Contacts of the helix formed by residues 347 - 365 (chain C) in PDB entry 3CQ6
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 VAL 347 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PRO* 3.7 20.4 - - + +
39C TYR* 3.6 36.8 - - + -
346C GLY* 1.3 73.6 - - - -
348C PRO* 1.3 76.5 - - + +
349C GLU* 4.3 7.9 - - + +
350C GLU* 2.9 45.1 + - + +
351C ASN* 3.0 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TYR* 4.3 12.3 - - + +
287C GLU* 3.4 35.0 - - + +
290C ARG* 4.1 2.9 - - - +
347C VAL* 1.3 85.7 - - + -
349C GLU* 1.3 57.5 + - - +
351C ASN* 3.1 4.3 + - - +
352C ASP* 2.8 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ILE* 5.0 3.3 - - + +
347C VAL* 3.2 7.9 - - + +
348C PRO* 1.3 79.2 - - - +
350C GLU* 1.3 62.3 + - + +
352C ASP* 3.6 11.0 + - + +
353C ALA* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 4.3 14.9 + - - -
29C ASP 4.5 8.1 - - - +
30C ILE* 3.9 35.6 - - + +
31C ARG 4.7 5.0 + - - +
32C LEU* 3.8 19.4 - - + +
38C PRO* 3.7 12.2 - - - +
346C GLY* 3.4 9.4 - - - -
347C VAL* 2.9 38.4 + - + +
349C GLU* 1.3 73.7 - - + +
351C ASN* 1.3 61.1 + - - +
353C ALA* 3.3 3.3 + - - +
354C PHE* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 4.6 3.6 - - - +
287C GLU* 2.6 31.4 + - - +
290C ARG* 3.8 3.6 - - - +
291C VAL* 3.7 23.1 - - + +
343C THR* 5.7 0.2 + - - -
344C THR 4.2 3.5 - - - +
345C ILE* 3.4 15.9 - - - +
346C GLY* 2.9 44.7 + - - -
347C VAL 3.0 4.6 + - - -
348C PRO 3.5 1.8 - - - +
350C GLU* 1.3 77.4 - - - +
352C ASP* 1.3 57.3 + - - +
354C PHE* 3.3 9.0 + - - +
355C LEU* 2.8 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C ARG* 3.0 32.8 + - - -
348C PRO* 2.8 25.5 + - - +
349C GLU* 3.6 11.2 - - + +
351C ASN* 1.3 72.1 - - - +
353C ALA* 1.3 56.9 + - - +
355C LEU* 3.4 5.4 + - - +
356C ASP* 2.9 40.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
30C ILE* 4.2 24.9 - - + -
330C VAL* 3.8 8.8 - - + +
349C GLU 3.2 11.2 + - - +
350C GLU 3.3 7.4 + - - +
352C ASP* 1.3 78.4 - - - +
354C PHE* 1.3 57.7 + - - +
356C ASP* 3.4 8.6 + - - +
357C ALA* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.8 14.6 - - + -
291C VAL* 3.7 23.3 - - + -
295C LEU* 3.7 21.1 - - + -
312C PHE* 3.8 18.2 - + - -
325C PHE* 3.6 26.7 - + - -
330C VAL* 4.0 20.3 - - + +
332C ILE* 4.2 3.8 - - + -
343C THR* 3.7 34.5 - - + -
350C GLU 2.9 14.4 + - - +
351C ASN* 3.6 11.0 - - - +
353C ALA* 1.3 76.4 - - - +
355C LEU* 1.3 82.1 + - + +
357C ALA* 3.4 2.3 + - - +
358C ALA* 2.8 26.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
290C ARG* 3.8 24.9 - - - +
291C VAL* 4.1 25.1 - - + +
294C ARG* 3.4 37.8 + - + +
295C LEU* 3.9 15.5 - - + -
298C LEU* 4.1 4.7 - - + +
351C ASN 2.8 25.5 + - - +
352C ASP* 3.8 5.6 - - - +
354C PHE* 1.3 98.3 - - + +
356C ASP* 1.3 62.2 + - - +
358C ALA* 3.8 3.4 - - + +
359C ALA* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C ASP* 2.9 29.9 + - - +
353C ALA* 3.7 7.9 - - - +
354C PHE 3.3 0.2 - - - -
355C LEU* 1.3 74.6 - - - +
357C ALA* 1.3 66.4 + - - +
359C ALA* 3.4 8.1 + - - +
360C GLU* 3.3 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 357 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C PHE* 3.8 20.9 - - + -
328C ARG* 4.0 28.0 - - + +
330C VAL* 4.1 12.6 - - + -
353C ALA 3.0 17.6 + - - +
354C PHE 3.6 4.7 - - - +
356C ASP* 1.3 77.8 - - - +
358C ALA* 1.3 56.8 + - - +
360C GLU* 3.2 6.2 + - - +
361C ILE* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 358 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LEU* 3.9 18.6 - - + -
298C LEU* 4.2 2.0 - - + -
300C TYR* 2.6 48.0 + - + +
325C PHE* 3.7 18.1 - - + -
354C PHE* 2.8 18.6 + - + +
355C LEU* 3.8 4.7 - - - +
356C ASP 3.3 0.2 - - - -
357C ALA* 1.3 74.0 - - - +
359C ALA* 1.3 65.1 + - - +
361C ILE* 4.3 0.2 - - - -
362C ILE* 3.1 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 359 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ARG* 5.5 4.9 - - - +
298C LEU* 3.9 24.1 - - + +
355C LEU 2.9 17.6 + - - +
356C ASP* 3.5 9.0 - - - +
358C ALA* 1.3 76.5 - - - +
360C GLU* 1.3 62.1 + - + +
362C ILE* 3.2 18.6 - - - +
363C LYS* 3.6 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C ARG* 2.9 37.9 + - - +
356C ASP* 3.5 15.3 - - - +
357C ALA* 3.2 7.2 + - - +
359C ALA* 1.3 77.9 - - + +
361C ILE* 1.3 63.5 + - - +
363C LYS* 3.5 34.4 + - - +
364C LEU* 3.7 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 361 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C TYR* 3.9 11.2 - - - +
315C PHE* 4.5 14.3 - - + -
321C ALA* 4.8 2.0 - - + -
324C ALA* 3.6 16.2 - - + +
325C PHE* 3.4 64.6 - - + +
328C ARG* 4.1 15.3 - - - +
357C ALA 2.9 17.6 + - - +
358C ALA* 4.3 0.9 - - - -
359C ALA 3.4 0.4 - - - -
360C GLU* 1.3 73.2 - - - +
362C ILE* 1.3 64.8 + - - +
363C LYS 3.1 2.5 - - - -
364C LEU* 3.0 24.1 + - + +
365C ASN 3.6 2.9 + - - -
366C LEU* 4.4 20.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 362 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C LEU* 3.1 42.4 - - + +
299C GLY* 3.7 13.7 - - - +
300C TYR* 3.2 40.0 + - + +
315C PHE* 6.0 1.1 - - - -
358C ALA 3.1 10.0 + - - +
359C ALA* 3.2 20.4 - - - +
361C ILE* 1.3 76.0 - - - +
363C LYS* 1.3 70.2 + - + +
365C ASN* 3.3 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 363 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C ALA 3.6 21.3 - - - +
360C GLU* 3.5 23.6 + - - +
361C ILE 3.1 0.4 - - - -
362C ILE* 1.3 80.5 - - + +
364C LEU* 1.3 67.0 + - + +
365C ASN* 3.3 5.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
324C ALA* 4.8 2.2 - - + -
328C ARG* 3.8 29.4 - - - +
360C GLU 3.7 13.5 - - - +
361C ILE* 3.0 17.5 + - + +
363C LYS* 1.3 78.5 - - + +
365C ASN* 1.3 69.5 + - - +
366C LEU* 3.9 34.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C SER* 5.3 1.7 + - - -
361C ILE 3.6 2.2 + - - -
362C ILE* 3.3 13.3 + - - +
363C LYS 3.2 7.7 - - - +
364C LEU* 1.3 82.4 - - - +
366C LEU* 1.3 67.0 + - - +
----------------------------------------------------------
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