Contacts of the helix formed by residues 294 - 312 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B GLU* 3.9 11.7 - - - -
171B GLN* 4.4 5.8 - - - -
173B TYR* 5.4 2.7 - - - -
190B THR 4.0 10.5 + - - +
291B ARG* 3.3 23.3 - - + +
292B PRO 3.1 5.3 + - - -
293B HIS* 1.3 76.1 - - - +
295B GLY* 1.3 67.9 + - - +
296B LEU* 3.8 9.4 - - - -
297B ASP* 3.7 30.5 - - - +
298B ASP* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ASP* 3.5 19.9 - - - +
136B GLU* 3.7 9.8 - - - +
153B GLU* 2.8 25.9 + - - -
155B PRO* 3.7 7.0 - - - -
293B HIS 3.6 2.6 + - - -
294B CYS* 1.3 70.3 - - - +
296B LEU* 1.3 57.2 + - - +
298B ASP* 3.3 5.1 + - - +
299B SER* 2.9 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B GLU* 3.2 6.4 + - - +
155B PRO* 3.7 11.1 - - + +
156B VAL 4.4 0.4 - - - +
157B VAL* 3.7 24.2 - - + -
169B THR* 3.9 23.8 - - - +
170B PHE 4.3 10.3 - - - +
171B GLN* 3.6 42.2 - - + +
294B CYS* 3.3 4.2 - - - -
295B GLY* 1.3 75.4 - - - +
297B ASP* 1.3 59.9 + - - +
299B SER* 3.1 4.6 + - - -
300B LYS* 2.9 50.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B TYR* 3.6 4.7 - - - +
289B ASP 4.3 5.4 - - - +
290B GLY* 3.7 10.0 - - - -
291B ARG* 3.2 40.6 + - - +
294B CYS* 3.4 19.3 + - - +
295B GLY 3.4 0.4 - - - -
296B LEU* 1.3 79.0 - - - +
298B ASP* 1.3 54.6 + - - +
300B LYS* 3.3 20.9 + - - +
301B ASN* 2.6 39.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A A 4.6 5.4 + - - -
134B ASP* 3.8 24.9 - - - +
136B GLU* 4.2 2.3 - - - +
277B LEU* 3.8 18.0 - - + +
288B TYR* 2.4 35.1 + - - -
292B PRO* 4.1 0.7 - - - +
293B HIS* 3.5 26.4 + - - -
294B CYS 3.0 14.1 + - - +
295B GLY 3.6 8.1 - - - +
297B ASP* 1.3 75.6 - - - +
299B SER* 1.3 58.7 + - - +
301B ASN* 3.2 3.2 + - - +
302B ILE* 2.9 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 3.7 23.9 + - - +
133B ILE 4.0 1.7 - - - -
134B ASP* 3.3 25.3 + - - +
155B PRO* 4.0 5.5 - - - +
157B VAL* 3.5 21.6 - - - +
295B GLY 2.9 14.7 + - - -
296B LEU* 3.4 10.5 - - - -
298B ASP* 1.3 76.1 - - - +
300B LYS* 1.3 56.1 + - - +
302B ILE* 3.4 5.5 + - - +
303B ALA* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B VAL* 4.0 11.0 - - + -
166B ILE* 4.3 16.7 - - + +
169B THR* 4.0 19.7 + - - +
289B ASP 5.7 1.1 - - - +
296B LEU* 2.9 40.3 + - - +
297B ASP* 3.6 23.3 + - - +
299B SER* 1.3 76.5 - - - +
301B ASN* 1.3 59.7 + - - +
303B ALA* 3.2 9.4 + - - +
304B ARG* 3.0 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 4.4 6.3 - - + -
281B LEU* 3.9 9.6 - - + +
288B TYR* 3.3 33.8 - - + -
289B ASP* 2.8 33.5 + - - -
297B ASP 2.6 29.1 + - - +
298B ASP 3.7 4.3 - - - +
300B LYS* 1.3 75.6 - - - +
302B ILE* 1.3 63.4 + - - +
304B ARG* 2.7 39.6 + - - +
305B ILE* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 3.8 10.3 - - + -
133B ILE 5.4 0.7 - - - +
134B ASP* 3.5 27.8 - - + +
228B LEU* 3.6 30.5 - - + -
230B ASP* 3.6 22.7 - - + +
260B ILE* 4.1 15.4 - - + +
277B LEU* 3.8 21.1 - - + -
298B ASP* 2.9 25.5 + - + +
299B SER* 3.6 10.1 - - - +
301B ASN* 1.3 72.7 - - - +
303B ALA* 1.3 60.0 + - - +
305B ILE* 3.2 8.7 + - + +
306B ALA* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 3.4 24.8 - - + +
157B VAL* 4.2 2.9 - - + -
159B LEU* 4.5 6.4 - - + +
166B ILE* 3.7 28.9 - - + -
299B SER 3.0 11.7 + - - +
300B LYS* 3.2 10.7 + - - +
302B ILE* 1.3 74.3 - - - +
304B ARG* 1.3 66.3 + - - +
306B ALA* 3.2 3.3 + - - +
307B VAL* 2.9 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ARG* 5.8 1.4 - - - +
166B ILE* 6.0 2.2 - - + -
281B LEU* 4.1 9.8 - - + +
286B MET* 3.8 35.1 - - + +
287B ASP 2.8 31.1 + - - +
288B TYR* 4.1 0.2 - - - +
289B ASP* 3.8 15.4 - - - +
300B LYS* 3.0 20.8 + - - +
301B ASN* 2.7 40.2 + - - +
303B ALA* 1.3 76.9 - - + +
305B ILE* 1.3 64.8 + - - +
307B VAL* 3.2 7.7 + - - +
308B ARG* 2.9 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ILE* 3.9 17.9 - - + -
264B TYR* 4.0 25.8 - - + -
277B LEU* 3.5 31.0 - - + -
280B MET* 3.8 27.1 - - + -
281B LEU* 3.8 20.6 - - + -
284B LEU* 4.2 16.8 - - + -
286B MET* 4.9 0.7 - - - -
301B ASN 3.0 10.8 + - - +
302B ILE* 3.2 9.6 + - + +
304B ARG* 1.3 76.1 - - - +
306B ALA* 1.3 57.3 + - - +
308B ARG* 3.3 3.9 + - - +
309B MET* 2.9 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ILE* 5.8 0.2 - - + -
132B ILE* 5.0 2.7 - - + -
159B LEU* 4.1 16.8 - - + -
228B LEU* 4.6 6.5 - - + -
260B ILE* 3.9 18.1 - - + +
302B ILE 2.9 19.2 + - - +
303B ALA* 3.2 5.8 + - - +
305B ILE* 1.3 70.1 - - - +
307B VAL* 1.3 60.0 + - - +
309B MET* 3.3 4.7 + - - +
310B LEU* 2.9 35.6 + - + +
316B LEU* 3.9 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LEU* 3.7 28.7 - - + -
164B LEU* 3.7 30.2 - - + +
165B GLU* 5.5 0.2 - - - -
166B ILE* 6.2 0.7 - - + -
303B ALA* 2.9 21.2 + - + +
304B ARG* 3.6 6.7 - - - +
306B ALA* 1.3 77.0 - - - +
308B ARG* 1.3 57.9 + - - +
310B LEU* 3.2 8.1 + - - +
311B GLN* 2.9 52.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU* 3.7 35.0 + - - +
96B ARG* 5.8 1.0 - - - +
105B ARG* 3.2 27.2 - - - +
268B TYR* 4.0 1.6 - - - +
284B LEU* 3.9 24.5 - - + -
286B MET* 3.5 34.4 - - + +
304B ARG 2.9 11.7 + - - +
305B ILE 3.7 3.6 - - - +
307B VAL* 1.3 78.1 - - - +
309B MET* 1.3 61.5 + - - +
311B GLN* 3.3 40.8 + - - +
312B ASP* 2.9 37.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ILE* 4.0 29.8 - - - -
263B SER 3.7 4.5 - - - +
264B TYR* 3.6 42.2 - - - +
267B PHE* 4.1 7.9 - - + -
268B TYR* 3.7 27.1 - - + +
284B LEU* 5.7 0.2 - - + -
305B ILE* 2.9 21.8 + - + +
306B ALA* 3.7 5.2 - - - +
308B ARG* 1.3 74.7 - - + +
310B LEU* 1.3 60.8 + - - +
312B ASP* 3.1 9.4 + - - +
313B GLY 3.2 0.3 + - - -
314B CYS* 3.0 55.3 + - + +
316B LEU* 3.9 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TYR* 3.5 32.8 - - + +
130B ILE* 4.9 1.3 - - + -
159B LEU* 4.6 13.5 - - + -
161B THR* 4.7 13.5 - - + +
164B LEU* 3.7 30.5 - - + -
306B ALA 2.9 24.2 + - - +
307B VAL* 3.7 4.7 - - - +
309B MET* 1.3 73.3 - - - +
311B GLN* 1.3 65.5 + - - +
313B GLY* 3.1 13.0 + - - -
314B CYS 3.5 20.0 - - - +
315B GLU* 5.1 0.4 - - - -
316B LEU* 4.4 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ASN* 4.0 7.6 + - - -
112B LYS* 4.6 8.0 + - - -
164B LEU* 3.7 23.4 - - + +
307B VAL* 2.9 36.4 + - - +
308B ARG* 3.3 41.5 + - - +
310B LEU* 1.3 75.6 - - - +
312B ASP* 1.3 60.6 + - - +
313B GLY* 3.1 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 4.4 0.2 - - - +
104B LYS 4.6 0.9 - - - +
105B ARG* 2.7 58.7 + - - +
108B ASN* 3.1 28.0 - - - +
267B PHE* 3.3 24.7 - - + -
268B TYR* 2.6 25.9 + - + -
308B ARG* 2.9 25.5 + - - +
309B MET 3.1 8.7 + - - +
311B GLN* 1.3 76.0 - - - +
313B GLY* 1.3 58.3 + - - +
314B CYS 3.5 0.4 - - - -
----------------------------------------------------------
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