Contacts of the helix formed by residues 366 - 377 (chain C) in PDB entry 2R2N
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 366 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C VAL* 4.1 12.3 - - + -
363C ILE* 4.2 9.4 - - + -
365C ASP* 1.3 72.3 + - - +
367C LYS* 1.3 66.9 + - - +
368C GLU 3.4 2.0 - - - -
369C LEU* 3.2 32.9 + - + -
370C ILE* 3.0 36.9 + - + +
383C PRO* 4.1 6.7 - - + -
384C GLY 4.5 0.4 - - - +
385C ASN* 5.1 0.2 - - - +
395C SER 2.9 16.7 + - - +
396C PRO* 4.4 6.7 - - + -
397C TYR 3.2 28.3 - - - +
398C LEU* 3.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 367 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C ASP* 3.3 20.5 + - - +
366C VAL* 1.3 79.7 - - - +
368C GLU* 1.3 51.4 - - - +
370C ILE* 3.8 0.2 - - - -
371C GLU* 2.7 77.1 + - - +
383C PRO* 4.2 14.1 - - + +
385C ASN* 3.7 33.4 - - + +
391C SER 5.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 368 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C ASP* 4.4 6.7 + - - +
366C VAL 3.4 0.4 - - - -
367C LYS* 1.3 74.9 - - - +
369C LEU* 1.3 69.1 + - - +
371C GLU* 5.1 0.2 - - - -
372C GLU* 2.9 67.3 + - + +
373C LYS* 3.3 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 369 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C VAL* 5.0 2.5 - - + -
363C ILE* 5.1 8.3 - - + -
365C ASP 4.9 1.2 + - - -
366C VAL* 3.2 37.6 + - + +
368C GLU* 1.3 80.7 - - - +
370C ILE* 1.3 59.6 + - + +
373C LYS* 3.2 15.4 + - + +
374C ALA* 2.9 25.1 + - + +
398C LEU* 4.9 1.1 - - + -
417C LEU* 3.6 29.8 - - + -
420C LEU* 3.5 31.4 - - + +
421C ILE* 3.9 13.7 - - + +
424C SER* 3.3 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 370 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C VAL* 3.0 24.3 + - + +
367C LYS 3.9 1.6 - - - +
369C LEU* 1.3 78.7 - - + +
371C GLU* 1.3 64.9 + - - +
372C GLU 3.4 0.5 + - - -
374C ALA* 3.5 12.9 + - + -
375C VAL* 3.1 27.4 + - + +
379C VAL 5.1 0.2 - - - +
380C LEU* 4.9 5.2 - - + -
381C MET* 3.1 29.4 - - + +
383C PRO* 3.3 28.5 - - + -
398C LEU* 2.7 40.8 - - + -
417C LEU* 5.9 1.8 - - + -
22D MET* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 371 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C LYS* 2.7 55.3 + - + +
368C GLU* 5.1 0.9 - - - -
370C ILE* 1.3 76.1 - - + +
372C GLU* 1.3 60.9 + - + +
375C VAL* 2.9 23.1 - - - +
383C PRO* 4.2 4.1 - - + +
22D MET* 3.6 31.2 - - + +
25D ILE* 5.6 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 372 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C GLU* 2.9 51.3 + - + +
371C GLU* 1.3 82.6 - - + +
373C LYS* 1.3 65.6 + - + +
374C ALA 3.9 0.2 - - - -
375C VAL* 3.8 6.4 - - - +
376C LYS* 3.7 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C GLU* 4.2 22.9 - - - +
369C LEU* 3.2 18.2 + - + +
372C GLU* 1.3 83.3 - - + +
374C ALA* 1.3 65.8 + - - +
375C VAL 3.4 0.2 - - - -
376C LYS* 3.4 14.8 + - - +
377C MET* 3.4 17.8 + - - +
420C LEU* 3.8 26.6 - - + +
423C GLU* 4.1 12.0 + - - +
424C SER* 3.0 37.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
369C LEU* 2.9 17.9 + - + +
370C ILE* 3.5 19.3 + - + +
373C LYS* 1.3 70.2 - - - +
375C VAL* 1.3 67.8 + - - +
377C MET* 2.9 13.5 + - - +
379C VAL* 3.1 42.7 + - + +
381C MET 5.8 1.1 - - - +
417C LEU* 6.0 5.2 - - + -
420C LEU* 3.5 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 375 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C ILE* 3.1 15.3 + - + +
371C GLU* 2.9 33.0 - - - +
372C GLU 3.8 7.2 - - - +
374C ALA* 1.3 75.3 - - - +
376C LYS* 1.3 60.3 + - + +
378C GLY* 2.8 21.9 + - - +
379C VAL 3.6 4.2 + - - -
380C LEU* 3.2 28.3 - - + -
22D MET* 5.5 1.3 - - - -
25D ILE* 3.9 35.2 - - + -
33D MET* 4.2 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 376 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C GLU 3.7 16.8 + - - +
373C LYS* 3.4 11.9 + - - +
374C ALA 3.2 0.6 - - - -
375C VAL* 1.3 80.8 - - + +
377C MET* 1.3 62.1 + - + +
378C GLY 3.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C LYS 3.5 13.9 - - - +
374C ALA 2.9 9.8 + - - +
376C LYS* 1.3 81.9 - - + +
378C GLY* 1.3 62.7 + - - +
379C VAL* 3.4 7.4 + - - +
416C VAL* 3.6 29.0 - - + +
419C GLN* 3.8 32.1 - - - +
420C LEU* 3.8 20.4 - - + -
----------------------------------------------------------
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