Contacts of the helix formed by residues 334 - 356 (chain C) in PDB entry 3ITX
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 ASP 334 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C THR* 1.3 74.4 + - - +
335C PRO* 1.3 67.4 - - - +
336C ILE* 2.9 21.3 + - - +
337C GLU* 2.9 41.5 + - + +
338C SER* 3.0 11.3 + - - -
406C TYR* 2.9 24.6 + - - -
412C ARG* 2.9 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLY 3.6 9.0 - - - +
59C VAL 3.1 36.3 - - - +
60C GLY 3.7 2.5 - - - +
61C THR* 3.7 33.0 - - - +
74C GLU* 5.2 2.2 - - - +
330C HIS* 4.0 17.9 + - + +
333C THR 3.2 9.4 - - - +
334C ASP* 1.3 86.4 - - - +
336C ILE* 1.3 60.8 + - - +
338C SER* 3.3 1.7 + - - -
339C LEU* 3.0 30.8 + - - +
412C ARG* 4.2 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C VAL* 4.9 7.0 - - + -
84C ASP* 3.7 30.5 - - + +
87C VAL* 3.9 16.8 - - + -
88C ILE* 4.0 15.9 - - + +
334C ASP* 2.9 8.2 + - - +
335C PRO* 1.3 78.2 - - + +
337C GLU* 1.3 63.3 + - - +
339C LEU* 3.5 2.1 + - - +
340C ILE* 3.0 37.7 + - + +
406C TYR* 3.7 22.9 - - + +
411C TYR* 3.7 30.5 - - + -
412C ARG* 3.6 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU* 3.7 27.4 - - + +
334C ASP* 2.9 25.4 + - + +
336C ILE* 1.3 77.1 - - - +
338C SER* 1.3 63.0 + - - +
340C ILE* 3.3 10.3 + - - +
341C ASN* 3.0 20.1 + - - +
403C VAL* 3.9 12.9 - - + +
406C TYR* 3.4 29.7 - - + -
407C ARG* 2.7 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU* 3.7 6.8 - - - +
293C ASP* 2.8 26.5 + - - +
330C HIS* 3.3 26.2 - - - -
333C THR* 2.6 31.1 + - - +
334C ASP 3.0 6.4 + - - -
335C PRO 3.8 3.6 - - - -
337C GLU* 1.3 78.3 - - - +
339C LEU* 1.3 57.7 + - - +
341C ASN* 3.3 1.2 + - - -
342C SER* 2.8 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 4.8 7.4 - - + -
55C PRO* 4.4 14.8 - - + +
58C GLY* 3.7 27.8 - - - +
59C VAL* 3.9 9.4 - - + -
88C ILE* 3.4 36.1 - - + +
326C ILE* 3.9 34.4 - - + +
328C GLN* 4.3 0.4 - - - +
330C HIS* 3.5 22.4 - - + +
335C PRO 3.0 18.1 + - - +
336C ILE 3.9 0.4 - - - +
338C SER* 1.3 76.4 - - - +
340C ILE* 1.3 57.9 + - - +
342C SER* 3.7 3.4 - - - -
343C ALA* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ILE* 4.1 16.8 - - + -
91C LEU* 4.1 25.1 - - + -
92C THR* 3.6 19.5 - - + +
336C ILE* 3.0 40.9 + - + +
337C GLU* 3.4 11.9 - - - +
339C LEU* 1.3 78.3 - - - +
341C ASN* 1.3 67.9 + - - +
343C ALA* 3.4 2.1 + - - +
344C ASN* 3.1 32.9 + - - +
402C PRO* 3.2 31.9 - - + +
403C VAL* 4.1 5.4 - - + +
406C TYR* 4.5 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU* 3.8 31.4 + - + +
372B MET* 5.9 0.6 - - - -
374B THR* 6.3 0.6 - - - +
375B GLU* 4.4 22.7 + - - +
293C ASP* 5.4 3.1 - - + +
294C ALA 5.0 0.2 - - - +
337C GLU 3.0 11.7 + - - +
338C SER 4.1 2.5 - - - +
340C ILE* 1.3 75.3 - - - +
342C SER* 1.3 59.9 + - - +
344C ASN* 3.5 17.2 - - - +
345C GLU* 2.9 29.5 + - - +
402C PRO* 5.3 0.9 - - - +
403C VAL* 3.2 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C ASP* 3.5 16.1 + - - +
294C ALA* 4.0 11.1 - - - +
326C ILE* 4.4 6.5 - - - -
328C GLN* 2.9 38.8 + - - -
338C SER 2.8 23.1 + - - -
339C LEU* 3.7 4.9 - - - -
341C ASN* 1.3 75.4 - - - +
343C ALA* 1.3 59.1 + - - +
345C GLU* 3.1 5.7 + - - +
346C ILE* 2.9 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C VAL* 4.5 3.3 - - + +
88C ILE* 5.2 0.2 - - + -
92C THR* 4.6 6.3 - - - +
94C ALA* 4.4 13.3 - - + +
95C THR* 3.9 26.7 - - + -
326C ILE* 4.1 10.7 - - + +
339C LEU 3.0 18.7 + - - +
340C ILE* 3.7 4.9 - - - +
342C SER* 1.3 76.5 - - - +
344C ASN* 1.3 64.4 - - - +
346C ILE* 3.3 7.8 + - - +
347C ARG* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C THR* 3.9 20.2 + - - +
94C ALA* 5.7 1.2 - - - +
340C ILE* 3.1 17.3 + - - +
341C ASN* 3.5 23.5 - - + +
343C ALA* 1.3 78.2 - - - +
345C GLU* 1.3 57.0 + - - +
347C ARG* 3.2 8.3 + - - +
348C ARG* 2.8 41.6 + - - +
386C GLU* 5.8 0.4 - - - +
389C LEU* 3.5 9.5 - - + +
393C ARG* 3.3 28.7 + - - +
402C PRO* 3.9 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LYS* 3.6 24.3 + - - +
382B ARG* 5.1 4.0 + - - -
294C ALA 3.3 27.6 - - - +
295C GLY* 3.7 9.6 - - - -
299C PRO* 3.9 15.6 - - - +
302C LEU* 3.7 7.4 - - + +
341C ASN 2.9 18.3 + - - +
342C SER 3.1 4.2 + - - +
344C ASN* 1.3 75.8 - - - +
346C ILE* 1.3 62.9 + - - +
348C ARG* 3.0 39.6 + - - +
349C ALA* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C PHE* 3.6 17.5 - - + -
52C VAL* 4.2 10.3 - - + -
282C PHE* 3.5 42.0 - - + -
294C ALA* 4.0 14.4 - - + -
302C LEU* 4.4 7.6 - - + -
306C PHE* 3.5 28.4 - - + -
326C ILE* 3.6 26.9 - - + -
342C SER 2.9 19.7 + - - +
343C ALA* 3.6 6.7 - - - +
345C GLU* 1.3 77.5 - - - +
347C ARG* 1.3 61.7 + - - +
349C ALA 3.4 1.0 + - - -
350C TYR* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL* 3.0 36.7 + - + +
48C GLU* 3.4 21.4 + - - +
50C PHE* 3.0 42.6 + - + -
51C PHE* 3.8 1.8 - - - -
52C VAL* 6.6 0.2 - - + -
92C THR 3.7 15.0 + - - -
93C ARG* 3.1 24.9 + - - +
94C ALA* 3.3 19.7 - - + +
343C ALA 3.0 14.9 + - - +
344C ASN* 3.7 10.5 - - - +
346C ILE* 1.3 75.1 - - + +
348C ARG* 1.3 60.5 + - - +
350C TYR* 3.6 7.6 - - - +
351C ALA* 2.8 31.5 + - - +
389C LEU* 3.8 15.9 + - + +
392C ALA* 4.4 10.7 - - - +
393C ARG* 4.9 8.6 - - - +
396C THR* 5.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ARG* 3.6 44.2 - - - +
344C ASN* 2.8 24.5 + - - +
345C GLU* 3.0 39.9 + - - +
347C ARG* 1.3 77.2 - - - +
349C ALA* 1.3 63.0 + - - +
351C ALA* 3.3 2.9 + - - +
352C GLN* 3.0 40.5 + - - +
384C ASP* 4.4 1.2 + - - -
385C VAL* 3.6 15.7 - - + +
386C GLU* 2.9 42.0 + - - +
389C LEU* 3.6 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C PRO 5.3 1.1 - - - +
302C LEU* 3.7 22.9 - - + -
303C PHE* 3.9 17.1 - - + +
306C PHE* 3.5 25.4 - - + +
345C GLU 3.0 11.4 + - - +
346C ILE 3.8 0.9 - - - +
348C ARG* 1.3 75.5 - - - +
350C TYR* 1.3 58.5 + - - +
352C GLN* 3.3 14.0 + - - +
353C ALA* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LYS* 3.6 42.1 + - - +
47C VAL* 4.2 6.7 - - + -
50C PHE* 3.7 46.9 - + + -
306C PHE* 3.7 29.9 - + + -
310C VAL* 4.2 11.2 - - + -
313C GLU* 5.6 0.3 + - - -
346C ILE 3.1 17.3 + - - +
347C ARG* 3.6 8.1 - - - +
349C ALA* 1.3 78.4 - - - +
351C ALA* 1.3 64.7 + - - +
353C ALA* 3.1 5.2 + - - +
354C LEU* 3.0 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C VAL* 4.5 6.3 - - + +
47C VAL* 3.9 20.2 - - + -
347C ARG 2.8 18.6 + - - +
348C ARG 3.7 4.0 - - - +
350C TYR* 1.3 77.0 - - - +
352C GLN* 1.3 63.7 + - - +
354C LEU* 3.0 24.6 + - - +
355C LEU* 3.3 17.9 + - - +
385C VAL* 4.0 22.7 - - + -
388C ILE* 5.1 1.6 - - + -
389C LEU* 4.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C PRO 5.8 0.2 + - - -
303C PHE* 3.5 17.0 - - + +
348C ARG* 3.0 41.1 + - - +
349C ALA* 3.7 11.2 - - - +
351C ALA* 1.3 76.2 - - - +
353C ALA* 1.3 62.7 + - - +
355C LEU* 3.1 16.4 + - - +
380C ALA* 3.3 36.8 - - - +
381C TYR* 3.2 38.5 - - - +
383C THR 3.1 21.8 - - - +
384C ASP* 4.9 0.7 - - - -
385C VAL* 4.0 9.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C PHE* 3.6 11.6 - - + -
306C PHE* 3.7 22.9 - - + +
307C ASN* 4.1 4.9 - - - +
310C VAL* 3.5 25.1 - - + +
349C ALA 2.9 14.5 + - - +
350C TYR 3.1 9.6 + - - +
352C GLN* 1.3 77.6 - - - +
354C LEU* 1.3 60.6 + - - +
355C LEU 3.3 0.5 + - - -
356C VAL* 3.4 10.1 + - - +
358C ARG* 3.1 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C VAL* 5.8 2.1 - - - +
43C VAL* 4.3 21.7 - - + +
46C LYS* 3.9 33.4 - - + -
47C VAL* 4.6 0.9 - - + -
310C VAL* 4.3 17.3 - - + -
313C GLU* 4.9 5.2 - - - +
350C TYR* 3.0 63.1 + - + +
351C ALA* 3.0 13.2 + - - +
353C ALA* 1.3 77.3 - - - +
355C LEU* 1.3 62.2 + - - +
356C VAL 3.3 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 355 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.9 26.7 - - + -
36C ARG* 4.3 9.2 + - - +
38C VAL* 4.2 18.8 - - + +
43C VAL* 4.0 30.1 - - + -
351C ALA 3.4 13.7 - - - +
352C GLN* 3.1 9.3 + - - +
354C LEU* 1.3 77.8 - - - +
356C VAL* 1.3 64.7 + - - +
357C ASP* 3.2 4.0 + - - +
380C ALA* 3.8 16.0 - - + +
383C THR* 3.7 37.5 - - + +
385C VAL* 3.7 18.6 - - + -
388C ILE* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C PHE* 3.9 11.7 - - + -
307C ASN* 4.0 0.7 - - - +
352C GLN 4.0 0.9 - - - +
353C ALA 3.6 15.7 - - - +
354C LEU 3.3 7.0 - - - +
355C LEU* 1.3 77.3 - - - +
357C ASP* 1.3 70.1 + - - +
358C ARG* 3.0 46.4 + - - +
361C LEU* 4.1 8.7 - - + -
376C THR* 4.6 6.5 - - + +
377C LEU* 3.9 30.7 - - + -
380C ALA* 3.7 20.8 - - + +
----------------------------------------------------------
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