Contacts of the helix formed by residues 357 - 369 (chain A) in PDB entry 1N9P
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 SER 357 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 5.0 0.2 - - - -
282A ASP* 2.9 41.2 + - - -
283A LEU 3.3 26.2 - - - -
284A SER* 3.6 7.6 - - - -
323A TRP* 4.7 0.4 - - - -
356A TYR* 1.3 75.5 - - - +
358A VAL* 1.3 60.2 + - - +
359A LYS 3.6 0.7 + - - -
360A GLU* 2.9 26.3 + - - +
361A GLN* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LYS* 5.3 6.5 - - - +
209A LEU* 4.0 27.1 - - + +
274A ILE* 3.5 47.8 - - + +
275A ASP* 4.3 2.0 - - - -
280A PHE 5.1 0.4 + - - -
281A TYR* 3.2 18.3 + - + +
283A LEU 4.6 1.0 + - - -
356A TYR 4.0 0.2 + - - -
357A SER* 1.3 73.3 - - - +
359A LYS* 1.3 63.3 + - - +
361A GLN* 3.2 15.6 + - - +
362A GLU* 3.0 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A TYR* 2.9 56.8 + - + +
282A ASP* 3.5 35.2 + - + +
358A VAL* 1.3 74.5 - - - +
360A GLU* 1.3 53.1 + - - +
362A GLU* 3.2 3.8 + - - +
363A GLU* 2.7 62.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ASP* 4.0 8.1 - - - +
284A SER* 3.9 9.0 + - - -
286A ARG* 3.3 29.3 + - - -
356A TYR* 3.3 16.8 - - + +
357A SER* 2.9 40.7 + - - +
359A LYS* 1.3 77.6 - - - +
361A GLN* 1.3 52.3 + - - +
363A GLU* 3.1 19.9 + - - +
364A MSE 2.8 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A MSE 4.3 21.1 - - - +
209A LEU* 4.6 10.3 + - - +
354A PRO* 4.1 24.2 - - - +
356A TYR* 4.1 20.5 + - + -
357A SER 2.9 18.5 + - - +
358A VAL* 3.2 27.1 + - - +
360A GLU* 1.3 74.6 - - - +
362A GLU* 1.3 60.4 + - + +
364A MSE 3.3 13.7 + - + +
365A LEU* 2.9 34.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
208A LYS* 5.1 6.8 + - - -
275A ASP* 5.1 2.8 - - - +
276A ALA* 4.8 7.7 + - - +
281A TYR* 2.6 40.0 + - - +
358A VAL* 3.0 25.2 + - + +
359A LYS 3.6 6.7 - - - +
361A GLN* 1.3 74.2 - - + +
363A GLU* 1.3 61.1 + - - +
365A LEU* 3.3 18.7 + - + +
366A LEU* 3.0 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ASP* 5.3 0.3 - - - +
359A LYS* 2.7 46.3 + - + +
360A GLU* 3.1 27.7 + - - +
362A GLU* 1.3 77.1 - - - +
364A MSE 1.3 58.1 + - + +
366A LEU* 3.4 14.4 + - + +
367A MSE 3.1 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TYR* 3.3 56.8 - - + -
360A GLU* 2.8 35.3 + - + +
361A GLN* 3.6 12.1 - - + +
362A GLU 3.2 0.2 - - - -
363A GLU* 1.3 75.7 - - + +
365A LEU* 1.3 63.7 - - - +
367A MSE 3.5 20.0 - - + +
368A SER* 3.1 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A GLN* 2.9 21.7 + - + +
362A GLU* 3.5 21.8 - - + +
363A GLU 3.2 0.4 - - - -
364A MSE 1.3 76.1 - - - +
366A LEU* 1.3 64.2 + - + +
368A SER* 2.5 28.7 + - - +
369A SER* 3.6 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLU* 3.0 17.9 + - + +
363A GLU* 3.6 15.5 - - + +
365A LEU* 1.3 77.8 - - + +
367A MSE 1.3 57.0 + - - +
368A SER 3.2 0.6 + - - -
369A SER* 3.0 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A GLU* 3.1 32.7 + - + +
364A MSE 3.5 24.9 - - + +
366A LEU* 1.3 77.1 - - - +
368A SER* 1.3 61.2 - - - +
369A SER 3.3 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A MSE 3.1 14.5 + - - -
365A LEU* 2.5 29.3 + - - +
366A LEU 3.2 0.4 - - - -
367A MSE 1.3 76.6 - - - +
369A SER* 1.3 63.5 + - - +
370A PRO* 3.2 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU 3.6 4.0 + - - -
366A LEU* 3.0 19.2 + - - +
367A MSE 4.1 6.1 - - - +
368A SER* 1.3 80.4 + - - +
370A PRO* 1.3 69.1 - - - +
----------------------------------------------------------
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