Contacts of the helix formed by residues 249 - 270 (chain E) in PDB entry 2GRA
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246E GLU* 2.7 20.1 + - - -
247E SER 3.5 1.0 - - - -
248E GLY* 1.3 72.3 - - - -
250E PHE* 1.3 66.8 + - - +
251E ARG* 3.4 3.8 - - - -
252E SER* 3.0 27.8 + - - -
253E LEU* 3.1 9.6 + - - +
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Residues in contact with PHE 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245E LEU* 3.3 64.3 + - + +
246E GLU* 4.4 2.1 + - - +
248E GLY 3.1 5.0 - - - -
249E GLY* 1.3 74.3 - - - +
251E ARG* 1.3 74.3 + - + +
253E LEU* 2.9 31.0 + - + +
254E LEU* 3.4 31.2 + - + +
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Residues in contact with ARG 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ASP* 4.1 17.8 + - - -
225E GLY* 6.3 0.6 - - - -
228E LYS* 4.3 17.4 - - - +
246E GLU* 3.3 38.0 + - - +
249E GLY* 5.0 1.8 - - - -
250E PHE* 1.3 85.6 - - + +
252E SER* 1.3 64.8 + - - +
254E LEU* 3.2 18.0 + - - +
255E ILE* 3.3 16.9 + - + +
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Residues in contact with SER 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E GLY* 3.0 18.5 + - - -
251E ARG* 1.3 78.4 - - - +
253E LEU* 1.3 60.0 + - - +
255E ILE* 2.7 33.4 + - - +
256E ASN* 2.7 28.3 + - - +
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Residues in contact with LEU 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E GLY 4.8 6.7 - - - +
249E GLY* 3.6 15.7 - - - +
250E PHE* 2.9 16.2 + - + +
252E SER* 1.3 86.2 + - - +
254E LEU* 1.3 66.3 + - + +
255E ILE 3.2 0.3 + - - -
256E ASN* 3.2 16.1 + - - +
257E ALA* 3.0 19.9 + - - +
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Residues in contact with LEU 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E TYR* 5.4 15.4 - - + -
250E PHE* 3.4 38.6 + - + +
251E ARG* 3.2 11.6 + - - +
252E SER 3.2 0.6 - - - -
253E LEU* 1.3 80.8 - - + +
255E ILE* 1.3 69.1 + - + +
257E ALA* 3.1 22.1 + - + +
258E VAL* 3.2 11.1 + - - +
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Residues in contact with ILE 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E ARG* 3.4 13.0 - - + +
252E SER* 2.7 24.2 + - - +
254E LEU* 1.3 77.0 - - + +
256E ASN* 1.3 72.2 + - - +
257E ALA 2.8 1.9 + - - -
258E VAL* 2.9 16.0 + - + +
259E GLU* 3.0 19.9 + - + +
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Residues in contact with ASN 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E SER* 2.7 29.9 + - - +
253E LEU* 3.4 16.9 - - - +
255E ILE* 1.3 78.9 - - - +
257E ALA* 1.3 65.6 + - - +
259E GLU* 3.5 16.6 - - - +
260E ALA* 2.8 26.3 + - - +
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Residues in contact with ALA 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E TYR* 3.3 34.6 + - + -
253E LEU 3.0 11.0 + - - +
254E LEU* 3.1 16.2 - - + +
255E ILE 2.8 1.4 + - - -
256E ASN* 1.3 78.5 - - - +
258E VAL* 1.3 66.1 + - - +
260E ALA* 3.4 4.6 - - - +
261E SER* 2.8 21.7 + - - -
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Residues in contact with VAL 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E ALA* 5.4 3.1 - - + +
172E GLY* 3.2 30.3 - - - +
173E LEU* 3.7 29.4 - - + +
180E TYR* 3.3 8.0 + - + -
254E LEU* 3.2 8.0 + - + +
255E ILE* 2.9 12.1 + - + +
257E ALA* 1.3 76.6 - - - +
259E GLU* 1.3 69.3 + - - +
261E SER* 3.4 2.3 - - - -
262E CYS* 2.9 22.0 + - + +
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Residues in contact with GLU 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E ILE* 3.0 19.9 + - + +
256E ASN* 3.5 19.9 - - - +
258E VAL* 1.3 79.3 - - - +
260E ALA* 1.3 57.0 + - - +
262E CYS* 2.7 29.9 + - - +
263E ILE* 2.8 31.3 + - + +
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Residues in contact with ALA 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E ASN 2.8 19.2 + - - +
257E ALA* 3.4 4.3 - - - +
259E GLU* 1.3 79.3 + - - +
261E SER* 1.3 65.9 + - - +
263E ILE* 3.8 8.5 - - - +
264E ARG* 3.1 23.2 + - - +
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Residues in contact with SER 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E THR* 3.5 3.1 + - - +
172E GLY* 2.8 26.3 + - - -
176E SER* 2.7 21.4 + - - -
180E TYR* 3.4 17.7 - - - -
257E ALA 2.8 9.7 + - - -
258E VAL 3.4 4.0 - - - -
260E ALA* 1.3 74.4 - - - +
262E CYS* 1.3 58.9 + - - +
264E ARG* 3.4 4.7 - - - +
265E THR* 2.8 32.1 + - - -
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Residues in contact with CYS 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ASP 4.0 13.2 - - - +
169E ALA* 3.9 27.1 - - - -
172E GLY* 4.4 3.6 - - - -
258E VAL* 2.9 12.3 + - + +
259E GLU* 2.7 16.2 + - - +
261E SER* 1.3 72.3 + - - +
263E ILE* 1.3 72.6 + - + +
265E THR* 2.9 13.6 + - - -
266E ARG* 3.0 43.0 + - - +
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Residues in contact with ILE 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E GLU* 2.8 40.1 + - + +
260E ALA* 3.8 7.6 - - - +
262E CYS* 1.3 70.7 - - + +
264E ARG* 1.3 52.7 + - - +
266E ARG* 2.5 55.0 + - + +
267E GLU* 2.7 40.6 + - + +
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Residues in contact with ARG 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E ALA 3.1 15.2 + - - +
261E SER* 3.4 4.5 - - - +
263E ILE* 1.3 79.6 - - - +
265E THR* 1.3 64.4 + - - +
266E ARG 3.1 0.2 + - - -
267E GLU* 3.2 34.3 + - - +
268E LEU* 3.2 45.6 + - + +
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Residues in contact with THR 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ALA* 4.7 9.0 - - + +
98E GLY* 4.0 26.1 - - - +
119E ARG* 5.3 0.7 - - - +
168E ASP* 3.4 35.0 - - - +
171E THR* 3.7 24.6 - - + +
261E SER* 2.8 16.6 + - - -
262E CYS* 2.9 11.9 + - - -
264E ARG* 1.3 76.7 - - - +
266E ARG* 1.3 59.7 + - - +
268E LEU* 3.6 20.2 + - - +
269E GLN 3.8 4.7 + - - -
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Residues in contact with ARG 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ASP* 3.2 33.2 - - - +
169E ALA* 5.8 0.8 - - - +
262E CYS* 3.0 35.5 + - - -
263E ILE* 2.5 38.9 + - + +
265E THR* 1.3 68.9 - - - +
267E GLU* 1.3 52.7 + - + -
268E LEU 2.8 11.3 + - - -
269E GLN* 3.4 12.8 - - - +
270E SER* 2.7 33.3 + - - +
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Residues in contact with GLU 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263E ILE* 2.7 43.4 + - + +
264E ARG* 3.2 39.1 + - - +
266E ARG* 1.3 70.9 - - + +
268E LEU* 1.3 57.9 - - - +
270E SER* 4.0 8.8 + - - -
271E MET* 3.2 30.1 - - - +
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Residues in contact with LEU 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E PRO* 5.4 8.3 - - + -
73E HIS* 4.6 31.2 - - + +
97E ALA* 5.0 19.3 - - + +
264E ARG* 3.2 50.5 - - + +
265E THR* 3.7 11.9 - - - +
266E ARG 2.8 2.6 + - - -
267E GLU* 1.3 79.5 - - - +
269E GLN* 1.3 63.1 + - - +
270E SER 2.9 4.3 - - - -
271E MET* 2.9 24.3 + - - +
272E ALA* 3.0 12.2 + - - +
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Residues in contact with GLN 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ALA 5.4 0.4 + - - -
98E GLY* 3.0 41.3 - - - +
99E VAL* 4.5 1.6 - - - +
100E THR* 4.4 8.7 + - - +
119E ARG* 4.6 1.4 + - - -
168E ASP* 3.6 23.3 - - - +
265E THR 3.8 5.2 + - - +
266E ARG* 3.4 18.8 - - - +
268E LEU* 1.3 77.7 - - - +
270E SER* 1.3 64.6 + - - +
271E MET 2.9 6.5 + - - -
272E ALA* 3.7 12.3 - - + -
273E ASP* 2.5 40.9 + - - +
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Residues in contact with SER 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E ARG* 2.7 24.9 + - - +
267E GLU* 4.1 9.2 - - - -
268E LEU 2.9 1.2 - - - -
269E GLN* 1.3 83.9 + - - +
271E MET* 1.3 65.4 + - - +
273E ASP* 4.7 3.8 - - - -
274E GLN* 3.2 14.4 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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