Contacts of the helix formed by residues 326 - 347 (chain C) in PDB entry 2OME
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 326 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C GLU* 2.8 26.2 + - - -
324C TRP 3.5 2.8 + - - -
325C TYR* 1.3 83.4 - - - +
327C GLU* 1.3 66.1 + - - +
328C GLN* 3.4 12.0 + - - -
329C ALA* 2.7 24.0 + - - +
330C SER* 3.0 20.3 + - - -
147D ARG* 4.2 0.2 - - - -
175D ALA 3.3 16.4 - - - -
176D ALA 4.1 2.0 - - - -
177D ARG 3.9 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 327 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C TYR* 4.0 17.5 + - - +
326C SER* 1.3 73.4 - - - +
328C GLN* 1.3 73.9 + - + +
330C SER* 3.4 3.3 + - - -
331C LEU* 3.2 23.6 + - + +
174D GLY* 6.4 0.7 - - - +
175D ALA 3.4 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C SER* 3.6 5.9 + - - -
327C GLU* 1.3 90.6 + - + +
329C ALA* 1.3 58.6 + - - +
331C LEU* 3.6 6.6 + - - +
332C GLU* 3.1 27.2 + - - +
176D ALA* 4.0 8.2 - - - +
177D ARG* 3.1 67.3 + - + +
181D GLU* 5.7 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 329 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ALA* 3.7 10.8 - - - +
130C ALA* 4.1 4.9 - - + -
133C GLU* 3.6 16.2 - - - +
324C TRP* 3.8 17.5 - - + +
326C SER* 2.7 25.0 + - - +
328C GLN* 1.3 72.3 - - - +
330C SER* 1.3 64.3 + - - +
332C GLU* 3.3 2.5 + - - +
333C MET* 3.1 30.0 + - + +
177D ARG* 3.5 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 330 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C TRP* 4.0 12.1 - - - -
325C TYR* 3.8 17.9 - - - -
326C SER 3.0 17.3 + - - +
327C GLU* 3.9 3.6 - - - -
329C ALA* 1.3 77.3 - - - +
331C LEU* 1.3 62.9 + - - +
333C MET* 3.6 8.2 - - - +
334C ARG* 3.2 30.2 + - - +
169D ARG* 3.1 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C VAL* 3.8 26.2 - - + -
327C GLU* 3.2 17.0 + - + +
328C GLN* 3.9 5.8 - - - +
330C SER* 1.3 80.3 - - - +
332C GLU* 1.3 64.0 + - - +
333C MET 3.2 0.3 + - - -
334C ARG* 3.2 3.9 + - - +
335C GLU* 2.9 55.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ARG* 2.9 33.2 + - - -
128C SER* 4.2 1.2 + - - +
129C ALA* 3.5 16.1 - - + +
328C GLN 3.1 14.8 + - - +
329C ALA 3.3 4.7 + - - +
331C LEU* 1.3 80.0 - - - +
333C MET* 1.3 57.1 + - - +
335C GLU* 3.5 10.4 + - - +
336C ALA* 3.0 30.8 + - + +
177D ARG* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 333 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C TYR* 5.5 1.6 - - - -
104C ILE* 3.7 36.6 - - + +
105C GLY* 4.2 8.1 - - - -
126C ILE* 3.9 19.5 - - + +
129C ALA* 3.6 18.4 - - + -
130C ALA* 3.8 24.5 - - + +
324C TRP* 3.6 38.1 - - + -
329C ALA 3.1 20.8 + - - +
330C SER* 3.6 8.5 - - - +
332C GLU* 1.3 75.0 - - - +
334C ARG* 1.3 64.2 + - + +
336C ALA* 3.6 1.3 - - - +
337C ALA* 2.9 29.8 + - - +
169D ARG* 6.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ASP* 3.4 51.9 + - - -
45C THR* 3.5 7.1 + - - +
46C VAL* 3.5 35.9 - - + +
47C GLU* 3.0 41.7 + - - +
82C TYR* 3.6 14.8 + - - +
104C ILE* 4.2 10.3 - - + -
330C SER* 3.2 21.4 + - - +
331C LEU 3.2 1.9 + - - +
333C MET* 1.3 78.4 - - + +
335C GLU* 1.3 58.0 + - - +
337C ALA* 3.2 4.3 + - - +
338C ALA* 2.9 30.0 + - - +
169D ARG* 3.5 30.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C VAL* 3.7 17.8 - - + +
50C ILE* 4.0 23.2 - - + +
331C LEU* 2.9 44.4 + - + +
332C GLU* 3.7 7.7 - - - +
334C ARG* 1.3 76.7 - - - +
336C ALA* 1.3 52.4 + - - +
338C ALA* 3.6 2.4 + - - +
339C THR* 2.7 36.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ILE* 3.7 26.9 - - + +
129C ALA* 6.0 0.2 - - + -
332C GLU* 3.0 21.1 + - + +
333C MET 3.6 4.9 - - - +
334C ARG 3.3 0.2 - - - -
335C GLU* 1.3 73.2 - - - +
337C ALA* 1.3 61.5 + - - +
339C THR* 3.4 7.2 + - - -
340C GLU* 3.1 26.3 + - - +
343C ARG* 4.8 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLU* 5.6 0.2 - - - +
80C MET* 4.6 9.4 - - - -
102C VAL* 3.7 21.4 - - + +
104C ILE* 3.7 23.8 - - + -
126C ILE* 3.6 11.2 - - + +
333C MET 2.9 17.7 + - - +
334C ARG 3.2 4.7 + - - +
336C ALA* 1.3 73.8 - - - +
338C ALA* 1.3 66.5 + - - +
340C GLU* 3.2 4.0 + - - +
341C ILE* 3.2 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLU* 4.1 15.5 - - + -
50C ILE* 3.6 30.3 - - + -
51C LEU* 3.6 28.9 - - + +
80C MET* 4.6 4.8 - - - -
334C ARG 2.9 16.2 + - - +
335C GLU* 3.8 3.4 - - - +
337C ALA* 1.3 75.7 - - - +
339C THR* 1.3 57.1 + - - +
341C ILE* 3.5 2.2 + - - +
342C ARG* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 4.4 11.0 - - + +
335C GLU 2.7 23.8 + - - -
336C ALA* 3.7 7.5 - - - -
337C ALA 3.2 0.4 - - - -
338C ALA* 1.3 73.2 - - - +
340C GLU* 1.3 65.5 + - - +
342C ARG* 3.3 14.4 + - + +
343C ARG* 3.1 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C VAL* 4.1 13.0 - - + -
124C CYS* 3.4 37.1 - - + +
125C ASN 4.5 1.6 - - - +
126C ILE* 5.2 3.1 - - + +
336C ALA 3.1 13.6 + - - +
337C ALA 3.2 8.9 + - - +
339C THR* 1.3 75.2 - - - +
341C ILE* 1.3 64.8 + - - +
343C ARG* 2.9 39.2 + - - +
344C ALA* 3.0 17.5 + - - +
353C LEU* 3.7 10.9 - - + +
354C ARG* 3.0 16.6 + - - +
355C ASN* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL* 3.9 30.3 - - + -
51C LEU* 3.7 19.1 - - + -
78C GLY* 4.3 1.1 - - - -
79C ALA 4.0 14.8 - - - +
80C MET* 3.9 16.8 - - + -
100C VAL* 4.0 19.5 - - + -
102C VAL* 3.7 22.0 - - + +
337C ALA 3.2 11.7 + - - +
338C ALA 3.6 7.4 - - - +
340C GLU* 1.3 76.1 - - - +
342C ARG* 1.3 65.7 + - - +
344C ALA* 2.9 17.2 + - - +
345C ILE* 3.1 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 2.8 42.5 + - - -
51C LEU* 3.9 13.1 - - + +
53C ASP* 2.7 39.0 + - - -
54C LEU* 3.7 26.8 - - + +
338C ALA 3.1 13.2 + - - +
339C THR* 3.3 19.5 - - + +
341C ILE* 1.3 78.3 - - - +
343C ARG* 1.3 58.8 + - + +
345C ILE* 3.4 3.9 + - - +
346C THR* 2.7 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C ALA 4.8 2.4 + - - -
339C THR* 3.1 36.3 + - + +
340C GLU* 2.9 52.5 + - - +
342C ARG* 1.3 76.8 - - + +
344C ALA* 1.3 58.2 + - - +
346C THR* 4.6 3.4 - - - +
347C GLY* 2.8 32.8 + - - +
352C SER* 3.5 34.1 - - - +
353C LEU* 4.6 1.3 - - + -
354C ARG* 3.4 37.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ARG* 5.4 0.3 + - - -
100C VAL* 3.7 29.6 - - + -
340C GLU 3.0 10.2 + - - +
341C ILE* 2.9 10.9 + - - +
343C ARG* 1.3 77.6 - - - +
345C ILE* 1.3 61.3 + - + +
347C GLY 3.3 13.4 - - - +
349C ILE* 3.6 29.6 - - + +
352C SER* 5.6 1.3 - - - -
353C LEU* 3.9 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C PRO* 4.9 20.4 - - + -
36C VAL* 4.3 5.8 - - + -
51C LEU* 4.8 3.1 - - + -
54C LEU* 4.4 28.9 - - + +
55C ALA* 3.9 26.0 - - + -
77C VAL* 5.7 9.2 - - + -
341C ILE* 3.1 32.1 + - + +
342C ARG* 3.9 5.8 - - - +
344C ALA* 1.3 81.5 - - + +
346C THR* 1.3 62.7 + - - +
347C GLY 3.6 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 3.5 19.9 - - + +
342C ARG* 2.7 21.0 + - - +
343C ARG* 4.3 3.4 - - - -
345C ILE* 1.3 78.3 - - - +
347C GLY* 1.3 58.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C ARG 2.8 14.5 + - - -
344C ALA 3.3 13.3 - - - +
345C ILE 3.8 3.5 - - - +
346C THR* 1.3 79.5 - - - +
348C ARG* 1.3 65.1 + - - -
349C ILE* 4.1 0.7 + - - +
352C SER* 3.4 13.2 - - - -
----------------------------------------------------------
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