Contacts of the helix formed by residues 368 - 375 (chain B) in PDB entry 6IWQ
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 THR 368 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ARG* 4.2 2.2 - - - +
366B PRO 4.2 3.6 - - - +
367B LEU* 1.3 80.1 - - - +
369B PRO* 1.3 76.7 - - + +
370B GLN* 3.8 5.2 - - - -
371B GLU* 3.2 15.1 + - - +
372B LYS* 3.2 20.0 + - - +
519B TYR* 3.0 30.1 + - + -
520B ASP* 3.4 38.8 - - + +
524B HIS* 6.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU 4.5 1.3 - - - +
368B THR* 1.3 91.6 - - + +
370B GLN* 1.3 64.0 + - + +
372B LYS* 3.1 13.1 + - + +
373B ARG* 2.9 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B THR* 3.1 2.8 - - - +
369B PRO* 1.3 84.0 - - + +
371B GLU* 1.3 61.4 + - - +
373B ARG* 3.4 41.1 + - - +
374B LEU* 3.5 16.1 + - + +
383B ARG* 4.9 4.1 + - - +
516B GLU* 4.7 2.8 - - - +
519B TYR* 3.6 50.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ARG* 3.5 25.9 + - - +
367B LEU* 3.6 18.8 - - + -
368B THR* 3.2 12.7 + - - +
369B PRO 3.2 0.2 - - - -
370B GLN* 1.3 74.6 - - - +
372B LYS* 1.3 64.8 + - - +
374B LEU* 3.1 22.2 + - - +
375B ARG* 3.1 20.6 - - - +
382B TYR* 4.7 2.6 - - + +
383B ARG* 2.6 62.4 + - - +
519B TYR* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU* 5.0 4.4 - - + +
368B THR 3.2 10.3 + - - +
369B PRO* 3.1 17.0 + - + +
371B GLU* 1.3 79.2 - - - +
373B ARG* 1.3 71.2 + - + +
375B ARG* 3.0 42.5 + - - +
378B LYS* 4.9 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B PRO* 2.9 34.4 + - + +
370B GLN* 3.5 38.5 + - - +
372B LYS* 1.3 87.1 - - + +
374B LEU* 1.3 65.2 + - + +
375B ARG 3.3 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B GLN* 3.6 17.5 - - + +
371B GLU* 3.1 16.3 + - - +
373B ARG* 1.3 82.0 - - + +
375B ARG* 1.3 61.4 + - + +
376B LYS 4.1 1.2 + - - -
380B GLU* 5.1 0.5 - - - +
383B ARG* 3.9 32.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B TYR* 4.9 0.8 - - - -
367B LEU* 3.9 17.4 - - - +
371B GLU* 3.1 23.3 - - - +
372B LYS* 3.0 31.4 + - - +
373B ARG 3.2 4.2 - - - +
374B LEU* 1.3 84.1 - - + +
376B LYS* 1.3 64.6 + - - +
377B THR 3.5 13.3 + - - +
378B LYS* 2.5 34.7 + - - +
379B THR 4.1 0.6 - - - -
380B GLU* 3.0 47.0 + - - +
381B PRO 4.2 4.7 - - - +
382B TYR* 3.5 34.6 - - - +
434B PRO* 4.6 2.2 - - - +
----------------------------------------------------------
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