Contacts of the helix formed by residues 329 - 346 (chain A) in PDB entry 1GZK
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 ARG 329 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A HIS* 3.5 30.0 - - + +
270A ASP* 5.8 4.0 - - - +
272A VAL* 3.8 16.3 - - + +
328A GLY* 1.3 69.6 - - - -
330A ALA* 1.3 64.6 + - - +
332A ASP* 3.0 22.2 + - - +
333A TRP* 4.0 1.9 + - - -
394A GLY 2.8 29.1 + - - -
395A GLY* 3.8 16.9 + - - -
396A GLY 2.9 22.4 + - - -
397A PRO* 4.3 8.6 - - - +
399A ASP* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLU* 3.6 7.4 - - - +
328A GLY 3.0 2.5 + - - +
329A ARG* 1.3 79.3 - - - +
331A VAL* 1.3 57.9 + - - +
333A TRP* 2.7 32.4 + - - +
334A TRP 2.9 9.5 + - - -
389A PRO* 3.7 20.9 - - + -
392A ARG* 3.0 22.4 + - - +
395A GLY* 4.4 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A VAL* 3.9 19.1 - - + -
274A ARG* 4.4 11.8 - - - -
276A ILE* 5.7 0.2 - - - +
318A ALA* 3.8 7.9 - - + -
320A GLU* 3.4 15.7 - - - +
321A VAL* 3.5 20.0 - - + -
326A ASP 3.5 22.2 - - - +
327A TYR* 4.0 9.2 - - + -
328A GLY 3.1 15.9 + - - +
330A ALA* 1.3 76.1 - - - +
332A ASP* 1.3 64.0 - - - +
334A TRP* 3.5 7.6 - - - +
335A GLY* 2.9 24.1 + - - -
392A ARG* 3.9 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 3.7 21.4 - - + +
267A HIS* 2.6 32.4 + - + +
272A VAL* 3.6 6.1 - - - +
273A TYR* 2.7 33.2 + - - +
274A ARG* 3.0 27.8 + - - -
276A ILE* 4.1 9.6 - - - +
329A ARG 3.0 11.1 + - - +
330A ALA 2.9 0.8 + - - -
331A VAL* 1.3 81.4 - - - +
333A TRP* 1.3 58.7 + - - +
335A GLY* 3.2 2.0 + - - +
336A LEU* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 3.8 26.7 - - + -
263A LEU* 3.7 32.8 - - + -
264A GLU 4.7 0.4 - - - -
267A HIS* 3.6 13.8 - + - -
329A ARG 4.1 10.5 - - - -
330A ALA* 2.7 10.6 + - - +
332A ASP* 1.3 73.1 - - - +
334A TRP* 1.3 67.0 + - - +
336A LEU* 3.0 29.7 + - + +
337A GLY 2.9 19.1 + - - -
384A LEU* 3.7 10.4 - - + +
392A ARG* 4.1 9.0 - - - -
393A LEU 3.5 17.9 - - - +
394A GLY* 3.0 35.5 + - - -
395A GLY 4.1 0.2 - - - -
399A ASP* 3.1 22.2 + - - -
400A ALA* 3.6 26.9 - - + -
403A VAL* 4.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A TYR* 2.9 29.5 + + - -
317A LEU 3.8 5.8 - - - -
318A ALA* 3.3 25.5 - - + +
319A PRO* 3.6 33.2 - - + -
330A ALA 2.9 4.6 + - - -
331A VAL 3.5 7.2 - - - +
333A TRP* 1.3 75.2 - - - +
335A GLY* 1.3 66.8 + - - +
337A GLY* 3.1 2.9 + - - -
338A VAL* 3.1 37.3 + - + +
349A PRO* 6.5 0.2 - - + -
350A PHE* 6.1 0.7 - + - -
362A ILE* 3.9 18.8 - - + -
367A ILE* 4.3 17.0 - - + -
384A LEU 3.6 10.8 - - - -
385A LEU* 3.4 48.0 - - + +
386A LYS 4.1 7.4 - - - -
387A LYS* 4.7 8.1 - - + -
392A ARG* 3.3 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ILE* 3.8 22.4 - - - +
331A VAL 2.9 15.9 + - - -
332A ASP 3.2 4.0 + - - -
333A TRP 3.2 0.4 - - - -
334A TRP* 1.3 86.2 - - - +
336A LEU* 1.3 58.4 + - - +
338A VAL* 3.6 5.8 + - - +
339A VAL* 3.0 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLY* 4.2 4.7 - - - +
259A ILE* 3.7 32.5 - - + -
260A VAL* 3.6 26.7 - - + -
263A LEU* 4.6 3.6 - - + -
276A ILE* 4.0 5.4 - - - +
332A ASP 2.9 13.8 + - - +
333A TRP* 3.0 29.8 + - + +
335A GLY* 1.3 75.4 - - - +
337A GLY* 1.3 60.3 + - - +
339A VAL* 3.2 3.8 + - + +
340A MET* 3.0 59.6 + - + +
384A LEU* 3.9 9.4 - - + -
403A VAL* 4.3 4.5 - - + -
409A PHE* 5.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A TRP 2.9 10.5 + - - -
334A TRP 3.1 2.6 + - - -
336A LEU* 1.3 75.3 - - - +
338A VAL* 1.3 59.7 + - - +
340A MET* 3.3 1.5 + - - -
341A TYR* 2.8 31.9 + - - +
381A LEU* 3.7 6.5 - - - +
384A LEU* 3.4 31.1 - - - +
385A LEU* 3.8 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ILE 6.1 0.2 - - - +
277A LYS* 6.4 2.2 - - + -
316A TYR* 4.2 23.1 - - + +
334A TRP* 3.1 41.0 + - + +
335A GLY* 4.0 5.8 - - - +
337A GLY* 1.3 74.9 - - - +
339A VAL* 1.3 64.6 + - + +
341A TYR* 3.7 6.7 - - - +
342A GLU* 3.2 22.2 + - - +
348A LEU* 3.5 29.0 - - + +
349A PRO* 4.8 6.1 - - + -
385A LEU* 3.6 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ILE* 4.4 9.4 - - + -
276A ILE* 3.9 9.2 - - + -
277A LYS* 3.6 30.5 - - - -
278A LEU* 3.8 14.1 - - + +
281A LEU* 3.8 24.0 - - + -
335A GLY 3.0 22.9 + - - +
336A LEU* 3.4 6.7 - - + +
337A GLY 3.1 0.2 - - - -
338A VAL* 1.3 81.0 - - + +
340A MET* 1.3 60.3 + - + +
342A GLU* 3.5 5.9 + - - +
343A MET* 3.2 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ALA* 4.9 9.9 - - + +
256A GLY* 3.8 19.5 - - - -
336A LEU* 3.0 38.0 + - + +
337A GLY* 4.4 0.4 - - - -
339A VAL* 1.3 76.7 - - + +
341A TYR* 1.3 61.3 + - - +
342A GLU 3.2 0.4 - - - -
343A MET* 3.5 19.1 - - + +
344A MET* 2.9 42.3 + - - +
380A LEU* 3.7 22.2 - - + -
381A LEU* 4.2 8.5 - - + -
384A LEU* 3.1 37.0 - - + -
408A PHE* 5.5 2.7 - - - -
409A PHE* 4.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A GLY 2.8 18.4 + - - +
338A VAL* 3.7 9.9 - - - +
340A MET* 1.3 75.9 - - - +
342A GLU* 1.3 58.3 + - - +
345A CYS* 2.9 47.7 + - + +
347A ARG* 3.3 31.0 + - + -
348A LEU 3.8 2.1 + - - -
349A PRO* 3.7 34.7 + - + +
367A ILE* 3.3 23.6 - - + +
368A ARG 2.8 23.0 + - - -
369A PHE* 3.9 15.9 - + - -
370A PRO* 4.4 3.7 - - + +
381A LEU* 3.7 16.9 - - + +
385A LEU* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PHE* 5.7 1.9 - - - -
241A LEU* 3.8 14.3 - - + +
278A LEU* 3.5 35.4 - - + +
279A GLU* 5.5 1.9 - - - +
338A VAL* 3.2 13.4 + - - +
339A VAL* 3.9 5.7 - - - +
340A MET 3.2 0.4 - - - -
341A TYR* 1.3 81.8 - - - +
343A MET* 1.3 56.7 + - - +
346A GLY* 2.7 34.8 + - - +
347A ARG* 3.6 28.4 - - - +
348A LEU* 3.8 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU* 3.3 26.9 - - + -
241A LEU* 4.2 14.4 - - + -
246A VAL* 2.7 25.3 - - - +
247A PHE* 2.7 32.9 + - + +
252A ALA* 4.1 16.8 - - + -
255A TYR* 3.3 44.2 - - + -
256A GLY* 5.7 0.2 - - - -
259A ILE* 6.1 0.7 - - + -
278A LEU* 5.2 1.8 - - + -
281A LEU* 5.3 0.4 - - + -
339A VAL* 3.2 27.6 + - + +
340A MET* 3.1 25.7 + - - +
342A GLU* 1.3 78.9 - - - +
344A MET* 1.3 52.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 2.7 22.5 - - - +
247A PHE 4.1 5.0 - - - +
249A GLU* 4.1 20.0 - - + +
252A ALA* 3.4 31.9 - - + -
340A MET* 2.9 20.5 + - - +
341A TYR 4.4 0.9 - - - +
343A MET* 1.3 74.6 - - - +
345A CYS* 1.3 56.2 + - - +
372A THR* 5.6 3.3 - - - +
373A LEU* 3.8 26.1 - - + +
377A ALA* 3.2 35.9 - - + +
380A LEU* 5.9 2.7 - - + -
381A LEU* 3.6 25.6 - - + -
408A PHE* 4.4 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ARG* 4.9 2.9 - - - -
246A VAL* 3.7 10.3 - - - +
341A TYR* 2.9 50.6 + - + +
344A MET* 1.3 78.8 - - - +
346A GLY* 1.3 59.1 + - - +
347A ARG* 3.4 24.6 + - - +
370A PRO* 3.5 39.0 - - + -
373A LEU* 4.1 15.3 - - - -
381A LEU* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU* 5.4 1.8 - - - +
245A ARG* 2.9 40.1 - - - +
246A VAL* 3.7 3.6 - - - +
342A GLU* 2.7 29.7 + - - +
345A CYS* 1.3 72.2 - - - +
347A ARG* 1.3 60.6 + - - +
----------------------------------------------------------
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