Contacts of the helix formed by residues 330 - 337 (chain A) in PDB entry 6TX0
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 ASP 330 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ASN 4.2 0.8 + - - +
329A PHE* 1.3 86.5 - - - +
331A TYR* 1.3 61.8 + - - +
332A LYS* 3.2 12.3 + - - +
333A ARG* 3.1 41.7 + - + +
334A PHE* 3.5 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 6.3 0.2 - - + -
123A HIS* 4.1 16.7 + + - -
173A TYR* 4.4 8.1 + - - -
174A LEU* 3.3 33.8 - - + +
177A CYS* 5.4 3.7 - - + -
313A TRP* 3.8 38.9 - + + -
317A ALA* 6.0 4.0 - - + -
329A PHE* 3.6 26.2 + - + -
330A ASP* 1.3 73.3 + - - +
332A LYS* 1.3 100.3 + - + +
334A PHE* 3.0 14.1 + - - +
335A ILE* 3.1 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ASP* 3.2 8.9 + - - +
331A TYR* 1.3 117.4 - - + +
333A ARG* 1.3 63.8 + - - +
335A ILE* 3.4 8.0 + - + +
336A LYS* 3.1 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ASP* 3.1 31.2 + - - +
332A LYS* 1.3 78.1 - - - +
334A PHE* 1.3 65.2 - - - +
336A LYS* 3.0 16.7 + - - +
337A PHE* 3.3 46.1 + - + -
354A LYS* 4.0 17.2 + - - +
355A GLU* 3.1 35.1 + - - +
358A ASN* 3.5 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 5.2 3.8 - - + -
308A ILE* 4.0 20.4 - - + -
313A TRP* 3.4 34.3 - + + -
329A PHE* 4.5 12.3 - + + -
330A ASP 3.5 5.5 + - - +
331A TYR* 3.0 12.3 + - - +
333A ARG* 1.3 77.1 - - - +
335A ILE* 1.3 64.5 + - - +
337A PHE* 3.2 13.1 + - - -
338A ALA* 3.2 26.9 + - + +
349A ILE* 4.9 12.8 - - + -
350A CYS 5.4 0.9 - - - -
351A ALA* 4.3 21.5 - - + -
355A GLU* 4.6 15.9 + - + +
359A LEU* 3.8 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 5.3 1.8 - - + +
177A CYS* 4.5 13.7 - - + +
178A LEU* 4.3 26.5 - - + +
181A ALA* 3.9 28.4 - - + +
185A LYS* 4.3 6.8 + - - -
313A TRP* 3.9 20.9 - - + -
331A TYR* 3.1 38.7 + - + +
332A LYS* 3.7 8.3 - - - +
333A ARG 3.1 0.2 - - - -
334A PHE* 1.3 80.8 - - - +
336A LYS* 1.3 66.0 + - + +
337A PHE 3.2 0.5 + - - -
338A ALA* 3.5 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LYS* 3.6 18.0 + - - +
332A LYS* 3.1 19.9 + - - +
333A ARG* 3.0 11.6 + - - +
335A ILE* 1.3 80.2 - - + +
337A PHE* 1.3 76.5 + - + +
521A TYR* 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ARG* 3.3 55.1 + - + +
334A PHE 3.2 7.7 + - - +
336A LYS* 1.3 91.1 - - + +
338A ALA* 1.3 58.5 + - - +
351A ALA* 3.6 3.4 - - - +
352A ARG* 3.1 40.9 + - + -
354A LYS* 3.4 27.8 - - - -
355A GLU* 3.9 22.4 - - + -
521A TYR* 3.2 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