Contacts of the helix formed by residues 331 - 356 (chain A) in PDB entry 3T79
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 PRO 331 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 5.5 7.4 - - + +
226A SER* 5.4 12.1 - - - -
330A LEU* 1.3 101.5 - - + +
332A PRO* 1.3 75.4 - - + +
333A ASP* 3.2 13.7 + - - +
334A ILE* 3.4 22.1 + - + +
335A GLN* 3.2 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU 3.3 5.3 - - - +
331A PRO* 1.3 83.3 - - + +
333A ASP* 1.3 72.2 - - - +
335A GLN* 3.5 16.0 + - + +
336A ALA* 4.1 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LYS* 5.7 8.1 - - + +
164A LEU 5.3 4.0 - - - +
331A PRO* 3.6 6.7 - - - +
332A PRO* 1.3 91.4 - - - +
334A ILE* 1.3 76.9 + - + +
336A ALA* 4.4 6.6 + - - +
337A VAL* 4.6 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.9 23.3 - - + +
162A LYS* 4.3 22.4 - - + -
225A LEU* 4.3 21.1 - - + +
231A ILE* 5.0 4.9 - - + -
330A LEU* 5.4 2.0 - - + -
331A PRO* 3.8 30.1 - - + +
333A ASP* 1.3 95.3 - - + +
335A GLN* 1.3 65.8 + - - +
336A ALA 3.4 0.2 - - - -
337A VAL* 3.1 12.7 - - + +
338A PHE* 2.8 53.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A PRO 3.2 20.0 + - - -
328A THR* 3.1 29.2 - - + +
330A LEU* 3.1 37.8 + - - +
331A PRO 3.2 15.5 + - - +
332A PRO* 3.8 11.2 - - + +
333A ASP 3.4 0.8 - - - -
334A ILE* 1.3 76.2 - - - +
336A ALA* 1.3 58.2 + - - +
338A PHE* 2.8 31.5 + - - +
339A ASP* 2.8 20.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A CYS* 3.6 31.5 - - + -
168A LEU* 4.4 8.5 - - + +
332A PRO 4.1 5.9 + - - +
333A ASP 4.8 5.6 - - - +
334A ILE 3.4 0.6 - - - -
335A GLN* 1.3 77.6 - - - +
337A VAL* 1.3 62.8 + - - +
339A ASP* 3.4 8.0 + - - +
340A LEU 3.0 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 4.9 9.2 - - + +
164A LEU* 4.3 30.5 - - + +
166A CYS* 3.8 16.9 - - + +
177A LEU* 4.0 13.5 - - + -
202A MET* 6.0 1.1 - - - -
206A TYR* 6.0 1.8 - - + -
333A ASP 4.6 4.7 - - - +
334A ILE* 3.1 22.0 - - + +
336A ALA* 1.3 76.2 - - - +
338A PHE* 1.3 70.7 + - + +
340A LEU* 2.7 24.0 + - - +
341A LEU* 2.9 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 5.0 11.2 - - + -
206A TYR* 4.8 9.6 - + - -
210A PHE* 4.7 18.8 - + - -
222A TYR* 4.7 13.2 - + - -
225A LEU* 3.2 28.5 - - + -
326A PHE* 3.9 35.3 - + + +
327A PRO 5.8 0.2 - - - -
330A LEU* 4.2 13.0 - - + -
334A ILE* 2.8 54.1 - - + -
335A GLN* 2.8 22.2 + - - +
337A VAL* 1.3 84.0 - - + +
339A ASP* 1.3 56.5 + - - +
341A LEU* 3.9 11.9 - - + +
342A ASN* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 4.4 14.2 - - - +
318A CYS* 5.2 5.2 - - - -
321A VAL* 5.8 1.4 - - - +
324A HIS* 5.1 8.5 + - - -
335A GLN* 2.8 19.7 + - + +
336A ALA* 3.6 11.4 - - - +
338A PHE* 1.3 73.2 - - - +
340A LEU* 1.3 61.7 + - - +
342A ASN* 3.3 15.1 + - - +
343A SER* 2.9 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A CYS* 4.4 9.0 - - - -
168A LEU* 4.3 4.5 - - + +
175A CYS* 4.1 26.0 - - + -
176A GLY* 3.4 35.4 - - - +
177A LEU* 3.7 24.5 - - + -
189A PRO* 5.3 1.1 - - + -
191A PHE* 6.0 0.9 - - + -
199A ILE* 5.3 5.6 - - + -
318A CYS* 4.2 18.2 - - - -
336A ALA 3.0 13.6 + - - +
337A VAL* 2.7 10.1 + - - +
339A ASP* 1.3 76.2 + - - +
341A LEU* 1.3 55.8 + - + +
343A SER* 2.7 26.1 + - - -
344A VAL* 2.9 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 4.3 9.6 - - + -
199A ILE* 5.5 2.5 - - + -
202A MET* 4.0 32.1 - - + +
203A ALA* 3.6 13.7 - - + +
206A TYR* 3.4 41.5 - - + -
326A PHE* 4.0 14.4 - - + -
337A VAL* 2.9 42.6 + - + +
338A PHE* 3.9 13.0 - - + +
340A LEU* 1.3 70.2 - - + +
342A ASN* 1.3 66.1 + - - +
344A VAL* 4.6 5.4 - - - +
345A LEU* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A VAL* 3.7 16.0 - - - +
323A VAL 3.1 22.6 + - - +
324A HIS* 3.8 18.3 + - - +
325A LEU* 3.1 28.2 + - - +
326A PHE* 3.7 19.1 + - + -
338A PHE 2.9 21.0 + - - +
339A ASP* 3.3 16.0 + - - +
340A LEU 3.2 0.2 - - - -
341A LEU* 1.3 75.6 - - - +
343A SER* 1.3 56.4 + - - +
345A LEU* 3.5 1.1 - - - +
346A VAL* 2.8 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A CYS* 3.6 17.9 - - - -
319A PRO* 3.0 41.2 + - - +
321A VAL* 4.1 16.6 + - - +
339A ASP* 2.9 13.0 + - - -
340A LEU* 2.7 16.4 + - - -
342A ASN* 1.3 71.0 - - - +
344A VAL* 1.3 57.2 + - - -
346A VAL* 3.8 1.0 - - - +
347A THR* 2.4 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PRO* 4.4 17.0 - - + -
190A ASN 5.9 1.1 - - - +
191A PHE* 4.5 17.3 - - + -
197A CYS* 4.9 1.8 - - - -
199A ILE* 4.4 14.1 - - + -
200A PHE* 3.7 37.7 - - + +
203A ALA* 5.1 1.1 - - + -
340A LEU* 2.9 33.5 + - + +
341A LEU* 4.1 5.6 - - - +
343A SER* 1.3 74.8 - - - +
345A LEU* 1.3 64.9 + - - +
347A THR* 2.9 7.5 + - - -
348A SER* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A PHE* 4.0 10.4 - - + -
203A ALA* 3.6 7.0 - - + +
204A VAL* 3.5 47.6 - - + +
207A TYR* 4.7 7.6 - - + -
325A LEU* 3.7 34.1 - - + -
326A PHE* 3.9 22.0 - - + -
341A LEU 2.9 19.9 + - - +
342A ASN* 3.5 3.4 - - - +
344A VAL* 1.3 77.5 - - - +
346A VAL* 1.3 58.4 + - + +
348A SER 3.3 0.3 + - - -
349A LEU* 2.8 46.0 + - + +
361A ILE* 4.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A VAL* 3.0 34.5 - - + -
323A VAL* 3.4 24.7 - - + +
325A LEU* 3.8 22.7 - - + -
342A ASN* 2.8 31.4 + - - +
343A SER 4.1 2.0 - - - +
345A LEU* 1.3 74.8 - - + +
347A THR* 1.3 63.4 + - - +
349A LEU* 4.4 5.6 - - - -
350A PRO* 3.4 15.2 - - - +
375A PHE* 3.8 22.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PHE* 4.3 21.1 - - + -
319A PRO* 3.5 22.4 - - + +
321A VAL* 5.4 3.5 - - - +
343A SER 2.4 30.4 + - - -
344A VAL* 3.3 7.4 - - - -
346A VAL* 1.3 81.5 - - - +
348A SER* 1.3 64.4 + - - +
350A PRO* 3.6 8.5 - - - +
381A PRO* 3.8 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ASN 5.4 0.3 + - - -
191A PHE* 5.0 8.0 + - - -
194A PRO* 3.4 35.4 - - - +
200A PHE* 3.6 28.7 - - - -
344A VAL* 2.9 12.7 + - - +
345A LEU 3.7 0.4 - - - -
347A THR* 1.3 80.3 - - - +
349A LEU* 1.3 64.2 + - - +
350A PRO* 3.3 3.4 - - - -
351A LEU* 3.1 15.2 + - - +
352A LEU 3.3 9.0 + - - -
381A PRO* 4.8 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A PHE* 4.4 7.9 - - + -
325A LEU* 3.7 29.8 - - + -
345A LEU* 2.8 25.8 + - + +
346A VAL* 4.3 3.8 - - - +
348A SER* 1.3 75.4 - - - +
350A PRO* 1.3 72.8 - - + +
352A LEU* 3.2 31.5 + - + +
353A TYR* 3.1 21.8 + - - +
361A ILE* 4.1 22.0 - - + -
362A PHE* 4.1 12.7 - - + -
367A LEU* 4.2 16.2 - - + -
375A PHE* 4.7 3.4 - - + -
376A LEU* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A VAL 3.4 16.6 - - - +
347A THR 3.6 8.7 - - - +
348A SER 3.4 3.6 - - - -
349A LEU* 1.3 93.0 - - + +
351A LEU* 1.3 64.5 + - - +
353A TYR* 3.2 13.2 + - + +
354A ARG* 3.2 16.8 + - - +
375A PHE* 4.2 24.2 - - + +
376A LEU* 4.1 21.8 - - + +
379A THR 4.4 10.5 - - - +
380A LEU* 4.2 5.8 - - + -
381A PRO* 3.8 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PRO* 4.0 23.3 - - + -
195A PHE* 3.9 28.7 - - + -
348A SER 3.1 12.0 + - - +
350A PRO* 1.3 79.1 - - - +
352A LEU* 1.3 66.2 + - - +
354A ARG* 2.8 17.8 + - + +
355A VAL* 3.1 18.1 + - + +
380A LEU* 4.3 17.9 - - + -
381A PRO* 3.7 15.9 - - + +
382A LEU* 3.9 24.5 - - + +
383A ASP 5.5 0.2 - - - +
384A ILE* 5.1 12.6 - - + -
387A GLN* 4.3 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TRP* 4.3 15.5 - - + -
195A PHE* 3.8 28.2 - - + -
200A PHE* 4.1 22.9 - - + -
204A VAL* 4.5 9.2 - - + -
348A SER 3.3 2.4 + - - -
349A LEU* 3.2 30.8 + - + +
351A LEU* 1.3 79.2 - - - +
353A TYR* 1.3 54.4 + - - +
356A PHE* 2.8 54.0 + - + -
359A HIS* 4.4 13.2 - - + +
361A ILE* 4.3 9.4 - - + -
362A PHE* 4.0 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU 3.1 7.7 + - - +
350A PRO* 3.4 11.2 - - + +
351A LEU 3.0 0.4 - - - -
352A LEU* 1.3 77.8 - - - +
354A ARG* 1.3 82.0 + - - +
357A PRO* 3.2 37.7 - - + +
362A PHE* 3.2 50.5 - + + -
373A ILE* 3.8 22.5 - - + +
376A LEU* 3.8 37.5 - - + -
377A THR* 4.7 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A PRO 3.4 13.2 - - - +
351A LEU* 2.8 10.3 + - + +
353A TYR* 1.3 92.6 - - + +
355A VAL* 1.3 63.1 + - + +
357A PRO* 4.4 3.3 - - - +
376A LEU 4.2 7.4 + - - +
377A THR* 3.4 45.7 + - - +
378A GLY 5.3 1.8 + - - -
380A LEU* 3.5 30.7 - - + +
384A ILE* 6.1 3.4 - - + -
400A THR* 4.8 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A PHE* 4.1 20.6 - - + -
351A LEU* 3.1 19.3 + - + +
352A LEU 4.0 0.9 - - - +
354A ARG* 1.3 77.8 - - + +
356A PHE* 1.3 99.2 + - + +
357A PRO* 3.0 13.3 - - - +
384A ILE* 4.4 22.0 - - + -
387A GLN* 5.8 1.8 - - + -
391A LEU* 5.8 9.9 - - + -
398A THR* 4.6 4.5 + - + +
400A THR* 3.5 16.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 4.2 17.5 - - + -
118A TRP* 3.9 21.8 - - + +
119A ASN* 3.2 38.1 - - + -
120A PRO* 3.1 30.1 - - + -
195A PHE* 4.3 9.0 - + - -
352A LEU* 2.8 36.5 + - + +
355A VAL* 1.3 104.2 - - + +
357A PRO* 1.3 55.5 - - - +
358A THR* 2.9 14.2 + - - +
359A HIS* 3.0 20.1 + - + +
362A PHE* 3.2 6.6 - - - -
394A LEU* 4.6 4.3 - - + -
398A THR* 4.1 15.0 - - + -
----------------------------------------------------------
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