Contacts of the helix formed by residues 312 - 327 (chain C) in PDB entry 3OMA
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 GLY 312 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C ILE 3.6 1.6 + - - -
311C PHE* 1.3 80.3 - - - +
313C TYR* 1.3 65.7 + - - +
314C LEU 3.1 4.9 + - - -
315C PRO* 3.2 18.9 - - - +
316C MET* 3.1 23.0 + - - +
365C SER* 4.9 1.7 + - - -
95D THR* 2.9 22.6 + - - -
96D HIS* 5.5 6.1 - - - -
101D GLU* 5.3 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 313 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C MET 3.9 0.2 + - - -
223C HIS* 3.6 33.6 - - + -
224C LYS* 4.8 1.6 - - - -
225C VAL 2.5 31.1 + - - -
226C PRO* 4.8 1.3 - - + -
227C LEU* 3.9 27.5 - - + +
230C TRP* 3.1 15.3 + + - -
310C ILE* 4.0 25.4 + - + +
311C PHE 3.4 2.2 - - - -
312C GLY* 1.3 74.5 - - - +
314C LEU* 1.3 81.7 + - + +
316C MET* 3.4 7.8 - - - +
317C VAL* 3.2 35.6 + - + +
95D THR* 5.8 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C HIS* 4.1 23.6 - - + -
230C TRP* 6.6 0.2 - - + -
312C GLY 3.1 0.4 + - - -
313C TYR* 1.3 97.1 - - + +
315C PRO* 1.4 74.3 - - + +
316C MET 3.2 1.3 - - - -
317C VAL* 3.1 14.3 + - + +
318C TYR* 3.0 53.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C GLY* 3.2 20.4 - - - +
314C LEU* 1.4 91.7 - - + +
316C MET* 1.3 52.0 + - + +
318C TYR* 3.2 10.9 + - + +
319C ALA* 2.7 37.2 + - - +
361C ILE* 4.3 19.7 - - + +
365C SER* 5.5 2.0 - - - +
9D CD 4.6 2.7 - - - -
96D HIS* 6.2 2.9 - - + +
101D GLU* 4.5 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C LEU* 4.0 15.5 - - + -
299C SER* 3.3 13.2 - - - +
310C ILE* 4.0 9.2 - - + -
311C PHE 3.8 10.1 - - - +
312C GLY 3.1 20.7 + - - +
313C TYR* 3.4 10.5 - - - +
314C LEU 3.2 0.2 - - - -
315C PRO* 1.3 73.9 - - - +
317C VAL* 1.3 62.7 + - - +
319C ALA* 3.4 4.7 + - - +
320C MET* 3.2 29.9 + - - +
361C ILE* 5.0 1.1 - - - +
362C MET* 3.7 31.4 - - + +
365C SER* 3.5 25.8 - - - +
366C TRP* 3.2 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C LEU* 3.8 16.4 - - + +
230C TRP* 3.8 56.8 - - + +
234C VAL* 5.3 0.3 - - - +
313C TYR* 3.2 27.1 + - + +
314C LEU* 3.1 15.1 + - + +
316C MET* 1.3 77.7 - - - +
318C TYR* 1.3 73.8 + - + +
320C MET* 3.3 11.3 + - + +
321C VAL* 3.2 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C LEU* 3.0 44.0 + - + +
315C PRO* 3.2 11.2 + - + +
317C VAL* 1.3 85.8 - - + +
319C ALA* 1.3 59.3 + - - +
321C VAL* 3.3 11.9 + - + +
322C ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C PRO 2.7 20.5 + - - +
316C MET 3.7 2.2 - - - +
317C VAL 3.3 0.2 - - - -
318C TYR* 1.3 71.6 - - - +
320C MET* 1.3 53.4 + - - +
322C ALA* 3.2 2.1 + - - +
323C ILE* 2.7 41.6 + - - +
358C PRO* 3.5 35.4 - - + +
361C ILE* 4.4 9.0 - - + -
362C MET* 3.7 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C LEU* 4.0 35.7 - - + +
230C TRP* 4.0 18.2 - - + -
231C SER* 3.8 24.0 - - - +
234C VAL* 3.5 22.5 - - + +
292C LEU* 4.0 22.0 - - + +
295C PHE* 4.5 7.2 - - - -
296C GLY* 5.2 1.6 - - - -
316C MET 3.2 16.4 + - - +
317C VAL* 3.6 9.2 - - + +
318C TYR 3.3 0.2 - - - -
319C ALA* 1.3 78.1 - - - +
321C VAL* 1.3 56.2 + - - +
323C ILE* 3.8 7.6 - - - +
324C GLY* 3.0 20.8 + - - -
362C MET* 3.6 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 321 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C TRP* 5.3 5.6 - - + -
234C VAL* 4.2 22.2 - - + +
317C VAL* 3.2 23.2 + - + +
318C TYR* 3.7 15.9 - - + +
319C ALA 3.3 0.2 - - - -
320C MET* 1.3 76.5 - - - +
322C ALA* 1.3 59.8 + - - +
324C GLY* 3.2 2.3 + - - -
325C VAL* 2.9 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C TYR 2.9 17.5 + - - +
319C ALA* 3.6 4.7 - - - +
321C VAL* 1.3 74.0 - - - +
323C ILE* 1.3 61.1 + - - +
325C VAL* 3.3 5.6 + - - +
326C LEU* 2.9 44.4 + - + +
358C PRO* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 323 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C TYR* 3.3 38.7 - - + -
292C LEU* 4.8 10.5 - - + -
295C PHE* 5.1 8.7 - - + -
319C ALA* 2.7 34.4 + - + +
320C MET* 3.8 8.5 - - - +
322C ALA* 1.3 71.3 - - - +
324C GLY* 1.3 58.0 + - - +
326C LEU* 4.0 3.7 - - - +
327C GLY* 2.9 29.5 + - - -
355C ILE* 3.9 10.7 - - + +
358C PRO* 3.6 23.6 - - + -
359C THR* 3.0 33.2 - - + +
362C MET* 5.1 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 324 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C VAL* 4.5 3.6 - - - -
238C LEU* 3.5 36.4 - - - +
288C TYR* 5.5 0.4 - - - -
292C LEU* 5.0 0.8 - - - +
320C MET 3.0 16.0 + - - -
321C VAL 3.2 4.2 + - - -
323C ILE* 1.3 78.8 - - - +
325C VAL* 1.3 60.9 + - - +
327C GLY* 3.6 4.9 + - - -
328C PHE* 3.5 21.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 325 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C VAL* 2.9 38.6 + - + +
322C ALA* 4.0 4.7 - - - +
324C GLY* 1.3 70.9 - - - +
326C LEU* 1.3 68.4 + - + +
328C PHE* 3.1 22.8 + - - +
329C VAL* 4.1 9.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C ALA* 2.9 29.2 + - + +
323C ILE 4.0 0.7 - - - +
325C VAL* 1.3 74.1 - - + +
327C GLY* 1.3 58.4 + - - +
328C PHE 2.8 11.5 + - - -
329C VAL* 3.0 34.6 + - + +
330C VAL* 3.4 10.4 - - + +
351C ALA* 4.8 5.4 - - + +
354C VAL* 3.8 34.8 - - + -
355C ILE* 3.6 27.6 - - + -
358C PRO* 4.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 327 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C LEU* 6.5 0.4 - - - -
284C HIS* 3.5 26.7 - - - +
285C PRO* 3.2 28.6 - - - +
288C TYR* 4.1 9.2 - - - -
323C ILE 2.9 17.5 + - - -
324C GLY 3.9 3.8 - - - -
325C VAL 3.2 0.8 - - - -
326C LEU* 1.3 75.6 - - - +
328C PHE* 1.3 59.2 + - - +
329C VAL 3.5 0.4 - - - -
330C VAL* 4.0 5.5 + - - +
331C TRP* 5.3 0.7 + - - +
355C ILE* 4.3 1.9 - - - +
----------------------------------------------------------
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