Contacts of the helix formed by residues 359 - 368 (chain A) in PDB entry 2P6U
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 LYS 359 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASP* 4.6 5.6 + - - +
356A LYS* 6.2 4.3 - - - +
357A ARG 4.5 4.3 - - - +
358A ILE* 1.3 77.4 - - - +
360A VAL* 1.3 67.1 + - - +
361A SER* 2.8 11.3 + - - +
362A GLU* 2.8 29.4 + - + +
363A TYR* 3.1 9.9 + - - +
397A TYR* 4.0 0.9 - - - -
403A GLU* 3.6 27.1 - - + +
706A PO4 2.7 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ILE 3.8 1.8 + - - -
359A LYS* 1.3 70.3 - - - +
361A SER* 1.3 48.7 + - - -
363A TYR* 3.4 1.6 + - - +
364A LYS* 2.7 57.8 + - + +
396A ARG* 3.8 29.4 - - + +
397A TYR* 3.8 23.3 - - + +
400A GLY 3.8 7.6 - - - +
401A GLU 3.3 26.9 - - - +
402A PRO* 3.3 14.1 - - + -
403A GLU* 2.5 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LYS* 2.8 9.6 + - - -
360A VAL* 1.3 73.9 - - - +
362A GLU* 1.3 56.7 + - - -
364A LYS* 3.1 7.3 + - - +
365A GLN* 2.7 37.2 + - - +
402A PRO* 4.1 8.6 - - - +
403A GLU* 2.8 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PRO* 3.8 23.1 - - + +
350A ARG* 4.4 18.0 + - - -
356A LYS* 5.8 2.3 - - - -
357A ARG 5.0 0.2 - - - +
358A ILE* 3.2 25.3 - - + +
359A LYS* 2.8 36.5 + - + +
361A SER* 1.3 76.3 - - - +
363A TYR* 1.3 57.3 + - - +
365A GLN* 3.2 13.8 + - - +
366A MET* 2.8 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLU* 2.5 46.9 + - - +
209A GLY 5.2 0.2 + - - -
345A VAL* 4.7 16.6 - - + -
348A LEU* 5.1 3.8 - - + -
358A ILE* 3.9 5.3 - - + +
359A LYS 3.1 4.9 + - - +
360A VAL 3.6 7.4 - - - +
362A GLU* 1.3 78.5 - - - +
364A LYS* 1.3 62.0 + - + +
366A MET* 3.0 11.9 + - + +
367A ALA* 2.7 52.4 + - + +
381A ALA* 4.5 5.9 + - + -
383A ILE* 3.2 39.6 - - + +
397A TYR* 3.3 51.6 - + + -
398A ILE* 4.2 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A THR* 6.1 2.0 - - - +
202A ARG* 5.5 2.8 + - - +
208A GLU* 3.1 27.9 + - - +
360A VAL* 2.7 36.5 + - + +
361A SER* 3.4 6.5 - - - +
363A TYR* 1.3 77.4 - - + +
365A GLN* 1.3 54.0 + - - +
367A ALA* 3.6 3.1 - - + +
368A GLY* 2.7 34.0 + - - -
397A TYR 3.2 16.3 + - - -
398A ILE 3.0 24.9 + - - -
400A GLY 3.9 16.1 + - - -
402A PRO* 4.9 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLU* 5.8 1.2 - - - +
330A PRO 5.8 2.4 + - - -
332A LEU 4.1 13.5 - - - +
361A SER 2.7 16.7 + - - +
362A GLU* 3.5 16.7 + - - +
364A LYS* 1.3 72.7 - - - +
366A MET* 1.3 66.8 + - - +
368A GLY* 2.9 18.7 + - - -
369A ARG* 3.2 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 3.7 53.4 - - + -
330A PRO* 4.7 17.3 - - + -
343A VAL* 3.6 12.2 - - - +
345A VAL* 4.1 25.8 - - + -
358A ILE* 3.9 20.0 - - + -
362A GLU* 2.8 50.3 + - + +
363A TYR* 3.3 12.1 - - - +
365A GLN* 1.3 75.8 - - + +
367A ALA* 1.3 63.8 + - - +
369A ARG* 3.2 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 3.7 15.3 - - + +
208A GLU* 4.6 2.0 - - - +
343A VAL* 4.6 2.9 - - - +
345A VAL* 5.2 0.6 - - - +
363A TYR* 2.7 47.5 + - + +
364A LYS* 3.7 4.9 - - + +
366A MET* 1.3 73.1 - - - +
368A GLY* 1.3 52.5 + - - +
369A ARG 2.6 13.9 + - - -
370A ALA* 2.9 23.6 + - - +
381A ALA* 3.6 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO 6.5 0.4 - - - -
49A THR* 3.9 22.6 + - - +
202A ARG* 4.5 21.9 + - - -
206A LEU* 4.7 1.8 - - - +
364A LYS 2.7 20.5 + - - -
365A GLN* 2.9 10.3 + - - -
367A ALA* 1.3 69.8 - - - +
369A ARG* 1.3 59.6 + - - +
370A ALA 3.5 0.9 - - - -
371A GLY* 4.8 3.4 + - - -
----------------------------------------------------------
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