Contacts of the helix formed by residues 371 - 378 (chain C) in PDB entry 4HH3
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 PRO 371 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C GLN 4.5 1.8 - - - +
370C LEU* 1.3 93.0 - - + +
372C PRO* 1.3 69.3 - - + +
373C SER* 3.1 11.0 - - - +
374C LYS* 2.9 36.7 + - + +
375C LEU* 3.8 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 372 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C LEU 3.4 6.4 - - - +
371C PRO* 1.3 83.3 - - + +
373C SER* 1.3 62.3 + - - +
375C LEU* 3.2 24.4 + - + +
376C LYS* 4.0 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C PRO* 3.1 11.5 + - - +
372C PRO* 1.3 79.5 - - - +
374C LYS* 1.3 67.5 + - - +
375C LEU 3.4 0.3 + - - -
376C LYS* 3.7 20.2 + - - +
377C ASP* 4.2 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 374 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C LEU* 3.9 31.4 - - + +
371C PRO* 2.9 26.2 + - + +
373C SER* 1.3 82.4 + - - +
375C LEU* 1.3 65.8 + - - +
377C ASP* 3.2 36.0 + - - +
378C SER* 3.8 4.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
363C VAL* 4.2 20.4 - - + -
367C LEU* 3.8 23.1 - - + +
368C ALA* 4.5 7.6 - - - +
370C LEU* 5.3 4.2 - - + +
371C PRO 3.8 2.7 + - - +
372C PRO* 3.2 20.2 + - + +
373C SER 3.2 0.4 - - - -
374C LYS* 1.3 78.9 - - - +
376C LYS* 1.3 64.1 + - + +
378C SER* 2.7 31.7 + - - +
380C ALA* 3.5 23.0 - - + +
381C ASP 4.2 2.5 - - - +
382C ALA* 3.8 25.6 - - - +
383C GLY* 4.3 7.9 - - - +
----------------------------------------------------------
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 PRO 4.2 12.6 - - - +
373C SER* 4.1 11.7 - - - +
374C LYS 3.2 1.0 + - - -
375C LEU* 1.3 80.0 - - + +
377C ASP* 1.3 66.0 + - - +
379C GLY* 3.3 13.0 + - - -
380C ALA 4.3 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C SER 4.2 9.2 - - - +
374C LYS* 3.2 29.2 + - - +
376C LYS* 1.3 79.3 - - - +
378C SER* 1.3 61.1 + - - +
379C GLY* 3.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LEU* 3.7 29.9 - - - +
347C VAL* 3.3 19.6 - - - +
348C SER* 4.4 11.8 + - - -
363C VAL* 5.3 1.4 - - - +
367C LEU* 5.9 3.0 - - - +
370C LEU* 6.6 0.2 - - - -
374C LYS 3.8 3.2 + - - -
375C LEU* 2.7 28.8 + - - +
377C ASP* 1.3 79.0 - - - +
379C GLY* 1.3 57.6 + - - +
380C ALA* 3.4 15.0 + - - +
----------------------------------------------------------
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