Contacts of the helix formed by residues 250 - 270 (chain C) 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 PHE 250 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184C ALA* 6.1 6.3 - - + -
245C LEU* 3.5 63.1 + - + +
246C GLU* 4.6 1.5 - - - +
248C GLY 3.0 3.4 - - - -
249C GLY* 1.3 77.0 - - - +
251C ARG* 1.3 71.7 + - + +
252C SER 3.2 7.8 - - - +
253C LEU* 4.1 12.7 - - + +
254C LEU* 3.7 38.9 + - + +
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Residues in contact with ARG 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C GLY* 6.4 0.6 - - - -
228C LYS* 4.7 19.8 - - - +
246C GLU* 3.2 42.1 + - - +
249C GLY* 4.8 2.2 - - - -
250C PHE* 1.3 83.3 - - + +
252C SER* 1.3 70.9 + - - +
254C LEU* 3.8 9.8 - - - +
255C ILE* 3.5 16.3 + - - +
186D ASP* 3.9 19.0 + - - -
190D ASP* 5.2 1.0 + - - -
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Residues in contact with SER 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C GLY* 2.8 18.7 + - - -
250C PHE 3.2 0.2 - - - +
251C ARG* 1.3 92.7 - - - +
253C LEU* 1.3 62.8 - - - -
254C LEU 2.1 24.7 + - - -
255C ILE* 2.7 15.6 + - - -
256C ASN* 3.7 12.6 - - - -
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C GLY 3.9 12.1 - - - +
249C GLY* 2.9 29.8 - - - +
250C PHE* 4.1 13.2 - - + +
252C SER* 1.3 77.2 - - - +
254C LEU* 1.3 54.7 + - + +
255C ILE 3.1 0.2 - - - -
256C ASN* 2.9 22.2 + - - +
257C ALA* 2.6 36.5 + - - +
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Residues in contact with LEU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C TYR* 5.1 20.7 - - + -
250C PHE* 3.7 42.6 - - + +
251C ARG* 3.8 7.6 - - - +
252C SER 2.1 15.2 + - - +
253C LEU* 1.3 72.9 - - + +
255C ILE* 1.3 65.5 + - + +
257C ALA* 2.9 10.3 + - + +
258C VAL* 2.8 26.2 + - + +
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Residues in contact with ILE 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C ARG 3.5 17.5 - - - +
252C SER* 2.7 16.3 + - - +
254C LEU* 1.3 71.5 - - + +
256C ASN* 1.3 73.6 + - - +
257C ALA 2.8 0.7 + - - -
258C VAL* 2.8 10.6 + - + +
259C GLU* 2.8 33.3 + - + +
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Residues in contact with ASN 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C SER* 3.7 9.0 - - - -
253C LEU* 3.1 35.2 + - - +
255C ILE* 1.3 78.5 - - - +
257C ALA* 1.3 56.1 + - - +
259C GLU* 3.0 16.6 + - - +
260C ALA* 2.9 30.5 + - - +
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Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C TYR* 3.7 26.9 + - + -
253C LEU 2.6 15.4 + - - +
254C LEU* 3.1 14.6 - - + +
255C ILE 2.8 0.6 + - - -
256C ASN* 1.3 68.2 - - - +
258C VAL* 1.3 58.4 + - - +
259C GLU 2.9 8.6 + - - -
260C ALA* 2.9 5.5 + - - +
261C SER* 2.9 26.5 + - - -
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Residues in contact with VAL 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C ALA 5.3 1.5 - - - +
172C GLY* 3.0 35.5 - - - +
173C LEU* 3.6 28.5 - - + +
180C TYR* 3.8 13.7 - - + -
254C LEU 2.8 17.8 + - - +
255C ILE* 3.9 8.5 - - + +
257C ALA* 1.3 72.1 - - - +
259C GLU* 1.3 57.9 + - - +
260C ALA 3.5 0.2 - - - -
261C SER 4.3 1.6 - - - -
262C CYS* 3.9 15.8 - - - +
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Residues in contact with GLU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C ILE* 2.8 25.5 + - + +
256C ASN* 3.4 12.7 - - - +
258C VAL* 1.3 79.5 - - + +
260C ALA* 1.3 63.1 + - - +
261C SER 3.6 0.4 - - - -
262C CYS* 4.7 2.6 - - - +
263C ILE* 2.7 44.1 + - + +
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C ASN 2.9 15.4 + - - +
257C ALA* 3.9 4.9 - - - +
259C GLU* 1.3 82.2 - - - +
261C SER* 1.3 63.6 + - - +
262C CYS 3.3 0.9 - - - -
263C ILE* 3.9 6.0 - - - +
264C ARG* 3.0 25.8 + - - +
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Residues in contact with SER 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C THR* 3.7 4.7 + - - +
172C GLY* 2.9 26.5 + - - -
176C SER* 2.8 23.5 + - - -
180C TYR* 3.5 11.4 - - - -
257C ALA 2.9 14.9 + - - -
260C ALA* 1.3 79.0 - - - +
262C CYS* 1.3 56.8 + - - +
264C ARG* 3.4 5.9 + - - +
265C THR* 2.9 27.8 + - - -
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Residues in contact with CYS 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ASP 3.4 26.5 - - - +
169C ALA* 4.2 12.3 - - - -
172C GLY* 3.8 3.8 - - - -
258C VAL 3.9 16.5 + - - +
259C GLU* 4.7 2.5 - - - +
260C ALA 3.3 0.4 - - - -
261C SER* 1.3 76.2 + - - +
263C ILE* 1.3 65.7 + - - +
264C ARG 2.9 1.3 - - - -
265C THR* 2.6 25.8 + - - -
266C ARG* 2.8 48.9 + - - +
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Residues in contact with ILE 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C GLU* 2.7 38.6 + - + +
260C ALA* 4.1 6.3 - - - +
262C CYS* 1.3 82.9 - - - +
264C ARG* 1.3 61.7 + - - +
266C ARG* 3.3 27.0 - - - +
267C GLU* 3.2 31.9 + - + +
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Residues in contact with ARG 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ALA 3.0 20.2 + - - +
261C SER* 3.4 5.6 - - - +
262C CYS 2.9 0.6 - - - -
263C ILE* 1.3 75.5 - - - +
265C THR* 1.3 65.4 + - - +
266C ARG 3.1 1.6 - - - -
267C GLU* 3.2 28.9 + - - +
268C LEU* 3.1 50.2 + - + +
271C MET* 5.4 9.9 - - - +
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Residues in contact with THR 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ALA* 4.3 6.9 - - + +
98C GLY* 4.1 17.0 - - - +
119C ARG* 4.7 0.9 - - - +
168C ASP* 3.8 31.6 - - - +
171C THR* 3.4 27.7 - - - +
261C SER 2.9 18.7 + - - -
262C CYS* 2.6 18.1 + - - -
264C ARG* 1.3 72.5 - - - +
266C ARG* 1.3 63.9 + - - +
268C LEU* 3.0 26.9 + - - +
269C GLN* 3.3 7.7 + - - +
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Residues in contact with ARG 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ASP 4.6 10.1 + - - -
168C ASP* 3.8 27.5 + - + +
169C ALA* 5.1 6.3 - - - +
262C CYS* 2.8 41.8 + - - +
263C ILE* 3.3 25.2 - - - +
265C THR* 1.3 77.4 - - - +
267C GLU* 1.3 54.9 + - + +
268C LEU 2.8 6.2 + - - -
269C GLN* 3.2 15.2 + - - +
270C SER* 2.7 34.3 + - - +
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Residues in contact with GLU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C ILE* 3.2 25.9 + - + +
264C ARG* 3.2 38.1 + - - +
266C ARG* 1.3 77.8 - - + +
268C LEU* 1.3 57.8 + - - +
270C SER* 3.7 9.3 + - - +
271C MET* 2.9 32.1 + - + +
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Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C PRO* 5.8 7.4 - - + -
97C ALA* 5.7 4.0 - - + +
98C GLY* 3.9 16.7 - - - +
264C ARG* 3.1 51.8 - - + +
265C THR* 3.0 15.0 + - - +
266C ARG 2.8 2.2 + - - -
267C GLU* 1.3 78.7 - - - +
269C GLN* 1.3 64.3 + - - +
271C MET* 3.1 29.1 - - - +
272C ALA* 3.1 8.5 + - - +
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Residues in contact with GLN 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLY* 2.9 25.7 + - - +
100C THR* 3.8 21.9 + - - +
119C ARG* 2.8 25.7 + - - +
168C ASP* 2.6 40.6 + - - +
265C THR 3.6 7.3 - - - +
266C ARG* 3.3 17.2 - - - +
268C LEU* 1.3 71.5 - - - +
270C SER* 1.3 62.4 + - - +
271C MET 2.5 16.6 + - - -
272C ALA* 2.7 16.5 + - - +
273C ASP* 3.3 13.1 - - - +
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Residues in contact with SER 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C ARG* 2.7 26.9 + - - +
267C GLU* 3.7 6.6 - - - +
269C GLN* 1.3 77.8 - - - +
271C MET* 1.3 51.5 + - - +
273C ASP* 3.7 9.4 - - - -
274C GLN* 2.6 38.4 + - - +
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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
------------------------------------------------------------
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