Contacts of the helix formed by residues 309 - 325 (chain A) in PDB entry 4LXZ
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 THR 309 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLY 2.8 25.6 + - - +
274A ASP* 3.6 7.7 + - - -
275A ARG* 3.0 16.3 + - - +
308A TYR* 1.3 72.8 - - - +
310A ILE* 1.3 58.7 + - - +
311A ARG* 3.3 35.9 - - + +
312A ASN* 2.9 45.8 + - - +
313A VAL* 3.1 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO 5.3 0.9 - - - +
36A LYS* 4.2 35.4 - - + -
38A HIS* 4.2 10.3 - - + -
39A ARG* 3.8 30.8 - - + +
42A MET* 3.6 27.7 - - + +
307A GLY 4.6 1.3 - - - +
308A TYR* 3.6 15.2 + - - +
309A THR* 1.3 68.9 - - - +
311A ARG* 1.3 68.5 + - - +
313A VAL* 3.3 7.2 + - - +
314A ALA* 3.0 24.3 + - - +
341A TYR* 3.9 18.4 - - + -
405A PG4 5.2 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A MET* 4.0 4.7 - - - +
273A GLY 5.5 1.0 + - - -
309A THR* 3.5 25.8 - - + +
310A ILE* 1.3 80.4 - - - +
312A ASN* 1.3 68.9 + - - +
315A ARG* 3.1 49.3 + - - +
341A TYR* 3.1 33.9 - - + +
342A PHE* 3.3 22.0 - - + -
343A GLY 4.6 3.3 + - - -
405A PG4 3.6 38.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 3.5 20.8 - - + +
272A SER 3.7 20.0 + - - -
273A GLY* 4.9 2.4 + - - -
283A VAL* 4.4 0.2 - - - +
309A THR* 2.9 31.1 + - + +
311A ARG* 1.3 81.6 + - - +
313A VAL* 1.3 60.0 + - + +
315A ARG* 3.1 29.7 + - - +
316A CYS* 2.9 30.7 + - - +
350A ILE* 3.4 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG* 3.9 18.4 - - + +
43A THR* 4.5 1.1 - - - +
268A ALA* 4.1 13.5 - - + +
274A ASP* 5.2 0.4 - - - +
307A GLY* 3.4 39.5 - - - +
308A TYR 3.9 0.2 - - - +
309A THR 3.1 15.1 + - - +
310A ILE* 3.3 10.1 + - - +
312A ASN* 1.3 77.2 - - + +
314A ALA* 1.3 63.5 + - - +
316A CYS* 3.2 1.9 + - - +
317A TRP* 3.0 64.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG 4.5 0.6 + - - +
42A MET* 3.9 11.0 - - + +
43A THR* 3.4 32.3 + - - +
46A LEU* 4.2 3.1 - - + -
310A ILE 3.0 16.7 + - - +
311A ARG 3.7 4.9 - - - +
313A VAL* 1.3 77.2 - - - +
315A ARG* 1.3 58.4 + - - +
318A THR* 2.7 34.3 + - - -
342A PHE* 3.9 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.4 3.8 - - + +
283A VAL* 4.2 7.0 - - + -
311A ARG* 3.1 40.2 + - - +
312A ASN* 3.1 27.9 + - - +
313A VAL 3.3 0.2 - - - -
314A ALA* 1.3 75.5 - - - +
316A CYS* 1.3 58.9 + - - +
319A TYR* 3.0 31.7 + - - +
333A LEU* 5.2 0.2 - - + -
342A PHE* 3.0 48.0 + - + +
343A GLY 5.5 0.2 + - - -
345A ASP* 3.1 16.0 + - - -
347A LYS 2.8 27.6 + - - +
348A LEU* 3.1 40.6 + - + +
349A HIS 5.2 0.2 - - - -
350A ILE* 3.6 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ALA* 4.2 10.3 - - + -
271A LEU* 3.7 20.0 - - + -
283A VAL* 3.9 12.7 - - + +
286A HIS* 3.3 44.9 - - - -
312A ASN 2.9 19.9 + - - +
313A VAL 3.6 4.0 - - - +
315A ARG* 1.3 77.0 - - - +
317A TRP* 1.3 57.7 + - + +
319A TYR* 3.4 1.9 + - - +
320A GLU* 2.9 43.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG* 3.6 29.8 - - + -
40A ILE* 4.4 9.6 - - + -
43A THR* 3.6 21.1 - - + -
140A TRP* 3.4 63.5 - + + -
266A CYS 2.9 22.0 + - - -
268A ALA* 4.0 9.9 - - + +
304A GLY* 3.5 17.0 - - - -
305A GLY 3.6 15.5 - - - -
306A GLY 3.8 12.8 - - - -
313A VAL* 3.0 31.5 + - + +
316A CYS* 1.3 76.7 - - + +
318A THR* 1.4 56.0 + - - +
320A GLU* 3.5 16.6 - - - -
321A THR* 2.7 37.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A THR* 3.4 21.0 + - - +
46A LEU* 3.6 16.5 - - + +
47A LEU* 3.8 18.8 + - + -
50A TYR* 3.6 36.3 - - + -
52A LEU* 3.9 3.0 - - + +
314A ALA 2.7 23.3 + - - -
315A ARG 3.7 3.4 - - - -
317A TRP* 1.4 74.2 - - - +
319A TYR* 1.4 63.9 + - - +
321A THR* 3.3 6.9 + - - -
322A ALA* 3.1 19.9 + - - +
329A ILE* 4.1 7.0 - - + -
348A LEU* 4.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A VAL* 3.7 21.1 - - + -
284A LYS* 4.4 17.5 - - + +
287A ALA* 3.4 33.2 - - + -
291A GLU* 4.2 11.2 + - - -
315A ARG 3.0 17.4 + - - +
316A CYS 3.8 0.2 - - - +
318A THR* 1.4 77.2 - - - +
320A GLU* 1.3 51.2 + - - +
322A ALA* 3.1 8.7 + - + +
323A VAL* 2.8 46.9 + - + +
327A CYS 6.0 1.1 - - - -
328A GLU* 6.4 0.7 - - - -
329A ILE* 4.4 17.9 - - + -
348A LEU* 3.9 15.5 - - + -
349A HIS* 3.6 32.9 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TRP* 4.0 13.9 - - + -
266A CYS* 3.8 9.5 - - - +
286A HIS* 2.5 36.6 + - - +
287A ALA* 3.2 34.1 + - + -
290A VAL* 3.8 22.1 - - + +
302A MET* 3.7 8.8 - - + +
316A CYS* 2.9 19.9 + - - +
317A TRP* 3.5 22.1 - - - +
319A TYR* 1.3 71.8 - - - +
321A THR* 1.4 60.1 + - - +
323A VAL* 3.4 7.1 + - - +
324A ALA* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 5.4 3.4 - - + -
18A TYR* 4.5 4.3 - - + -
47A LEU* 3.8 13.4 - - + +
52A LEU* 4.4 4.9 - - + -
56A MET* 3.7 38.8 - - + -
138A VAL* 4.6 4.3 - - + +
140A TRP* 3.0 24.3 + - - -
302A MET* 5.3 0.2 - - - -
317A TRP 2.7 22.6 + - - -
318A THR 3.3 5.1 + - - -
320A GLU* 1.4 76.0 - - - +
322A ALA* 1.3 62.8 + - - +
324A ALA* 3.1 8.7 + - - +
325A LEU* 3.0 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.9 17.4 - - + +
318A THR 3.1 12.9 + - - +
319A TYR* 3.1 12.1 + - + +
321A THR* 1.3 74.6 - - - +
323A VAL* 1.3 58.2 + - - +
325A LEU* 3.2 4.3 + - - +
326A ASP 3.0 7.4 + - - -
327A CYS 2.9 46.4 + - - +
329A ILE* 3.8 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ALA* 4.3 4.7 - - + +
290A VAL* 3.8 21.5 - - + -
291A GLU* 3.6 38.1 - - + +
294A LYS* 3.4 14.4 - - + +
319A TYR* 2.8 54.1 + - + +
320A GLU* 3.7 7.2 - - - +
321A THR 3.2 0.2 - - - -
322A ALA* 1.3 72.5 - - - +
324A ALA* 1.4 65.0 + - - +
326A ASP* 3.0 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LYS* 4.8 2.4 + - - +
16A VAL* 3.7 18.2 - - + +
136A MET* 3.2 39.5 - - - +
138A VAL* 4.9 2.5 - - + -
290A VAL* 4.8 0.9 - - - +
294A LYS* 3.3 17.1 - - - +
302A MET* 4.0 15.5 - - + -
320A GLU 2.9 15.3 + - - +
321A THR* 3.3 13.0 - - - +
323A VAL* 1.4 75.0 - - - +
325A LEU* 1.3 58.5 + - - +
326A ASP* 4.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 4.2 12.5 + - - +
14A LYS 5.0 7.4 - - - +
16A VAL* 3.8 19.1 - - + +
52A LEU* 4.0 43.7 - - + +
55A LYS* 3.4 37.0 + - + +
56A MET* 3.8 24.0 - - + -
321A THR* 3.0 18.7 + - + +
322A ALA 3.6 6.7 - - - +
323A VAL 3.1 0.2 - - - -
324A ALA* 1.3 78.3 - - - +
326A ASP* 1.4 69.9 + - - +
327A CYS* 3.3 9.8 + - + +
----------------------------------------------------------
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