Contacts of the helix formed by residues 257 - 268 (chain B) in PDB entry 3ER8
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 GLU 257 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LYS* 6.0 6.1 - - - -
244B ARG 6.0 0.9 - - - +
246B LYS 4.0 7.4 - - - +
247B VAL* 4.9 8.7 - - + +
255B ASN* 2.4 35.9 + - - +
256B GLN* 1.3 78.5 + - - +
258B TYR* 1.3 68.4 + - - +
259B ASP* 3.3 6.1 - - + +
260B TYR* 2.9 26.1 + - + +
261B PHE 3.3 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.9 30.5 - - + -
9B PRO* 3.7 19.1 - - + +
10B PHE* 3.0 40.9 + + - +
239B LEU* 4.3 4.5 - - + +
243B VAL* 3.7 33.0 - - + +
244B ARG* 3.4 44.9 + - + -
246B LYS* 3.4 15.7 + - + +
248B VAL* 4.1 10.8 - - + -
256B GLN 3.2 3.2 + - - -
257B GLU* 1.3 69.7 - - - +
259B ASP* 1.3 59.6 + - - +
261B PHE* 2.7 29.1 + + - +
262B HIS* 2.7 28.3 + + + -
----------------------------------------------------------
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
----------------------------------------------------------
199B PRO* 4.0 3.7 - - + +
200B PHE* 3.0 44.5 + - + +
244B ARG* 3.0 54.6 + - - +
257B GLU* 3.0 5.0 + - + +
258B TYR* 1.3 76.2 + - - +
260B TYR* 1.3 54.3 + - + +
262B HIS* 2.7 13.1 + - - +
263B MET* 2.5 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LYS* 5.5 6.5 - - - -
34B LEU* 3.0 32.6 - - + +
200B PHE* 3.4 20.9 - + - -
251B PHE* 3.9 5.3 - - + -
253B TYR* 4.8 4.1 - + + -
255B ASN* 2.7 61.1 + - + +
257B GLU* 2.9 23.0 + - + +
259B ASP* 1.3 77.8 - - + +
261B PHE* 1.3 56.0 + - - +
263B MET* 3.5 25.0 - - + +
264B TYR* 3.1 26.9 + - - +
287B GLN* 3.9 12.3 - - - -
291B PHE* 3.8 24.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.7 31.9 - - + -
7B ASP 4.4 3.1 - - - -
8B LYS* 3.9 22.4 - - - -
9B PRO* 3.7 25.0 - - + +
248B VAL* 3.4 38.1 - - + -
250B ASN* 5.7 2.9 - - - -
251B PHE* 3.3 44.6 - + + -
257B GLU 3.3 2.5 + - - +
258B TYR* 2.7 20.1 + + - +
260B TYR* 1.3 74.5 - - - +
262B HIS* 1.3 56.7 + - - -
264B TYR* 3.4 11.3 - - - +
265B PHE* 3.6 28.7 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PRO* 3.8 17.9 - - + -
10B PHE 3.4 20.9 + - - -
11B MET* 3.8 24.1 - - - -
197B LEU* 3.8 28.8 + - + -
198B GLN 4.2 2.2 + - - -
199B PRO* 3.5 32.9 - - + +
239B LEU* 6.6 0.2 - - + -
244B ARG* 6.3 0.4 - - - -
258B TYR* 2.7 27.5 + + + +
259B ASP* 2.7 13.6 + - - +
261B PHE* 1.3 76.2 - - - +
263B MET* 1.3 62.4 + - - +
264B TYR 3.2 0.6 + - - -
265B PHE* 3.4 8.1 + - - +
266B MET* 3.3 15.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.8 0.2 - - - -
44B LEU* 3.7 37.2 - - + -
199B PRO* 4.5 3.5 - - + +
200B PHE* 4.0 9.6 - - + -
253B TYR* 5.1 0.2 - - + -
259B ASP 2.5 16.5 + - - +
260B TYR* 3.5 37.7 - - + +
262B HIS* 1.3 69.1 - - - +
264B TYR* 1.3 67.1 + - - +
266B MET* 3.4 13.4 + - - +
267B LEU* 3.3 31.3 + - + +
283B VAL* 5.8 0.4 - - + -
287B GLN* 3.4 34.1 - - - +
290B ILE* 6.2 0.4 - - - -
291B PHE* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PHE* 3.5 30.1 - + + -
252B ASP 5.6 1.6 - - - -
253B TYR* 4.2 10.1 - + + -
260B TYR 3.1 18.2 + - - +
261B PHE 3.4 7.9 - - - +
263B MET* 1.3 80.3 - - - +
265B PHE* 1.3 81.8 + + - +
266B MET 3.0 5.9 + - - -
267B LEU 3.2 0.3 + - - -
268B ARG* 3.0 37.0 + - + +
279B THR* 3.6 18.9 - - + +
280B LYS* 3.8 21.2 + - + +
283B VAL* 3.5 43.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASP 4.0 7.0 - - - -
8B LYS* 3.5 31.9 - - + -
9B PRO* 3.3 32.5 - - + -
11B MET* 4.0 17.9 - - + +
251B PHE* 5.7 0.2 - + - -
261B PHE* 3.6 26.9 + + - -
262B HIS 3.4 3.7 + - - +
263B MET 3.4 0.4 - - - -
264B TYR* 1.3 99.1 - + - +
266B MET* 1.3 58.3 + - - +
268B ARG* 3.1 55.8 + - - +
269B THR* 3.3 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B MET* 3.9 14.1 - - + -
44B LEU* 2.9 41.3 - - + +
45B GLY* 4.2 5.4 - - - -
48B PHE* 3.4 36.0 - - + -
196B MET* 4.5 10.8 - - + -
197B LEU 5.3 0.2 - - - +
199B PRO* 3.4 33.7 - - + -
262B HIS* 3.3 18.2 - - + +
263B MET* 3.6 9.0 - - - +
264B TYR 3.0 0.4 + - - -
265B PHE* 1.3 78.2 - - - +
267B LEU* 1.3 66.1 + - + +
269B THR* 2.7 27.2 + - - -
270B VAL* 3.8 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 3.6 23.1 - - + +
47B LEU* 4.0 15.5 - - + -
263B MET* 3.3 29.1 + - + +
264B TYR 3.2 3.2 + - - +
266B MET* 1.3 75.3 - - + +
268B ARG* 1.3 55.2 + - - +
269B THR 2.8 5.4 - - - -
270B VAL* 2.5 39.1 + - + +
282B LYS* 4.4 1.2 - - - -
283B VAL* 4.2 17.5 - - + +
286B LEU* 3.4 26.9 - - + +
287B GLN* 3.9 28.9 - - + +
290B ILE* 3.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B MET* 6.2 0.4 - - - +
55B ARG* 4.8 1.0 + - - -
264B TYR* 3.0 21.1 + - + +
265B PHE* 3.1 67.4 + - - +
267B LEU* 1.3 75.9 - - - +
269B THR* 1.3 70.2 + - + +
270B VAL 3.4 2.4 + - - +
279B THR* 4.0 23.3 - - + +
282B LYS* 3.6 16.7 + - - +
283B VAL* 3.8 9.1 - - + +
376C ASP* 4.6 8.7 + - - +
377C THR* 4.3 28.4 + - + +
----------------------------------------------------------
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