Contacts of the helix formed by residues 360 - 370 (chain A) in PDB entry 5NKS
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 GLU 360 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 4.0 15.3 - - + -
356A ASN* 3.2 24.7 + - - +
357A GLY* 3.4 14.2 + - - -
358A ILE 3.4 0.4 - - - -
359A GLU* 1.3 96.4 + - + +
361A ARG* 1.3 54.9 + - - +
362A MET 3.5 2.0 - - - -
363A SER* 3.3 8.8 + - - +
364A MET* 2.8 35.1 + - + +
420A ILE* 3.7 36.4 - - + +
425A HIS* 4.5 1.9 - - - +
427A LEU* 5.0 3.0 - - - +
432A ASN* 2.9 24.0 + - - -
434A PHE* 3.7 10.5 - - + -
439A CYS* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY* 3.5 5.7 - - - -
70A VAL 3.3 32.8 + - - +
71A ASP* 3.5 13.7 + - - +
101A THR* 2.9 26.8 + - - +
280A THR* 3.4 24.2 - - - +
329A THR* 3.0 42.0 + - - +
330A GLY* 3.6 29.6 - - - +
331A SER 4.1 1.6 - - - +
357A GLY 3.2 9.9 + - - +
358A ILE* 4.1 6.5 - - - +
359A GLU 3.4 2.4 - - - -
360A GLU* 1.3 76.0 - - - +
362A MET* 1.3 70.0 + - - +
364A MET* 3.8 0.3 - - - +
365A VAL* 2.9 32.5 + - + +
384A THR* 3.2 22.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 4.1 17.7 - - + -
67A PRO 4.4 0.9 - - - +
69A GLY* 3.8 21.5 - - - +
99A GLY 3.2 26.1 + - - +
100A GLY* 3.9 15.0 - - - +
101A THR* 3.8 13.7 + - - +
358A ILE 5.4 0.2 + - - -
360A GLU 3.5 0.4 - - - -
361A ARG* 1.3 83.8 - - - +
363A SER* 1.3 58.8 + - - +
365A VAL* 4.7 1.3 - - - -
366A TRP* 3.0 25.3 + - - +
380A PHE* 3.3 35.3 - - + -
384A THR* 3.7 29.2 - - - +
410A VAL* 5.0 1.3 - - + -
412A TRP* 3.7 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLY* 4.9 1.6 + - - -
359A GLU 5.4 1.5 + - - -
360A GLU* 3.3 10.3 + - - -
362A MET* 1.3 75.6 - - - +
364A MET* 1.3 61.3 + - - +
366A TRP* 3.7 1.2 - - - +
367A GLU* 2.8 31.0 + - - +
412A TRP* 3.7 9.9 - - - -
418A LYS* 6.6 0.2 - - - -
420A ILE* 6.1 1.3 - - - -
439A CYS* 3.8 15.6 - - - +
440A ARG 3.8 2.4 - - - +
441A GLY 2.8 25.7 + - - -
442A ALA* 3.8 9.0 - - - +
443A PRO* 4.2 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 3.9 16.6 - - + +
283A LEU* 4.4 9.6 - - + +
284A GLY* 3.6 27.8 - - - +
360A GLU* 2.8 21.6 + - + +
361A ARG 3.9 2.5 - - - +
363A SER* 1.3 70.7 - - - +
365A VAL* 1.3 62.7 + - + +
367A GLU* 3.8 3.9 - - - +
368A LYS* 2.9 39.8 + - + +
420A ILE* 3.8 18.8 - - + -
434A PHE* 3.9 25.4 - - + -
437A VAL* 4.0 14.6 - - + -
439A CYS* 3.8 23.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 6.3 0.9 - - - -
283A LEU* 3.9 16.4 - - + -
321A LEU* 5.4 0.2 - - + -
329A THR* 3.7 31.2 - - + +
361A ARG* 2.9 25.9 + - + +
362A MET 3.8 3.4 - - - +
364A MET* 1.3 76.8 - - + +
366A TRP* 1.3 57.2 + - - +
368A LYS* 4.9 0.4 - - - -
369A CYS* 2.8 54.6 + - + +
380A PHE* 3.7 21.5 - - + -
383A VAL* 4.1 13.5 - - + -
384A THR* 4.0 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A MET* 3.8 26.2 - - + -
66A LEU* 4.8 2.5 - - + -
362A MET 3.0 17.6 + - - +
363A SER 3.7 4.5 - - - +
365A VAL* 1.3 78.3 - - - +
367A GLU* 1.3 56.5 + - - +
370A VAL* 2.9 56.7 + - + +
371A ALA* 2.9 22.7 + - + +
377A GLU* 4.0 14.6 - - + -
380A PHE* 3.5 47.6 - + + -
412A TRP* 3.3 31.9 - + + -
414A PRO* 3.6 28.9 + - + +
440A ARG* 3.1 25.5 - - - +
441A GLY* 3.8 5.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A SER 2.8 20.5 + - - +
364A MET* 3.8 6.7 - - - +
366A TRP* 1.3 75.7 - - - +
368A LYS* 1.3 71.4 + - + +
371A ALA* 3.5 13.0 - - - +
372A SER* 3.8 6.6 + - - -
437A VAL* 5.6 1.8 - - + -
438A GLU 3.7 16.7 - - - +
439A CYS* 3.8 24.5 - - + -
440A ARG* 2.8 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 3.3 29.4 + - + +
284A GLY* 5.5 1.6 - - - -
314A ALA* 4.0 15.4 - - + +
315A ASP* 3.1 25.6 + - - +
318A THR* 3.3 32.5 - - + +
364A MET* 2.9 32.2 + - + +
365A VAL* 4.2 2.0 - - - +
367A GLU* 1.3 83.1 - - + +
369A CYS* 1.3 59.6 + - - +
372A SER* 2.6 25.2 + - - -
374A LYS* 4.3 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 5.5 0.9 - - - -
318A THR* 3.9 21.1 - - - -
321A LEU* 4.0 19.3 - - - -
365A VAL* 2.8 36.2 + - + +
368A LYS* 1.3 79.6 - - - +
370A VAL* 1.3 58.9 + - + +
372A SER* 3.0 16.9 + - - -
374A LYS* 3.1 2.9 + - - -
375A MET* 2.9 59.2 + - + -
380A PHE* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A TRP* 2.9 53.5 + - + +
369A CYS* 1.3 75.7 - - + +
371A ALA* 1.3 62.7 + - - +
372A SER 3.1 1.8 - - - -
373A GLY* 3.0 19.6 + - - -
375A MET* 3.4 14.7 - - + +
376A ASP* 3.9 10.1 - - - +
377A GLU* 4.4 7.4 - - + +
380A PHE* 3.7 34.5 - - + -
----------------------------------------------------------
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