Contacts of the helix formed by residues 333 - 340 (chain A) in PDB entry 3H13
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 LEU 333 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LEU* 4.7 0.7 - - + -
319A GLN* 2.8 44.3 + - + +
320A SER* 3.7 3.4 - - - +
321A VAL* 4.1 21.3 - - + +
331A LEU 3.4 0.4 + - - -
332A PRO* 1.3 71.3 - - - +
334A HIS* 1.3 58.3 + - - +
336A ILE* 2.8 41.4 + - + +
337A ARG* 3.1 20.4 + - - +
357A ILE* 4.1 10.1 - - + -
359A ASN* 5.3 3.1 - - - +
403A TRP* 3.6 27.5 - - + +
405A LEU* 4.0 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLN* 4.8 3.2 + - - +
332A PRO* 3.4 26.2 - - + +
333A LEU* 1.3 79.1 + - - +
335A HIS* 1.3 85.6 + + - +
337A ARG* 3.6 34.7 - - - +
338A ARG* 3.0 30.5 + - - +
341A MET* 5.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU* 4.4 11.3 - - + +
332A PRO* 3.1 38.8 + - + +
334A HIS* 1.3 111.9 + + - +
336A ILE* 1.3 68.2 + - - +
338A ARG* 3.4 38.2 + - - +
339A MET* 3.4 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ILE* 5.1 0.2 - - + -
293A LEU* 3.8 33.0 - - + -
310A CYS* 5.7 1.3 - - - -
312A LEU* 3.8 29.2 - - + -
321A VAL* 4.3 10.8 - - + -
331A LEU* 4.3 11.4 - - + -
332A PRO 3.7 9.0 - - - +
333A LEU* 2.8 28.5 + - + +
335A HIS* 1.3 76.3 - - - +
337A ARG* 1.3 67.5 + - - +
339A MET* 3.0 26.5 + - - +
340A PHE* 3.6 6.4 - - + -
355A PHE* 4.0 26.2 - - + -
357A ILE* 6.2 0.4 - - + -
403A TRP* 4.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLN* 6.2 0.2 - - - +
333A LEU* 3.5 17.7 - - - +
334A HIS* 3.6 33.2 - - - +
336A ILE* 1.3 77.0 - - - +
338A ARG* 1.3 61.7 + - - +
340A PHE 3.0 11.8 + - - -
341A MET* 3.4 12.7 - - + +
355A PHE* 4.7 3.6 - - - -
401A PHE* 3.4 37.2 - - + -
403A TRP* 3.2 62.8 - - + +
466A TRP* 4.9 11.4 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
334A HIS* 3.0 21.4 + - - +
335A HIS* 3.4 41.7 + - - +
336A ILE 3.0 0.4 - - - -
337A ARG* 1.3 79.0 - - - +
339A MET* 1.3 59.0 + - + +
340A PHE 3.2 0.7 + - - -
341A MET* 3.4 26.4 + - + +
344A SER* 2.8 19.9 + - - -
397A ARG* 5.9 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A SER* 4.0 11.9 - - - +
293A LEU* 3.3 25.6 - - + +
294A GLY* 3.0 42.8 - - - +
297A ALA* 3.5 19.4 - - + +
331A LEU* 6.4 1.3 - - - -
335A HIS* 3.4 17.7 - - - +
336A ILE* 3.0 12.0 + - - +
338A ARG* 1.3 79.3 - - + +
340A PHE* 1.3 65.3 + - + +
341A MET 3.5 0.4 - - - -
344A SER* 3.5 19.4 + - - +
345A CYS* 3.8 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU* 3.8 42.8 - - + -
296A PHE* 4.2 5.4 - - + -
297A ALA* 3.6 24.7 - - + -
308A PHE* 3.3 41.1 - + - -
336A ILE* 3.6 17.7 - - + -
337A ARG 3.0 7.5 + - - +
339A MET* 1.3 87.3 - - + +
341A MET* 1.3 63.5 + - - +
345A CYS* 3.7 10.5 - - - +
348A LEU* 4.2 12.3 - - + -
353A LYS* 3.1 28.6 - - + +
355A PHE* 3.8 19.7 - + + -
401A PHE* 3.6 14.4 - - + -
----------------------------------------------------------
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