Contacts of the helix formed by residues 249 - 270 (chain D) in PDB entry 2GER
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 GLY 249 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D GLU 3.2 12.3 + - - -
247D SER 3.3 1.2 - - - -
248D GLY* 1.3 81.3 - - - +
250D PHE* 1.3 64.9 + - - +
251D ARG* 3.1 3.8 - - - -
252D SER* 2.9 31.4 + - - -
253D LEU* 3.2 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ALA* 6.3 4.7 - - + -
245D LEU* 3.5 62.6 + - + +
246D GLU* 4.5 2.5 + - - +
248D GLY 3.3 2.9 - - - -
249D GLY* 1.3 76.5 - - - +
251D ARG* 1.3 68.9 + - + +
253D LEU* 3.7 13.7 + - + +
254D LEU* 3.5 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ASP* 5.3 6.3 + - - -
224D PRO* 6.2 1.6 - - - +
225D GLY* 5.8 4.8 - - - +
228D LYS* 4.7 21.6 - - - +
246D GLU* 3.4 32.4 + - - +
249D GLY* 3.0 1.3 + - - -
250D PHE* 1.3 83.2 - - + +
252D SER* 1.3 67.7 + - - +
254D LEU* 3.1 16.3 + - - +
255D ILE* 3.2 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D GLY* 2.9 17.6 + - - -
251D ARG* 1.3 76.5 - - - +
253D LEU* 1.3 72.2 + - - +
254D LEU 2.5 2.4 + - - -
255D ILE* 2.4 42.3 + - - -
256D ASN* 2.8 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D GLY 4.4 12.8 - - - +
249D GLY 3.2 13.2 + - - +
250D PHE* 3.9 15.3 - - + +
252D SER* 1.3 89.8 + - - +
254D LEU* 1.3 59.9 + - + +
255D ILE 3.4 0.2 - - - -
256D ASN* 3.8 18.3 - - + +
257D ALA* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D TYR* 5.1 19.3 - - + -
250D PHE* 3.5 45.0 + - + +
251D ARG* 3.1 11.0 + - - +
252D SER 2.5 5.5 + - - -
253D LEU* 1.3 78.0 - - + +
255D ILE* 1.3 66.8 + - + +
257D ALA* 3.5 8.8 + - + +
258D VAL* 3.2 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D ARG* 3.5 20.4 - - + +
252D SER* 2.4 28.4 + - - +
254D LEU* 1.3 65.1 - - + +
256D ASN* 1.3 61.2 + - - +
257D ALA 2.5 14.6 + - - -
258D VAL* 2.7 22.1 + - + -
259D GLU* 2.8 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D SER* 2.8 28.3 + - - +
253D LEU* 3.8 20.2 - - + +
255D ILE* 1.3 78.7 - - - +
257D ALA* 1.3 64.3 + - - +
259D GLU* 3.9 10.2 - - - +
260D ALA* 3.0 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D TYR* 2.9 38.0 + - + -
253D LEU 3.2 16.9 + - - +
254D LEU* 3.5 11.2 - - + +
255D ILE 2.5 4.9 + - - -
256D ASN* 1.3 76.7 - - - +
258D VAL* 1.3 70.4 + - - +
260D ALA* 3.7 2.3 - - - +
261D SER* 3.0 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D ALA 6.0 0.7 - - - +
172D GLY* 3.0 34.0 - - - +
173D LEU* 3.4 22.0 - - + +
180D TYR* 2.9 13.8 + - + -
254D LEU 3.2 8.6 + - - +
255D ILE* 2.7 17.1 + - + +
257D ALA* 1.3 74.6 - - - +
259D GLU* 1.3 86.7 + - + +
261D SER* 2.9 12.8 + - - -
262D CYS* 3.0 9.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D ILE* 2.8 28.8 + - + +
256D ASN* 3.9 8.9 - - - +
258D VAL* 1.3 86.6 - - + +
260D ALA* 1.3 58.2 + - + +
262D CYS* 2.7 30.1 + - - +
263D ILE* 3.0 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ASN 3.0 18.5 + - - +
257D ALA* 3.7 2.5 - - - +
259D GLU* 1.3 85.4 - - + +
261D SER* 1.3 60.5 - - - +
263D ILE* 3.5 9.6 + - - +
264D ARG* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D THR* 4.0 1.9 + - - +
172D GLY* 3.3 12.8 + - - -
176D SER* 2.8 24.0 + - - -
180D TYR* 3.4 20.9 - - - -
257D ALA 3.0 4.8 + - - -
258D VAL 2.9 12.8 + - - -
260D ALA* 1.3 73.6 - - - +
262D CYS* 1.3 59.2 + - - +
264D ARG* 3.5 6.3 + - - +
265D THR* 3.1 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D ASP* 3.3 35.7 - - - +
169D ALA* 3.6 12.1 - - - -
172D GLY* 4.1 6.7 - - - -
258D VAL* 3.0 9.3 + - + +
259D GLU* 2.7 16.3 + - - +
261D SER* 1.3 76.5 - - - +
263D ILE* 1.3 65.3 + - + +
265D THR* 3.0 14.3 + - - -
266D ARG* 3.0 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D GLU* 3.3 40.2 - - + +
260D ALA* 3.8 8.7 - - - +
262D CYS* 1.3 75.7 - - + +
264D ARG* 1.3 56.8 + - - +
266D ARG* 3.1 19.2 + - + +
267D GLU* 2.8 55.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D ALA 3.1 17.5 + - - +
261D SER* 3.7 7.4 - - - +
263D ILE* 1.3 74.9 - - - +
265D THR* 1.3 63.7 + - - +
267D GLU* 4.5 19.3 + - - +
268D LEU* 2.9 58.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ALA* 3.3 31.1 - - + +
98D GLY* 3.5 11.3 - - - +
168D ASP* 4.6 14.4 - - - +
171D THR* 4.0 25.2 - - + +
261D SER* 3.1 17.8 + - - -
262D CYS* 3.0 9.4 + - - +
264D ARG* 1.3 79.2 - - - +
266D ARG* 1.3 62.0 + - - +
268D LEU* 3.5 16.3 - - - +
269D GLN* 3.6 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D ASP 5.5 3.4 + - - -
168D ASP* 3.7 28.7 - - + +
169D ALA* 5.2 6.5 - - - +
262D CYS* 3.0 39.8 + - - +
263D ILE* 3.5 19.2 - - + +
264D ARG 3.0 0.2 - - - -
265D THR* 1.3 75.7 - - - +
267D GLU* 1.3 53.1 + - + +
268D LEU 2.5 10.4 + - - -
269D GLN* 2.7 5.5 + - - -
270D SER* 2.5 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D ILE* 2.8 43.3 + - + +
264D ARG* 4.1 19.8 + - - +
266D ARG* 1.3 71.7 - - + +
268D LEU* 1.3 59.6 + - - +
270D SER* 3.6 12.0 + - - -
271D MET* 3.1 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D PRO* 4.6 14.1 - - + -
97D ALA* 3.5 35.7 - - + +
264D ARG* 2.9 54.3 + - + +
265D THR* 3.5 8.1 - - - +
266D ARG 2.5 4.4 + - - -
267D GLU* 1.3 72.5 - - - +
269D GLN* 1.3 59.0 + - + +
271D MET* 3.1 25.0 + - - +
272D ALA* 3.6 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ALA 4.7 1.1 + - - +
98D GLY* 3.1 35.2 - - - +
99D VAL* 2.8 28.7 + - - +
100D THR* 3.2 19.8 + - - +
103D SER* 5.1 3.1 + - - -
168D ASP* 5.4 3.8 - - - +
265D THR 3.7 3.6 - - - +
266D ARG* 2.7 9.5 + - - +
268D LEU* 1.3 71.5 - - - +
270D SER* 1.3 51.9 + - - +
271D MET 2.7 16.6 + - - -
272D ALA* 2.9 30.2 + - - +
273D ASP* 2.6 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D ARG* 2.5 48.8 + - - +
267D GLU* 3.6 8.9 + - - -
268D LEU 3.3 0.6 - - - -
269D GLN* 1.3 68.4 - - - +
271D MET* 1.3 57.1 + - - +
273D ASP* 4.3 3.8 - - - -
274D GLN* 2.4 33.3 + - - +
----------------------------------------------------------
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