL* 3.5 10.5 - - - +
370A TRP 3.0 0.4 - - - -
371A SER* 1.3 76.4 - - - +
373A GLY* 1.3 65.6 + - - +
375A LEU* 3.1 13.4 + - + +
376A LEU* 2.9 48.3 + - + +
418A VAL* 5.3 0.9 - - + -
422A CYS* 4.8 6.3 - - - -
433A PHE* 3.9 15.5 - + + -
436A LEU* 4.0 23.6 - - + -
440A LEU* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A VAL 3.3 4.8 + - - -
370A TRP 3.0 4.6 + - - -
372A PHE* 1.3 78.0 - - - +
374A ILE* 1.3 60.9 + - - +
376A LEU* 3.2 15.7 + - - +
377A TRP 3.2 7.8 + - - -
419A MET* 3.7 5.2 - - - +
422A CYS* 3.9 18.0 - - - +
423A TRP* 3.1 34.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LYS 3.9 15.0 - - - +
352A TRP* 3.4 43.1 - - + +
370A TRP* 3.3 17.2 + - - +
371A SER 3.7 6.3 - - - +
373A GLY* 1.3 73.5 - - - +
375A LEU* 1.3 57.9 + - - +
377A TRP* 3.1 7.4 + - - +
378A GLU* 2.8 26.4 + - + +
386A PRO* 3.8 23.3 - - + -
387A TYR* 3.8 22.0 - - + +
405A MET* 3.9 8.1 - - + -
423A TRP* 3.2 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 5.6 0.9 - - + -
295A SER* 6.1 0.4 - - - -
298A VAL* 4.6 10.8 - - + -
315A LEU* 4.1 19.1 - - + +
316A ALA* 3.4 32.8 - - - +
317A ALA* 3.5 10.1 - - + +
320A VAL* 4.0 13.9 - - + -
352A TRP* 4.8 0.2 - - - -
371A SER 3.1 18.1 + - - +
372A PHE* 3.1 28.0 + - + +
374A ILE* 1.3 76.3 - - - +
376A LEU* 1.3 63.5 + - + +
378A GLU* 3.3 18.7 - - - +
379A ILE* 3.2 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A SER* 3.5 31.4 - - - +
372A PHE* 2.9 35.2 + - + +
373A GLY* 3.5 9.6 - - - +
374A ILE 3.1 0.2 - - - -
375A LEU* 1.3 75.9 - - + +
377A TRP* 1.3 67.9 + - - +
379A ILE* 3.0 20.3 + - + +
380A TYR* 3.0 23.7 + - + -
415A VAL* 4.3 12.8 - - + -
418A VAL* 3.5 34.3 - - + -
419A MET* 3.5 22.0 - - + -
422A CYS* 5.5 0.4 - - - -
440A LEU* 5.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLY 3.2 5.6 + - - +
374A ILE 3.1 7.5 + - - +
376A LEU* 1.3 79.2 - - - +
378A GLU* 1.3 67.5 + - - +
380A TYR 3.3 0.7 + - - -
381A SER* 2.5 47.3 + - - -
384A ARG* 3.5 45.8 - - + -
385A VAL 3.6 9.4 - - - -
386A PRO* 3.5 25.6 - - + -
388A PRO* 3.8 21.1 - - + -
405A MET* 3.6 38.4 - - + +
406A ASP 3.2 19.6 + - - +
408A PRO* 3.3 32.7 - - + +
416A TYR* 5.8 0.2 - + - -
419A MET* 3.4 17.6 - - - -
423A TRP* 4.1 2.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A VAL* 4.4 8.8 - - + +
278A LEU* 4.6 1.1 - - - -
316A ALA* 4.3 0.3 - - - +
317A ALA* 2.9 40.3 + - + +
318A ARG* 4.8 1.2 + - - +
352A TRP* 3.1 40.5 + - - +
374A ILE 2.8 13.7 + - - +
375A LEU* 3.3 21.1 - - - +
377A TRP* 1.3 84.7 - - - +
379A ILE* 1.3 59.9 + - - +
381A SER* 3.3 2.4 + - - -
382A PHE 3.2 2.3 + - - -
383A GLY* 2.9 30.7 + - - -
384A ARG 4.2 9.9 - - - +
386A PRO* 4.2 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 4.3 20.6 - - + -
278A LEU* 3.8 16.2 - - + +
291A LEU* 3.7 29.3 - - + +
294A PHE* 4.4 17.7 - - + -
295A SER* 3.7 23.8 - - - +
298A VAL* 5.8 1.3 - - + -
317A ALA* 5.3 0.9 - - + -
375A LEU* 3.2 29.1 + - + +
376A LEU* 3.0 10.6 + - + +
378A GLU* 1.3 75.4 - - + +
380A TYR* 1.3 75.9 + - + +
381A SER 3.0 4.9 - - - -
382A PHE* 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ARG* 4.3 1.0 + - - -
288A GLY* 4.8 4.5 + - - -
291A LEU* 3.6 28.8 - - + +
292A LEU* 3.7 30.0 + - - +
295A SER* 3.9 17.5 + - - -
376A LEU* 3.0 22.7 + - + +
377A TRP 3.3 0.2 + - - -
379A ILE* 1.3 81.9 - - + +
381A SER* 1.3 55.9 + - - +
382A PHE* 3.4 13.6 - + - -
408A PRO* 3.1 36.0 - - + +
409A ASP 3.8 13.2 + - - +
410A GLY 5.1 2.2 - - - -
411A CYS* 4.0 18.6 - - + -
412A PRO* 4.1 21.3 - - + -
415A VAL* 3.5 34.8 - - + +
419A MET* 5.0 0.9 - - + -
449A HIS* 5.3 3.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ARG* 5.8 0.2 - - - +
377A TRP* 2.5 46.3 + - - -
378A GLU 3.4 5.6 - - - -
379A ILE 3.0 0.4 - - - -
380A TYR* 1.3 77.2 - - - +
382A PHE* 1.3 73.0 + - - +
383A GLY 3.3 0.7 + - - -
384A ARG* 3.7 30.4 + - - +
408A PRO* 3.7 8.1 - - - +
409A ASP 5.6 1.1 - - - +
510B GLU* 4.6 10.2 - - - +
----------------------------------------------------------
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