Contacts of the helix formed by residues 376 - 388 (chain C) in PDB entry 4OGB
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 ILE 376 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C MET* 4.2 10.5 - - + -
276C HIS* 3.9 29.2 - - + +
277C MET* 4.8 11.4 - - + -
319C LEU* 3.9 24.5 - - + -
372C PHE* 3.0 38.3 + - + +
374C ASP 3.7 0.2 - - - -
375C TYR* 1.3 114.6 - - + +
377C VAL* 1.3 68.5 + - - +
378C HIS 3.5 1.3 - - - -
379C PRO* 3.4 2.8 - - - +
380C LEU* 3.2 25.1 + - - +
502C 2SR 4.7 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C LEU* 3.7 17.7 - - + +
322C PRO* 3.9 20.9 - - + -
323C THR* 4.5 0.7 - - + -
372C PHE* 3.0 51.7 + - + +
373C ILE* 3.9 10.3 - - + -
376C ILE* 1.3 79.9 - - + +
378C HIS* 1.3 61.4 + - - +
380C LEU* 3.8 3.0 - - - +
381C TRP* 3.1 43.3 + - + +
399C LEU* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C ILE* 2.6 32.5 + - + +
374C ASP* 4.8 4.3 - - - +
377C VAL* 1.3 71.2 - - - +
379C PRO* 1.4 63.7 - - + +
382C GLU* 2.8 73.7 + - + +
396C LEU* 3.9 7.0 - - + +
399C LEU* 3.7 22.2 - - + +
400C GLU* 3.0 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C LEU* 3.8 19.9 - - + +
284C LYS* 4.8 8.2 - - - +
373C ILE 3.6 1.6 - - - +
374C ASP 3.5 22.2 - - - +
375C TYR* 3.7 14.1 - - - +
376C ILE 3.4 10.5 - - - +
378C HIS* 1.4 96.3 - - + +
380C LEU* 1.3 56.7 + - - +
382C GLU* 3.9 9.5 - - + +
383C THR* 2.7 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C HIS* 4.2 8.5 - - + -
280C LEU* 3.9 22.6 - - + +
283C LEU* 4.5 3.8 - - + -
312C ASN* 4.2 13.2 - - - +
315C HIS* 3.6 36.8 - - + +
316C CYS* 3.7 35.0 - - - -
319C LEU* 3.9 20.6 - - + -
376C ILE 3.2 17.7 + - - +
377C VAL 3.8 3.8 - - - +
379C PRO* 1.3 78.5 - - - +
381C TRP* 1.3 63.2 + - + +
383C THR* 3.2 4.0 + - - -
384C TRP* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TRP* 3.7 36.8 - + - -
175C LEU* 3.8 14.6 - - + -
316C CYS* 3.5 35.5 + - + +
319C LEU* 3.1 20.0 + - - +
320C SER* 3.9 3.4 - - - -
323C THR* 3.4 17.2 - - + +
377C VAL* 3.1 36.9 + - + +
378C HIS 4.2 0.4 - - - +
380C LEU* 1.3 83.1 - - + +
382C GLU* 1.3 56.6 + - - +
384C TRP* 3.6 35.1 - + + +
385C ALA* 2.7 36.0 + - - +
392C ALA* 4.9 3.4 - - + -
395C ILE* 3.8 22.7 - - + -
396C LEU* 4.1 18.1 - - + +
399C LEU* 4.2 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C HIS* 2.8 47.3 + - + +
379C PRO* 3.9 9.8 - - - +
381C TRP* 1.3 77.2 - - - +
383C THR* 1.3 57.1 + - - +
385C ALA* 3.4 5.6 + - - +
386C ASP* 3.0 42.5 + - - +
396C LEU* 4.0 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C LEU* 3.5 13.4 - - + +
283C LEU* 3.7 24.0 - - + +
284C LYS* 3.6 39.6 - - + +
287C VAL* 3.6 11.0 - - + +
379C PRO 2.7 21.4 + - - -
380C LEU 3.2 4.6 + - - -
381C TRP 3.1 0.2 - - - -
382C GLU* 1.3 76.6 + - - +
384C TRP* 1.3 65.1 + - - +
386C ASP* 3.4 6.4 + - - +
387C LEU* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C LEU* 3.6 16.8 - - + +
181C LEU* 4.3 8.7 - - + -
283C LEU* 4.0 12.4 - - + +
309C VAL* 3.9 24.2 - - + -
312C ASN* 4.5 3.4 - - + -
313C MET* 3.8 46.0 - - + -
316C CYS* 4.0 24.7 - - - -
380C LEU 2.9 14.2 + - - +
381C TRP* 3.6 29.6 - + - +
383C THR* 1.3 77.5 - - - +
385C ALA* 1.3 62.8 + - - +
387C LEU* 3.1 28.8 + - + +
388C VAL* 3.1 42.8 + - + +
392C ALA* 4.2 5.6 - - + -
513C EDO 3.5 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C TRP 2.7 22.1 + - - +
382C GLU* 3.6 8.7 - - - +
383C THR 3.2 0.2 - - - -
384C TRP* 1.3 73.2 - - - +
386C ASP* 1.3 55.2 + - - +
388C VAL* 3.2 1.5 + - - -
389C HIS* 2.7 40.9 + - + +
392C ALA* 4.2 30.8 + - + +
393C GLN* 5.6 5.2 - - + +
396C LEU* 4.4 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C VAL* 4.2 19.6 - - + +
290C LYS* 3.3 20.1 + - - -
382C GLU* 3.0 30.0 + - - +
383C THR* 3.9 7.0 - - - +
384C TRP 3.3 0.2 - - - -
385C ALA* 1.3 78.6 - - - +
387C LEU* 1.3 62.0 + - - +
388C VAL 3.5 0.2 + - - -
389C HIS* 3.7 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ALA* 5.0 0.9 - - - +
283C LEU* 4.1 13.9 - - + -
286C MET* 3.9 24.0 - - + +
287C VAL* 3.8 24.2 - - + +
290C LYS* 3.3 25.1 + - + +
298C LEU* 3.8 36.6 - - + +
309C VAL* 4.6 11.7 - - + -
383C THR 3.1 13.3 + - - +
384C TRP* 3.1 41.4 + - + +
386C ASP* 1.3 78.3 - - - +
388C VAL* 1.3 62.2 + - + +
389C HIS 3.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C THR* 4.0 17.5 - - + -
180C ALA* 3.8 19.7 - - + +
181C LEU* 4.7 6.1 - - + -
290C LYS* 5.0 0.7 - - - +
298C LEU* 4.8 2.0 - - + -
384C TRP* 3.1 49.2 + - + +
385C ALA 4.1 0.7 - - - +
387C LEU* 1.3 89.0 - - + +
389C HIS* 1.3 56.8 + - - +
391C ASP* 2.8 49.8 + - + +
392C ALA* 4.0 14.8 - - + -
513C EDO 4.1 2.9 - - - +
----------------------------------------------------------
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