Contacts of the helix formed by residues 368 - 383 (chain C) in PDB entry 2O2C
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 ASN 368 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C HIS* 3.6 8.9 + - - -
360C PHE* 3.0 52.6 + - - -
363C ALA* 3.2 18.2 + - - +
364C PRO 3.1 11.9 + - - +
365C PRO* 3.4 12.6 + - + +
366C GLU 3.6 0.6 - - - -
367C GLN* 1.3 75.0 - - - +
369C VAL* 1.3 66.6 + - - +
370C PRO* 3.5 5.2 - - - +
371C LEU* 3.3 20.5 + - + +
372C LEU* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 369 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C VAL* 3.9 24.0 - - + +
89C VAL* 3.7 26.7 - - + -
99C LEU* 5.1 9.0 - - + +
101C LEU* 3.8 32.5 - - + +
356C ILE* 6.2 1.1 - - + -
359C HIS* 3.1 13.6 + - + +
367C GLN 3.7 0.2 + - - -
368C ASN* 1.3 70.0 - - - +
370C PRO* 1.4 72.4 - - + +
371C LEU 3.1 0.5 + - - -
372C LEU* 3.1 5.1 + - - +
373C LEU* 2.9 22.5 + - + +
529C LEU* 5.2 0.2 - - + -
545C MET* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 370 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C ILE* 4.5 5.6 - - + -
359C HIS* 3.8 12.3 - - + -
360C PHE* 3.6 28.9 - - + -
368C ASN* 3.5 7.0 - - - +
369C VAL* 1.4 100.3 - - + +
371C LEU* 1.3 58.4 + - - +
373C LEU* 3.6 6.3 + - + +
374C ALA* 3.1 24.3 + - - +
545C MET* 3.6 33.2 - - + +
548C HIS* 3.7 17.7 - - + -
549C LYS* 3.7 8.7 - - - +
552C VAL* 4.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 371 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU* 4.0 9.9 - - + -
120C ALA* 3.9 24.0 - - + -
125C ILE* 4.1 14.4 - - + -
360C PHE* 4.4 5.0 - - + -
365C PRO* 3.5 42.8 - - + +
368C ASN* 3.3 23.4 + - + +
369C VAL 3.2 0.8 - - - -
370C PRO* 1.3 74.3 - - - +
372C LEU* 1.3 60.8 + - - +
374C ALA* 3.3 3.5 + - - +
375C LEU* 3.0 40.4 + - + +
552C VAL* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 372 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C VAL* 4.0 11.9 - - + -
101C LEU* 4.5 5.6 - - + -
103C TYR* 3.7 46.4 - - + +
113C LYS* 4.6 9.9 - - + -
117C LEU* 4.4 15.5 - - + -
365C PRO 4.0 12.3 - - - +
366C GLU 3.5 22.9 - - - +
368C ASN 3.0 27.5 + - - +
369C VAL* 3.7 3.6 - - - +
371C LEU* 1.3 73.9 - - - +
373C LEU* 1.3 65.6 + - - +
375C LEU* 3.3 7.5 + - + +
376C VAL* 3.0 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LEU* 4.0 25.0 - - + +
369C VAL 2.9 15.1 + - - +
370C PRO 3.9 4.9 - - - +
372C LEU* 1.3 76.5 - - - +
374C ALA* 1.3 61.4 + - - +
376C VAL* 3.6 6.4 + - - +
377C GLY* 3.2 18.0 + - - -
389C HIS* 6.3 0.2 - - + -
458C ASP* 4.3 9.6 - - - +
527C ASN* 3.5 30.3 + - + +
529C LEU* 5.0 3.1 - - + -
545C MET* 3.9 40.6 - - + -
546C TYR* 4.2 9.6 - - + -
549C LYS* 4.0 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 374 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C PRO 3.1 19.4 + - - +
371C LEU 3.5 5.2 - - - +
372C LEU 3.2 0.2 - - - -
373C LEU* 1.3 79.5 - - - +
375C LEU* 1.3 57.7 + - - +
377C GLY 3.2 0.2 + - - -
378C VAL* 2.9 29.1 + - - +
549C LYS* 3.5 30.7 - - + +
552C VAL* 3.7 20.0 - - + -
553C GLN* 3.1 17.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LEU* 3.4 60.6 - - + +
117C LEU* 3.9 23.1 - - + +
119C LEU* 5.2 2.0 - - + -
120C ALA* 4.4 6.5 - - + -
371C LEU* 3.0 31.8 + - + +
372C LEU* 3.3 8.9 + - + +
374C ALA* 1.3 72.8 - - - +
376C VAL* 1.3 61.2 + - + +
378C VAL* 3.3 3.8 + - + +
379C TRP* 3.0 28.9 + - - +
552C VAL* 4.8 2.7 - - + -
556C ILE* 3.4 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 376 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C TYR* 4.0 29.8 - - + +
106C SER* 4.8 4.3 - - - -
108C ILE* 3.7 27.4 - - + -
116C LEU* 5.7 0.7 - - + -
372C LEU* 3.0 21.2 + - + +
373C LEU* 3.8 6.5 - - - +
374C ALA 3.4 0.2 - - - -
375C LEU* 1.3 74.6 - - + +
377C GLY* 1.3 61.9 + - - +
379C TRP* 3.4 2.6 + - - +
380C TYR* 3.2 51.2 + - + -
527C ASN* 4.0 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C LEU 3.2 12.4 + - - -
374C ALA 3.2 0.2 + - - -
375C LEU 3.2 0.2 - - - -
376C VAL* 1.3 75.1 - - - +
378C VAL* 1.3 57.7 + - - +
380C TYR* 3.2 5.6 + - - +
381C ILE* 2.9 38.3 + - - +
389C HIS* 6.0 5.4 - - - -
456C PRO* 6.5 0.7 - - - -
549C LYS* 5.3 3.6 - - - -
553C GLN* 3.5 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TRP* 4.3 17.3 - - + -
116C LEU* 4.9 3.1 - - + -
119C LEU* 4.4 14.6 - - + -
374C ALA 2.9 19.6 + - - +
375C LEU* 3.3 8.5 + - + +
377C GLY* 1.3 72.7 - - - +
379C TRP* 1.3 60.5 + - - +
381C ILE* 4.6 2.2 - - - +
382C ASN* 2.9 51.5 + - - +
383C PHE* 3.8 5.6 - - + -
553C GLN* 4.1 15.0 - - + +
556C ILE* 4.0 25.6 - - + -
557C TRP* 4.4 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LEU* 3.5 49.8 - - + -
62C LEU* 4.1 0.9 - - + -
63C TYR* 3.8 23.3 - + + -
67C GLY* 5.4 3.4 - - - -
107C HIS 3.0 19.7 + - - -
108C ILE* 3.7 20.8 - - + +
112C ILE* 3.7 36.3 - - + -
116C LEU* 4.2 11.6 - - + +
375C LEU 3.0 13.1 + - - +
376C VAL* 3.4 9.4 - - - +
378C VAL* 1.3 77.9 - - - +
380C TYR* 1.3 69.2 + + - +
383C PHE* 3.2 53.5 + + - +
384C PHE* 3.3 33.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 380 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C SER* 3.4 6.8 - - - -
107C HIS* 2.7 50.8 + - - -
108C ILE* 5.1 0.2 - - + -
376C VAL* 3.2 40.6 + - + +
377C GLY* 3.9 7.2 - - - +
379C TRP* 1.3 86.9 - + - +
381C ILE* 1.3 59.1 + - + +
384C PHE* 3.3 32.5 - + + +
385C GLY 3.0 10.9 + - - -
386C ALA* 2.9 25.5 + - + +
454C LEU* 3.8 16.6 - - + -
456C PRO* 3.8 27.4 - - + -
525C PRO* 3.3 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C GLY* 2.9 27.1 + - - +
378C VAL 4.2 1.1 - - - +
380C TYR* 1.3 75.8 - - + +
382C ASN* 1.3 75.9 + - - +
385C GLY* 3.2 23.4 - - - -
386C ALA 3.4 20.6 - - - +
387C VAL* 5.7 2.2 - - - -
427C LEU* 3.6 21.6 - - + +
428C THR 3.5 17.9 - - - +
430C PRO* 3.7 37.2 - - + -
553C GLN* 4.4 6.1 - - - +
557C TRP* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TRP* 3.6 29.5 - - + -
60C GLN* 5.0 2.6 - - - +
378C VAL* 2.9 28.6 + - - +
381C ILE* 1.3 81.3 - - - +
383C PHE* 1.3 69.8 + - + +
385C GLY* 4.5 1.1 - - - -
426C THR* 3.7 5.9 - - - -
427C LEU* 2.9 43.3 + - - +
557C TRP* 2.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TRP* 3.8 54.3 - + - -
59C LEU* 3.6 37.2 - - + -
60C GLN* 3.7 45.8 - - + +
63C TYR* 3.2 36.6 + - + -
116C LEU* 5.5 0.2 - - + -
378C VAL* 3.8 16.6 - - + -
379C TRP* 3.2 31.6 + + + +
382C ASN* 1.3 82.5 - - + +
384C PHE* 1.3 63.0 + - - +
385C GLY 3.3 1.5 + - - -
----------------------------------------------------------
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