Contacts of the helix formed by residues 337 - 341 (chain A) in PDB entry 3RAW
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 337 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASP* 3.0 22.9 + - - +
284A LEU 5.6 1.1 + - - -
285A LYS* 3.3 24.3 + - + +
336A ALA* 1.3 73.0 - - - +
338A ARG* 1.3 71.3 + - - +
339A HIS* 4.2 9.9 - - + +
340A TYR* 3.0 40.3 + - + +
341A ARG* 3.3 5.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ALA 3.6 2.0 + - - -
337A THR* 1.3 75.6 - - + +
339A HIS* 1.3 68.6 + - + +
340A TYR 3.1 1.0 + - - -
341A ARG* 3.2 38.7 + - - +
376A THR* 3.6 11.4 - - + +
377A HIS* 3.3 44.8 + - - +
378A GLU* 3.7 5.4 - - - +
379A ASN* 2.9 38.2 + - - +
382A HIS* 3.1 33.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A THR* 3.0 7.6 + - + +
338A ARG* 1.3 79.5 - - + +
340A TYR* 1.3 78.9 + - + +
341A ARG 3.4 1.1 + - - -
362A CYS* 3.8 15.1 - - - +
372A THR* 3.6 22.7 + - + +
374A PHE* 3.3 39.8 + - - +
375A GLN* 3.4 27.6 + - - -
376A THR* 3.2 31.7 + - - -
382A HIS* 4.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU 3.6 17.3 - - - +
285A LYS* 3.6 20.4 - - + -
286A PRO* 3.2 24.3 - - + +
336A ALA* 4.1 4.8 - - + +
337A THR* 3.0 26.2 + - + +
339A HIS* 1.3 98.7 + - + +
341A ARG* 1.3 60.3 + - - +
342A PRO* 3.7 2.1 - - - +
358A TRP* 3.6 11.5 - - - -
359A SER* 2.7 31.1 + - - +
362A CYS* 3.8 26.2 - - + -
363A ILE* 4.0 17.7 - - + -
366A GLU* 2.5 35.0 + - - -
372A THR* 4.4 5.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ILE* 3.5 23.9 - - - +
335A VAL 3.0 21.1 + - - +
336A ALA* 2.7 24.7 + - + -
337A THR* 3.3 5.1 + - - +
338A ARG* 3.2 63.3 + - - +
339A HIS 3.4 0.6 - - - -
340A TYR* 1.3 76.7 - - - +
342A PRO* 1.3 74.1 - - + +
345A VAL* 3.6 22.7 - - + -
346A ILE* 4.3 14.1 - - + +
358A TRP* 3.5 8.2 + - - -
379A ASN* 4.4 4.2 + - - -
382A HIS* 3.4 19.1 - - + -
386A MET* 3.7 1.9 - - - +
----------------------------------------------------------
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