Contacts of the helix formed by residues 342 - 366 (chain C) in PDB entry 2VF7
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 342 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ARG 6.0 0.2 + - - -
338C ARG* 2.9 26.2 + - + +
339C VAL 4.2 1.9 - - - +
340C LYS 3.1 2.4 + - - -
341C ASN* 1.3 85.3 + - - +
343C PRO* 1.4 70.0 - - + +
344C GLU* 5.1 2.5 - - - +
345C GLN* 3.2 50.5 + - + +
346C ALA* 4.0 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C VAL 4.1 11.7 - - - +
340C LYS 4.1 12.3 - - - +
341C ASN 4.3 0.7 - - - -
342C ARG* 1.4 89.5 - - + +
344C GLU* 1.4 70.0 + - + +
346C ALA* 3.8 7.8 + - + +
347C ILE* 3.7 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ARG* 4.5 27.0 + - - +
342C ARG* 3.6 3.3 - - + -
343C PRO* 1.4 81.6 - - + +
345C GLN* 1.3 68.7 + - + +
347C ILE* 3.4 13.6 - - - +
348C ALA* 3.4 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ARG 4.0 9.7 + - - +
127C ALA* 3.6 31.1 - - - +
128C GLY 4.2 9.8 + - - +
338C ARG* 5.7 8.0 + - - +
342C ARG* 3.2 52.4 + - + +
343C PRO 3.5 0.6 - - - -
344C GLU* 1.3 82.6 - - + +
346C ALA* 1.3 63.0 + - + +
347C ILE 3.3 0.2 - - - -
348C ALA* 3.4 10.7 - - + +
349C LEU* 2.9 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C GLU* 5.8 1.0 - - - +
332C GLU* 6.0 0.9 - - - +
335C HIS* 5.2 11.6 + - + +
338C ARG* 4.4 10.3 - - + +
339C VAL* 4.6 18.2 - - + +
342C ARG 4.0 14.7 + - - +
343C PRO* 3.8 5.1 + - + +
344C GLU 3.4 0.6 - - - -
345C GLN* 1.3 83.1 - - + +
347C ILE* 1.3 60.7 + - + +
349C LEU* 3.4 22.4 - - + +
350C GLN* 3.5 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C GLU* 5.2 9.2 - - - +
343C PRO 3.7 13.2 - - - +
344C GLU* 3.4 17.0 - - - +
346C ALA* 1.3 78.7 - - + +
348C ALA* 1.3 63.4 + - - +
349C LEU 3.5 0.2 - - - -
350C GLN* 3.9 9.0 - - + +
351C ARG* 3.5 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ARG* 5.2 9.9 - - + +
127C ALA* 6.0 1.8 - - + +
344C GLU* 3.4 30.7 + - - +
345C GLN* 3.1 15.2 + - + +
347C ILE* 1.3 78.5 - - - +
349C LEU* 1.3 60.9 + - - +
351C ARG* 3.3 29.7 - - - +
352C MET* 3.4 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LEU* 5.2 4.2 - - + +
127C ALA* 3.8 22.4 - - + +
304C PHE* 4.0 20.0 - - + -
327C TYR* 3.7 40.4 - - + +
332C GLU* 4.7 15.5 - - - +
335C HIS* 6.2 0.7 - - - +
338C ARG* 4.9 11.0 - - - +
345C GLN* 2.9 26.8 + - + +
346C ALA* 3.4 23.6 - - - +
348C ALA* 1.3 74.8 - - - +
350C GLN* 1.3 58.3 + - - +
352C MET* 3.7 9.3 - - - +
353C ALA* 2.7 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C TYR 3.7 13.7 - - - +
328C ALA* 2.9 27.9 + - - +
330C GLU* 3.7 34.2 + - + +
346C ALA 3.5 18.4 + - - +
347C ILE* 3.9 10.3 - - + +
349C LEU* 1.3 80.4 - - - +
351C ARG* 1.3 73.7 + - - +
353C ALA* 3.7 1.6 - - - +
354C ALA* 2.8 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C MET* 4.9 7.7 - - - +
126C ARG* 4.4 11.5 - - - +
347C ILE 3.5 9.7 + - - +
348C ALA* 3.3 17.6 + - - +
350C GLN* 1.3 88.6 + - - +
352C MET* 1.3 107.0 + - - +
354C ALA* 3.4 6.7 + - - +
355C ASP* 2.7 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU 5.4 1.1 - - - +
122C MET* 4.1 24.2 - - + +
123C LEU* 3.9 38.1 - - + +
126C ARG* 3.6 34.8 - - + -
127C ALA* 5.2 1.6 - - - -
348C ALA* 3.4 17.7 + - + +
349C LEU* 3.4 8.0 + - - +
350C GLN 3.3 0.6 - - - -
351C ARG* 1.3 118.6 - - - +
353C ALA* 1.3 64.0 + - - +
354C ALA 3.3 0.5 + - - -
355C ASP* 3.3 22.0 - - - +
356C LEU* 3.4 18.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
123C LEU* 4.5 8.2 - - + +
304C PHE* 5.9 0.2 - - + -
324C LEU* 4.0 17.3 - - + +
327C TYR* 4.2 9.2 - - + -
328C ALA* 3.6 22.4 - - + +
349C LEU* 2.7 23.3 + - + +
350C GLN 3.9 2.5 - - - +
352C MET* 1.3 73.1 - - - +
354C ALA* 1.3 61.5 + - - +
356C LEU* 3.9 9.0 - - - +
357C VAL* 3.2 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C ALA* 3.6 12.3 - - + +
329C GLU* 5.8 1.1 - - - +
350C GLN* 2.8 34.5 + - - +
351C ARG* 3.4 9.0 - - - +
352C MET 3.2 0.2 - - - -
353C ALA* 1.3 78.2 - - - +
355C ASP* 1.3 58.5 + - - +
357C VAL* 3.3 3.8 + - - +
358C LYS* 3.0 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 355 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU* 4.6 16.8 - - - +
351C ARG* 2.7 23.7 + - - +
352C MET* 3.3 10.1 - - - +
354C ALA* 1.3 75.1 - - - +
356C LEU* 1.3 67.2 + - - +
358C LYS* 3.0 12.9 + - + +
359C ARG* 2.7 56.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LEU* 4.0 38.7 - - + +
119C LEU* 3.8 35.9 - - + +
120C LEU* 4.6 10.5 - - + +
123C LEU* 3.9 23.1 - - + -
320C VAL* 6.1 0.9 - - + -
324C LEU* 3.7 23.3 - - + -
352C MET* 3.4 19.4 + - + +
353C ALA 3.9 1.6 - - - +
355C ASP* 1.3 81.9 + - - +
357C VAL* 1.3 51.2 + - - +
359C ARG* 3.2 9.1 + - - +
360C LEU* 2.8 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C SER* 4.1 17.3 + - - +
324C LEU* 3.8 26.7 - - + +
325C ARG* 4.0 38.4 - - + +
328C ALA* 4.6 6.5 - - + -
329C GLU* 5.6 4.5 - - - +
353C ALA 3.2 18.7 + - - +
354C ALA 3.7 5.2 - - - +
355C ASP 3.2 0.2 - - - -
356C LEU* 1.3 75.3 - - - +
358C LYS* 1.3 62.8 + - + +
360C LEU* 3.9 5.7 - - - +
361C ASP* 3.0 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 358 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C ALA* 3.0 20.7 + - - +
355C ASP* 3.0 13.0 + - + +
357C VAL* 1.3 78.3 - - + +
359C ARG* 1.3 59.6 + - + +
361C ASP* 3.2 21.2 - - - +
362C VAL* 3.5 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 359 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C THR* 4.8 10.7 + - - +
116C LEU* 3.7 14.6 - - + -
119C LEU* 3.8 34.0 - - - +
355C ASP* 2.7 38.7 + - - +
356C LEU 3.4 4.9 - - - +
358C LYS* 1.3 72.9 - - + +
360C LEU* 1.3 63.4 + - - +
361C ASP 3.2 0.7 + - - -
362C VAL* 3.5 7.6 + - - +
363C LEU* 3.2 21.9 + - - +
395C TYR* 3.6 69.9 + - + +
397C ASN* 6.0 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LEU* 3.7 24.2 - - + -
317C LEU* 3.4 42.4 - - + +
320C VAL* 3.9 19.1 - - + -
321C SER* 3.9 34.1 - - - +
324C LEU* 4.0 14.1 - - + -
356C LEU* 2.8 27.4 + - + +
357C VAL* 4.0 5.4 - - - +
359C ARG* 1.3 70.2 - - - +
361C ASP* 1.3 58.7 + - - +
362C VAL 3.4 0.2 - - - -
363C LEU* 3.2 6.0 + - + +
364C LEU* 2.8 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 361 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C SER* 5.4 1.5 + - - -
357C VAL 3.0 15.4 + - - +
358C LYS* 3.2 17.8 - - - +
360C LEU* 1.3 74.9 - - - +
362C VAL* 1.3 59.0 + - - +
364C LEU* 3.0 8.6 + - - +
365C HIS* 2.9 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 362 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C LYS 3.5 16.6 - - - +
359C ARG 3.7 7.0 - - - +
360C LEU 3.4 0.4 - - - -
361C ASP* 1.3 80.8 + - - +
363C LEU* 1.3 60.9 + - - +
365C HIS* 3.8 5.5 + - - +
366C LEU* 3.3 24.8 + - + +
391C ALA* 4.0 11.0 - - - +
394C LEU* 3.5 46.2 - - + +
395C TYR* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 363 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C THR* 4.0 12.6 - - + -
116C LEU* 4.7 5.2 - - + -
317C LEU* 4.0 23.3 - - + -
359C ARG 3.2 24.2 - - - +
360C LEU* 3.2 12.0 + - - +
362C VAL* 1.3 75.6 - - - +
364C LEU* 1.3 65.5 + - + +
366C LEU* 3.3 7.4 + - - +
368C LEU* 3.2 33.0 + - + +
388C LEU* 3.5 31.9 - - + -
391C ALA* 3.6 22.0 - - + -
392C THR 5.3 0.2 - - - +
395C TYR* 3.4 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 364 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C LEU* 3.6 35.9 - - + +
318C ALA* 3.8 26.5 - - + -
321C SER* 4.5 8.7 - - - +
360C LEU* 2.8 33.7 + - + +
361C ASP* 3.4 7.2 - - - +
363C LEU* 1.3 73.5 - - + +
365C HIS* 1.3 56.1 + - - +
366C LEU 3.1 4.3 - - - -
367C GLY* 3.1 20.8 + - - -
368C LEU 4.1 0.5 + - - -
369C GLY* 3.9 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C ASP* 2.9 24.2 + - - +
362C VAL* 4.1 6.5 - - - +
364C LEU* 1.3 75.0 - - - +
366C LEU* 1.3 58.8 + - - +
367C GLY 3.3 0.6 + - - -
419C ALA* 3.5 29.4 - - + +
422C SER* 5.4 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C VAL* 3.3 20.8 + - + +
363C LEU* 3.3 7.4 + - - +
364C LEU 3.1 1.2 - - - -
365C HIS* 1.3 78.4 - - - +
367C GLY* 1.3 58.8 + - - +
368C LEU* 4.0 13.3 - - + +
387C ARG* 4.3 34.0 - - + +
390C LEU* 4.9 3.8 - - + -
391C ALA* 4.0 19.1 - - + +
394C LEU* 4.1 10.3 - - + -
412C LEU* 5.5 3.1 - - - +
416C ASP* 5.3 5.1 - - - +
419C ALA* 4.2 17.8 - - - +
420C LEU* 4.3 15.3 - - + -
423C ALA* 3.6 33.2 - - + -
----------------------------------------------------------
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