Contacts of the helix formed by residues 373 - 381 (chain A) in PDB entry 2Z82
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 373 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LEU 3.6 8.4 + - - +
372A MET* 1.3 80.6 - - - +
374A GLU* 1.3 70.7 + - - +
375A GLU* 4.2 7.0 - - + +
376A TYR* 3.0 37.7 + - + +
377A LEU* 2.8 20.3 + - - +
398A HIS* 3.5 29.2 - - + +
399A LEU* 3.9 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A VAL* 1.3 72.5 - - - +
375A GLU* 1.3 65.6 + - - +
377A LEU* 2.8 17.3 + - - +
378A LYS* 2.8 12.0 + - - +
398A HIS 4.3 2.1 - - - +
399A LEU* 3.6 9.6 - - - +
400A ARG* 2.9 33.5 + - - +
401A SER* 3.1 14.9 + - - +
404A LYS* 3.5 48.2 - - + +
405A THR* 3.4 18.4 + - - +
408A ILE* 3.6 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A VAL* 3.3 5.9 + - + +
374A GLU* 1.3 79.0 - - + +
376A TYR* 1.3 78.0 + - + +
378A LYS* 3.6 32.8 - - - +
379A ASN* 3.9 5.9 + - - +
404A LYS* 4.7 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A PHE* 3.4 46.9 - + + +
350A LEU* 3.7 25.0 - - + +
371A LEU 5.9 0.7 - - - -
372A MET* 4.5 1.3 - - + -
373A VAL* 3.0 29.3 + - + +
375A GLU* 1.3 89.2 + - + +
377A LEU* 1.3 64.5 + - - +
378A LYS 3.2 0.4 - - - -
379A ASN* 3.4 3.9 + - + +
380A SER* 2.8 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LEU* 6.3 0.2 - - + -
372A MET* 3.9 24.1 - - + +
373A VAL 2.8 14.1 + - - +
374A GLU* 3.3 8.7 - - - +
376A TYR* 1.3 75.5 - - - +
378A LYS* 1.3 66.4 + - - +
380A SER* 2.9 7.3 + - - -
381A ALA* 2.8 28.1 + - + +
386A TRP* 5.4 6.3 - - + -
392A LEU* 5.6 0.4 - - + -
394A LEU* 4.1 24.2 - - + -
399A LEU* 4.1 20.2 - - + -
405A THR* 4.2 24.2 - - + +
408A ILE* 4.1 22.7 - - + -
409A LEU* 4.6 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLU 2.8 9.9 + - - +
375A GLU* 3.6 28.3 - - - +
377A LEU* 1.3 77.4 - - - +
379A ASN* 1.3 61.5 + - - +
381A ALA 3.4 17.2 - - - +
382A CYS* 3.5 5.0 + - - +
404A LYS* 5.8 7.3 - - - +
408A ILE* 3.5 31.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 3.8 12.0 - - + +
352A PRO* 3.7 7.6 - - - +
353A CYS* 2.9 54.8 + - - +
375A GLU 3.9 4.6 + - - +
376A TYR* 3.4 12.3 + - + +
377A LEU 3.1 0.6 - - - -
378A LYS* 1.3 78.0 - - - +
380A SER* 1.3 64.7 + - - +
381A ALA 3.3 0.3 + - - -
382A CYS* 3.3 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 3.8 1.4 - - - +
351A VAL* 3.1 47.5 + - - -
356A SER* 2.9 22.2 + - - -
372A MET* 3.7 13.0 - - - +
376A TYR 2.8 15.4 + - - -
377A LEU* 2.9 11.7 + - - -
379A ASN* 1.3 78.7 + - - +
381A ALA* 1.3 58.2 + - - +
382A CYS* 4.5 0.2 - - - -
385A ALA* 3.4 9.9 - - - +
386A TRP* 3.8 14.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 2.8 19.8 + - + +
378A LYS 3.4 6.8 - - - +
380A SER* 1.3 71.3 - - - +
382A CYS* 1.3 62.4 + - - +
385A ALA* 3.6 8.7 - - + -
386A TRP* 4.2 17.9 - - + -
408A ILE* 4.1 10.9 - - + +
409A LEU* 4.4 19.1 - - + -
411A THR* 2.7 35.2 + - - +
412A LEU* 4.9 3.4 - - + -
----------------------------------------------------------
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