Contacts of the helix formed by residues 249 - 266 (chain B) in PDB entry 4EMX
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 ASP 249 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B HIS* 2.5 42.4 + - - -
244B GLU* 2.9 30.2 + - + +
247B HIS* 3.1 22.5 - - - +
248B GLY* 1.3 76.1 - - - +
250B LEU* 1.3 57.7 + - - +
252B GLU* 3.2 30.1 - - + +
253B CYS* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.0 16.9 - - + +
25B ILE* 3.5 13.9 - - + -
26B ALA* 3.5 34.1 - - + +
29B GLN* 3.5 24.9 - - - +
70B PHE* 6.2 1.8 - - - -
106B LYS* 5.9 0.4 - - - +
149B PHE 5.6 1.1 - - - +
151B ALA* 3.8 23.4 - - + +
245B CYS* 3.5 31.0 - - - +
248B GLY* 3.2 18.7 + - - +
249B ASP* 1.3 76.0 - - - +
251B LEU* 1.3 59.6 + - + +
252B GLU* 3.8 0.4 + - - -
253B CYS* 3.2 4.8 - - - +
254B ALA* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ARG* 4.0 14.1 - - + -
14B LEU* 3.5 26.5 - - + +
19B PHE* 3.6 37.0 - - + +
22B LEU* 3.6 29.4 - - + -
23B VAL* 4.1 5.4 - - + +
66B LEU* 3.7 17.7 - - + -
70B PHE* 3.6 34.1 - - + -
249B ASP 3.4 0.4 - - - -
250B LEU* 1.3 78.0 - - + +
252B GLU* 1.3 62.7 + - - +
254B ALA 3.5 0.5 + - - -
255B ASP* 3.0 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU* 4.1 6.3 - - - +
10B ARG* 3.6 35.0 - - - +
66B LEU* 3.5 31.1 - - - +
67B HIS* 5.4 0.9 - - - -
244B GLU* 3.4 24.7 - - + +
249B ASP* 3.2 37.5 - - + +
251B LEU* 1.3 73.1 + - - +
253B CYS* 1.3 58.9 + - - +
255B ASP* 3.3 0.9 + - - +
256B ASP* 2.9 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TYR* 3.9 13.0 - - - -
152B PRO* 4.0 4.3 - - - -
241B VAL* 3.5 14.9 - - - +
244B GLU* 3.5 10.2 + - - +
245B CYS* 2.0 56.5 - - - +
249B ASP 3.0 15.4 + - - +
250B LEU 3.2 9.2 - - - +
252B GLU* 1.3 77.6 - - - +
254B ALA* 1.3 63.4 + - - +
256B ASP* 3.8 1.4 - - - +
257B ARG* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.9 10.7 - - + +
22B LEU* 3.6 37.5 - - + -
152B PRO* 4.1 23.2 - - + +
155B LEU* 5.0 3.4 - - + -
250B LEU 2.9 14.4 + - - +
251B LEU 4.1 0.7 - - - +
253B CYS* 1.3 73.3 - - - +
255B ASP* 1.3 63.8 + - - +
257B ARG* 3.4 2.0 + - - +
258B ALA* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ARG* 2.8 30.1 + - - +
13B ASP* 2.4 49.9 - - - +
14B LEU* 4.1 12.7 - - + +
251B LEU 3.0 19.2 + - - +
252B GLU 3.7 0.4 - - - +
253B CYS 3.1 0.4 - - - -
254B ALA* 1.3 80.5 - - - +
256B ASP* 1.3 57.2 + - - +
258B ALA* 3.3 6.4 + - - +
259B ASP* 3.1 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ARG* 4.8 9.8 + - - -
237B ASP* 5.5 1.4 - - - +
240B LYS* 3.8 22.2 + - + -
241B VAL* 3.6 19.6 - - + +
244B GLU* 2.5 34.7 - - - +
252B GLU* 2.9 15.7 + - - +
253B CYS 4.0 0.2 - - - +
255B ASP* 1.3 72.7 - - - +
257B ARG* 1.3 60.7 + - - +
259B ASP* 3.6 16.2 - - - +
260B LEU* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TYR* 3.2 34.6 + - - +
152B PRO* 3.4 38.4 + - - +
153B GLU* 2.8 37.6 + - - +
156B PHE* 5.8 0.2 - - - +
241B VAL* 3.7 14.9 - - + +
253B CYS 2.9 17.0 + - - +
254B ALA 3.6 3.6 - - - +
256B ASP* 1.3 75.4 - - - +
258B ALA* 1.4 64.4 + - - +
260B LEU* 3.2 8.0 + - + +
261B ALA* 3.1 23.0 + - - +
283B LEU 5.3 0.2 + - - -
284B LEU* 4.3 13.7 + - - +
287B SER* 3.0 40.2 + - - +
288B HIS* 3.8 5.3 - - - +
291B ALA* 5.9 0.4 - - - +
603B CL 3.5 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 6.0 2.5 - - + -
254B ALA 3.0 13.1 + - - +
255B ASP* 3.3 11.9 + - - +
257B ARG* 1.4 74.8 - - - +
259B ASP* 1.3 58.9 + - - +
261B ALA* 3.5 6.6 + - - +
262B LYS* 3.0 29.4 + - - +
283B LEU* 5.6 15.6 - - + +
287B SER* 4.9 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASP* 5.7 0.2 - - - +
255B ASP* 3.1 24.6 + - - +
256B ASP* 3.6 21.2 - - - +
258B ALA* 1.3 74.0 - - - +
260B LEU* 1.3 59.2 + - - +
262B LYS* 3.4 14.2 + - - +
263B TYR* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 3.8 28.5 - - + +
237B ASP* 3.7 28.3 - - + +
238B LEU* 3.8 47.3 - - + +
241B VAL* 4.7 4.3 - - + -
256B ASP 3.0 19.0 + - - +
257B ARG* 3.2 11.1 + - + +
259B ASP* 1.3 74.4 - - - +
261B ALA* 1.3 57.9 + - - +
263B TYR* 3.3 6.0 + - + +
264B ILE* 2.9 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ARG 3.1 8.5 + - - +
258B ALA* 3.8 6.1 - - - +
260B LEU* 1.3 71.7 - - - +
262B LYS* 1.3 66.9 + - - +
264B ILE* 3.9 2.8 - - - +
265B CYS* 2.9 31.0 + - - -
283B LEU* 5.8 1.1 - - + +
286B LYS* 4.1 15.7 - - + -
287B SER* 3.6 24.7 - - - +
290B ILE* 4.0 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ALA 3.0 17.6 + - - +
259B ASP* 3.6 13.9 - - - +
261B ALA* 1.3 77.3 - - - +
263B TYR* 1.3 63.0 + - - +
265B CYS* 3.2 4.2 + - - +
266B GLU* 3.1 54.5 + - + +
283B LEU* 6.3 2.9 - - + -
286B LYS* 5.0 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLU* 2.8 35.5 + - - -
233B LYS* 3.2 38.2 - - - +
234B LEU* 3.9 20.4 - - + -
237B ASP* 5.4 1.3 - - - +
259B ASP 2.9 20.2 + - - +
260B LEU* 3.3 8.7 + - + +
262B LYS* 1.3 75.5 - - - +
264B ILE* 1.3 64.2 + - + +
266B GLU* 3.4 9.4 + - - -
267B ASN* 3.0 54.2 + - - +
271B ILE* 4.4 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B PHE* 5.1 7.4 - - + -
234B LEU* 3.9 27.4 - - + -
260B LEU* 2.9 39.0 + - + +
261B ALA* 3.9 6.5 - - - +
263B TYR* 1.3 74.9 - - - +
265B CYS* 1.3 63.1 + - - +
267B ASN 3.1 12.5 + - - -
268B GLN* 3.4 12.5 + - - +
271B ILE* 3.9 17.0 - - + +
275B LEU* 3.7 27.6 - - + -
290B ILE* 3.9 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ALA 2.9 22.0 + - - +
262B LYS* 3.2 4.5 + - - +
264B ILE* 1.3 74.9 - - - +
266B GLU* 1.3 61.4 + - + +
267B ASN 3.4 0.4 - - - -
268B GLN* 3.0 21.4 + - - +
279B CYS* 2.0 59.2 - - + +
286B LYS* 3.7 20.0 - - + +
290B ILE* 3.9 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LYS* 3.1 50.9 + - + +
263B TYR* 4.0 8.6 - - - +
265B CYS* 1.3 79.7 - - + +
267B ASN* 1.3 68.3 + - - +
268B GLN 3.6 1.6 - - - -
269B ASP* 4.8 1.0 - - - +
----------------------------------------------------------
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