Contacts of the helix formed by residues 294 - 312 (chain E) in PDB entry 4QOZ
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 CYS 294 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E GLU* 4.2 8.5 - - - -
171E GLN* 4.5 4.0 - - - -
173E TYR* 6.0 1.3 - - - -
190E THR 4.0 10.0 + - - +
291E ARG* 3.3 28.2 - - + +
292E PRO 3.1 5.1 + - - -
293E HIS* 1.3 77.8 - - - +
295E GLY* 1.3 67.5 + - - +
296E LEU* 3.3 16.3 + - - -
297E ASP* 3.7 19.7 - - - +
298E ASP* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 295 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E ASP* 3.8 18.0 - - - +
136E GLU* 3.6 13.6 - - - +
153E GLU* 2.9 27.5 + - - -
155E PRO* 3.7 7.3 - - - +
294E CYS* 1.3 71.4 - - - +
296E LEU* 1.3 61.1 + - - +
298E ASP* 3.5 3.4 + - - +
299E SER* 3.0 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E GLU* 3.2 7.2 + - - +
155E PRO* 3.9 15.5 - - + +
157E VAL* 3.9 22.2 - - + -
169E THR* 4.0 22.4 - - - +
170E PHE 4.3 6.5 - - - +
171E GLN* 3.3 41.3 - - + +
294E CYS* 3.4 4.2 - - - -
295E GLY* 1.3 74.0 - - - +
297E ASP* 1.3 60.7 + - - +
299E SER* 3.2 4.6 + - - -
300E LYS* 2.9 50.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 297 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E TYR* 3.3 6.3 - - - +
289E ASP 4.2 3.3 - - - +
290E GLY* 3.4 13.5 - - - -
291E ARG* 2.7 47.4 + - - +
294E CYS* 3.4 13.0 + - - +
296E LEU* 1.3 77.8 - - - +
298E ASP* 1.3 62.6 + - - +
300E LYS* 3.2 16.7 + - - +
301E ASN* 2.7 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 298 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D A 4.7 5.4 + - - -
134E ASP* 3.4 22.1 - - - +
136E GLU* 4.1 6.6 - - - +
277E LEU* 3.9 17.2 - - + +
288E TYR* 2.3 36.5 + - - -
292E PRO* 3.8 0.2 - - - +
293E HIS* 3.1 32.1 + - - -
294E CYS 2.9 18.5 + - - +
295E GLY* 3.8 3.6 - - - +
297E ASP* 1.3 75.1 - - - +
299E SER* 1.3 58.3 + - - +
301E ASN* 3.2 3.0 + - - +
302E ILE* 2.9 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 299 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E ILE* 3.5 28.6 + - - +
134E ASP* 3.4 24.6 + - - +
155E PRO* 3.7 8.3 - - - +
157E VAL* 3.5 19.7 - - - +
295E GLY 3.0 17.8 + - - -
296E LEU* 3.4 10.1 - - - -
298E ASP* 1.3 76.0 - - - +
300E LYS* 1.3 63.2 + - - +
302E ILE* 3.4 4.4 + - - -
303E ALA* 3.0 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 300 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E VAL* 3.9 11.4 - - + -
166E ILE* 4.0 18.3 - - + +
169E THR* 3.9 24.7 + - - +
289E ASP 5.7 1.6 - - - +
296E LEU* 2.9 37.5 + - + +
297E ASP* 3.6 19.8 + - - +
299E SER* 1.3 76.3 - - - +
301E ASN* 1.3 60.6 + - - +
303E ALA* 3.0 11.6 + - - +
304E ARG* 3.0 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 301 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E LEU* 4.3 11.0 - - + -
281E LEU* 4.3 4.6 - - + +
288E TYR* 3.2 33.0 - - + -
289E ASP* 2.9 34.1 + - - +
297E ASP 2.7 27.7 + - - +
298E ASP 3.8 3.6 - - - +
300E LYS* 1.3 75.4 - - - +
302E ILE* 1.3 65.5 + - - +
304E ARG* 2.8 40.4 + - - +
305E ILE* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 302 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E ILE* 3.6 12.1 - - + -
133E ILE 5.4 0.4 - - - +
134E ASP* 3.3 30.7 - - + +
228E LEU* 3.6 31.2 - - + -
230E ASP* 3.6 26.9 - - + +
260E ILE* 4.3 13.6 - - + +
277E LEU* 3.9 19.3 - - + -
280E MET* 6.0 0.9 - - + -
298E ASP 2.9 19.8 + - - +
299E SER* 3.6 9.6 - - - +
301E ASN* 1.3 76.1 - - - +
303E ALA* 1.3 57.1 + - - +
305E ILE* 3.2 7.8 + - + +
306E ALA* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E ILE* 4.2 13.0 - - + +
157E VAL* 4.1 11.2 - - + -
159E LEU* 4.3 9.5 - - + +
166E ILE* 4.1 23.8 - - + -
299E SER 3.0 13.1 + - - +
300E LYS 3.0 13.0 + - - +
302E ILE* 1.3 76.3 - - - +
304E ARG* 1.3 54.7 + - - +
306E ALA* 3.1 7.3 + - - +
307E VAL* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 304 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E ARG* 5.7 1.6 - - - +
166E ILE* 5.9 3.6 - - + -
281E LEU* 4.2 8.7 - - + +
286E MET* 3.8 34.8 - - - +
287E ASP* 2.8 30.1 + - - +
289E ASP* 3.8 16.5 - - - +
300E LYS* 3.0 17.9 + - + +
301E ASN* 2.8 42.9 + - - +
303E ALA* 1.3 75.3 - - + +
305E ILE* 1.3 63.1 + - - +
307E VAL* 3.2 9.8 + - - +
308E ARG* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 305 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E ILE* 3.8 19.1 - - + -
264E TYR* 4.0 26.9 - - + -
277E LEU* 3.6 30.5 - - + -
280E MET* 3.7 28.0 - - + -
281E LEU* 3.7 23.6 - - + +
284E LEU* 4.2 3.6 - - + -
286E MET* 3.7 13.5 - - + -
301E ASN 3.0 8.7 + - - +
302E ILE* 3.2 9.4 + - + +
304E ARG* 1.3 75.5 - - - +
306E ALA* 1.3 63.9 + - - +
308E ARG* 3.2 3.9 + - - +
309E MET* 2.9 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E ILE* 5.9 0.2 - - + -
132E ILE* 5.0 2.5 - - + -
159E LEU* 4.1 15.5 - - + -
228E LEU* 4.6 7.9 - - + -
260E ILE* 4.0 15.0 - - + -
302E ILE 2.9 14.0 + - - +
303E ALA* 3.1 8.3 + - - +
305E ILE* 1.3 76.8 - - - +
307E VAL* 1.3 56.9 + - - +
309E MET* 3.3 4.5 + - - +
310E LEU* 2.9 34.8 + - - +
316E LEU* 3.8 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 307 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E LEU* 3.7 22.7 - - + -
164E LEU* 3.6 34.0 - - + +
165E GLU* 5.4 0.2 - - - -
166E ILE* 6.4 0.4 - - + -
303E ALA* 2.8 18.5 + - + +
304E ARG* 3.2 10.7 + - - +
306E ALA* 1.3 76.3 - - - +
308E ARG* 1.3 58.2 + - - +
310E LEU* 3.1 10.0 + - - +
311E GLN* 2.9 52.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 308 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E GLU* 3.6 34.2 + - - +
96E ARG* 5.6 1.8 - - - +
105E ARG* 3.3 18.0 - - - +
268E TYR* 3.9 9.0 - - - +
284E LEU* 3.9 25.8 - - + -
286E MET* 4.4 9.9 - - + -
304E ARG 3.0 12.7 + - - +
305E ILE 3.2 6.7 + - - +
307E VAL* 1.3 76.8 - - - +
309E MET* 1.3 63.7 + - - +
311E GLN* 3.2 39.6 + - - +
312E ASP* 2.9 51.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 309 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E ILE* 3.8 31.9 - - - -
263E SER* 3.7 8.5 - - - +
264E TYR* 3.5 44.6 - - + +
267E PHE* 4.3 5.8 - - + -
268E TYR* 3.7 24.7 - - + +
284E LEU* 5.3 0.4 - - + -
305E ILE* 2.9 18.3 + - + +
306E ALA 3.7 6.5 - - - +
308E ARG* 1.3 76.1 - - - +
310E LEU* 1.3 61.8 + - - +
312E ASP* 3.2 7.1 + - - +
313E GLY 3.3 0.2 + - - -
314E CYS* 2.8 57.8 + - + +
316E LEU* 4.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E SER* 4.6 20.2 - - - +
130E ILE* 4.8 2.2 - - + -
159E LEU* 4.8 9.4 - - + -
161E THR* 4.5 20.6 - - + +
164E LEU* 3.9 29.2 - - + -
306E ALA 2.9 23.2 + - - +
307E VAL 3.1 3.8 + - - +
309E MET* 1.3 77.6 - - - +
311E GLN* 1.3 57.4 + - - +
313E GLY* 2.9 19.8 + - - -
314E CYS 3.3 20.7 - - - +
315E GLU* 4.9 0.4 - - - -
316E LEU* 3.9 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 311 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E ASN* 4.2 6.6 + - - -
112E LYS* 5.2 4.9 + - - -
164E LEU* 3.6 25.3 - - + +
307E VAL* 2.9 39.5 + - - +
308E ARG* 3.2 40.2 + - - +
309E MET 3.3 0.2 - - - -
310E LEU* 1.3 76.5 - - - +
312E ASP* 1.3 60.1 + - - +
313E GLY 3.1 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 312 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E LYS 4.8 0.7 - - - +
105E ARG* 2.8 57.8 + - - +
108E ASN* 3.1 27.6 - - - +
267E PHE* 3.6 17.4 - - + -
268E TYR* 2.7 29.5 + - + +
308E ARG* 2.9 31.7 + - - +
309E MET 3.2 5.5 + - - +
311E GLN* 1.3 75.4 - - - +
313E GLY* 1.3 59.7 + - - +
314E CYS 3.4 0.7 - - - -
----------------------------------------------------------
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