Contacts of the helix formed by residues 360 - 370 (chain A) in PDB entry 5X1A
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* 3.9 9.2 - - + -
333A HIS* 5.7 0.2 - - - -
356A ASN* 3.1 24.9 + - - +
357A GLY* 3.4 15.4 + - - -
358A THR 3.4 0.2 - - - -
359A GLU* 1.3 95.0 + - + +
361A ARG* 1.3 63.7 + - - +
362A MET 3.3 2.8 + - - -
363A SER* 3.3 8.6 + - - -
364A VAL* 2.9 36.4 + - + +
420A ILE* 3.8 30.0 - - + +
425A HIS* 4.2 8.7 - - - +
432A ASN* 3.0 23.2 + - - -
434A PHE* 3.9 5.3 - - + -
----------------------------------------------------------
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* 3.6 5.9 - - - -
70A ILE 3.4 33.1 + - - +
71A ASP* 3.5 12.2 + - - +
101A THR* 2.9 27.0 + - - +
280A THR* 3.3 25.7 - - - +
329A THR* 2.9 34.2 + - - +
330A GLY* 3.7 28.3 - - - +
331A SER 4.4 0.9 - - - +
357A GLY 3.2 8.9 + - - +
358A THR* 3.9 7.4 + - - +
359A GLU 3.5 2.4 - - - -
360A GLU* 1.3 76.8 - - - +
362A MET* 1.3 69.5 + - + +
364A VAL* 3.3 1.9 + - - +
365A ILE* 3.1 40.1 + - + +
384A THR* 3.2 22.8 + - - +
----------------------------------------------------------
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 ILE* 3.6 31.0 - - + -
67A PRO 4.6 0.9 - - - +
69A GLY* 3.6 20.9 - - - +
99A GLY 3.8 14.1 + - - +
100A GLY* 3.1 35.7 - - - +
101A THR* 3.9 5.4 + - - +
359A GLU 5.0 0.2 + - - -
360A GLU 3.4 0.4 - - - -
361A ARG* 1.3 92.8 - - - +
363A SER* 1.3 57.4 + - - +
365A ILE* 4.7 0.2 - - - -
366A TRP* 3.0 24.3 + - - +
380A PHE* 3.3 20.4 - - + -
384A THR* 3.7 34.3 - - + +
412A TRP* 3.7 12.3 - - + -
----------------------------------------------------------
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 3.5 + - - -
359A GLU 5.2 3.1 + - - -
360A GLU* 3.3 12.4 + - - -
362A MET* 1.3 78.6 - - - +
364A VAL* 1.3 58.0 + - - +
366A TRP 3.3 1.0 + - - -
367A ASP 3.0 23.6 + - - -
412A TRP* 3.7 9.9 - - - -
420A ILE* 5.8 2.5 - - - -
439A CYS* 3.3 20.6 - - - -
440A ARG 3.4 3.8 - - - +
441A GLY 2.8 28.1 + - - -
442A SER* 3.9 7.3 - - - -
443A PRO* 4.7 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 3.9 20.2 - - + +
283A LEU* 3.9 16.6 - - + +
284A GLY* 3.7 26.5 - - - +
360A GLU* 2.9 30.2 + - + +
361A ARG 3.8 3.4 - - - +
363A SER* 1.3 75.4 - - - +
365A ILE* 1.3 59.7 + - + +
367A ASP* 3.3 0.9 + - - +
368A LYS* 2.8 40.2 + - + +
420A ILE* 4.2 16.8 - - + -
434A PHE* 5.0 4.7 - - + -
437A MET* 4.5 9.9 - - + -
439A CYS* 3.9 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 6.4 0.2 - - - -
283A LEU* 4.1 20.4 - - + -
318A ASN* 4.6 7.0 - - - +
321A LEU* 4.6 5.8 - - + -
329A THR* 3.4 39.5 - - + +
361A ARG* 3.1 27.3 + - + +
362A MET 4.0 3.1 - - - +
364A VAL* 1.3 73.8 - - + +
366A TRP* 1.3 66.9 + - - +
368A LYS 4.5 0.2 - - - +
369A ALA* 2.8 36.0 + - + +
370A VAL* 3.5 0.7 + - - +
375A MET* 4.6 1.1 - - - -
380A PHE* 3.7 20.2 - - + -
383A VAL* 4.2 15.9 - - + -
384A THR* 4.0 12.3 - - + -
----------------------------------------------------------
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* 3.6 29.6 - - + -
362A MET 3.0 18.4 + - - +
363A SER 3.6 5.2 - - - +
365A ILE* 1.3 76.2 - - - +
367A ASP* 1.3 58.2 + - - +
370A VAL* 3.1 39.5 + - + +
371A VAL* 3.0 41.7 + - + +
377A GLU* 4.0 12.3 - - + -
380A PHE* 3.6 43.4 - + + -
412A TRP* 3.4 24.7 - + + -
414A PRO* 3.3 37.0 + - + +
440A ARG* 3.4 16.8 - - - +
441A GLY* 3.8 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A SER 3.0 17.5 + - - +
364A VAL* 3.7 2.7 - - - +
366A TRP* 1.3 79.8 - - - +
368A LYS* 1.3 76.1 + - + +
371A VAL* 3.6 17.3 - - - +
372A THR* 3.6 13.9 - - - +
437A MET* 5.8 2.6 - - - +
438A GLU 3.9 7.5 - - - +
439A CYS* 3.6 20.9 - - - -
440A ARG* 2.9 34.9 + - - +
----------------------------------------------------------
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 3.6 21.3 - - - +
284A GLY* 4.8 10.2 + - - +
314A PRO* 4.3 12.0 - - - +
315A ASP* 3.7 24.9 + - - +
318A ASN* 3.5 23.9 - - - +
364A VAL* 2.8 30.8 + - + +
367A ASP* 1.3 87.6 - - + +
369A ALA* 1.3 54.5 + - - +
372A THR* 2.7 27.2 + - + +
374A LYS* 4.1 10.2 + - - +
437A MET* 5.5 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ASN* 3.6 17.7 - - + +
322A SER* 4.2 6.5 - - - +
365A ILE* 2.8 16.9 + - + +
368A LYS* 1.3 79.2 - - - +
370A VAL* 1.3 59.2 + - - +
372A THR* 3.4 5.4 - - - -
374A LYS* 2.9 30.2 + - - +
375A MET* 2.9 40.6 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
365A ILE 4.2 1.3 - - - +
366A TRP* 3.1 59.3 + - + +
369A ALA* 1.3 75.7 - - - +
371A VAL* 1.3 70.0 + - + +
372A THR 3.1 1.1 - - - -
373A GLY* 2.9 14.7 + - - -
375A MET* 3.4 33.0 - - + +
376A ASP* 4.2 8.5 - - - +
377A GLU 4.6 1.1 - - - +
380A PHE* 3.8 21.1 - - + -
----------------------------------------------------------
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