Contacts of the helix formed by residues 254 - 272 (chain B) in PDB entry 2GH1
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 THR 254 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ILE* 3.9 4.2 - - - +
252B GLY 5.3 1.8 - - - +
253B LEU* 1.3 80.3 - - - +
255B TYR* 1.3 60.1 + - - +
256B ASP* 3.4 8.2 + - - +
257B ASN* 3.1 34.8 + - - +
258B ALA* 3.1 26.5 + - - +
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Residues in contact with TYR 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B LYS* 5.5 3.8 + - - -
245B VAL* 3.8 22.8 - - + +
249B ILE* 4.1 18.4 - - + +
254B THR* 1.3 74.2 - - - +
256B ASP* 1.3 74.8 + - - +
258B ALA* 3.5 2.0 + - - +
259B LEU* 2.9 60.4 + - + +
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Residues in contact with ASP 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B THR* 3.4 6.9 + - - +
255B TYR* 1.3 89.4 - - - +
257B ASN* 1.3 64.4 + - - +
259B LEU* 3.2 7.5 + - - +
260B ALA* 2.9 31.2 + - - +
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Residues in contact with ASN 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B VAL* 3.7 38.3 - - + +
171B LYS* 5.6 5.4 - - - +
253B LEU* 4.4 9.7 - - + +
254B THR* 3.1 33.5 + - - +
256B ASP* 1.3 82.6 - - - +
258B ALA* 1.3 58.3 + - - +
260B ALA* 3.3 5.0 + - - +
261B GLN* 2.9 28.8 + - - +
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Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B PHE* 3.9 5.0 - - - -
245B VAL* 3.6 36.8 - - + +
248B LEU* 3.9 24.2 - - + -
249B ILE* 4.2 2.2 - - + +
253B LEU* 4.6 2.4 - - + +
254B THR 3.1 20.5 + - - +
255B TYR 3.8 0.2 - - - +
257B ASN* 1.3 78.8 - - - +
259B LEU* 1.3 57.7 + - - +
261B GLN* 3.2 4.0 + - - +
262B TYR* 2.9 26.5 + - - +
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LYS* 3.6 33.9 - - - +
245B VAL* 4.6 6.7 - - + +
255B TYR* 2.9 54.4 + - + +
256B ASP* 3.6 7.9 - - - +
258B ALA* 1.3 72.9 - - - +
260B ALA* 1.3 66.9 + - - +
262B TYR* 3.0 7.3 + - + +
263B GLU* 3.0 53.1 + - + +
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Residues in contact with ALA 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLN* 3.8 26.0 + - + +
168B VAL* 4.8 2.7 - - + -
256B ASP 2.9 16.4 + - - +
257B ASN* 3.6 9.0 - - - +
259B LEU* 1.3 75.9 - - - +
261B GLN* 1.3 62.0 + - - +
263B GLU* 3.7 8.1 + - - +
264B ALA* 3.1 23.6 + - - +
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Residues in contact with GLN 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B MSE 5.8 0.9 - - - +
165B GLN* 4.0 13.5 - - - +
168B VAL* 3.9 17.8 - - + +
169B LEU* 3.3 38.1 - - - +
172B LEU* 5.8 0.4 - - + -
244B PHE* 3.6 11.4 - - + -
248B LEU* 3.5 27.1 - - + -
257B ASN 2.9 13.5 + - - +
258B ALA 3.3 9.6 - - - +
260B ALA* 1.3 76.6 - - - +
262B TYR* 1.3 64.6 + - - +
264B ALA* 3.2 6.5 + - - +
265B GLU* 3.0 47.9 + - - +
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Residues in contact with TYR 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B PRO* 3.6 20.4 - - + +
239B GLY 3.4 26.2 + - - -
241B LYS* 3.5 51.1 + - + +
244B PHE* 3.4 39.7 - + + -
245B VAL* 4.7 4.0 - - + -
258B ALA 2.9 9.3 + - - +
259B LEU* 3.4 10.3 - - - +
261B GLN* 1.3 76.3 - - - +
263B GLU* 1.3 67.7 + - + +
264B ALA 3.1 0.7 + - - -
265B GLU* 3.1 4.0 + - - +
266B LEU* 2.8 57.0 + - + +
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Residues in contact with GLU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B GLU 4.9 0.4 - - - -
241B LYS* 5.1 3.2 + - - +
259B LEU* 3.0 44.2 + - + +
260B ALA* 4.1 7.0 + - - +
262B TYR* 1.3 84.0 - - + +
264B ALA* 1.3 56.4 + - - +
266B LEU* 3.6 12.9 - - + +
267B ARG* 2.9 29.1 + - - +
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B GLU 3.6 13.7 - - - +
163B PHE* 3.5 30.3 - - - +
164B ILE* 4.6 0.2 - - - -
165B GLN* 4.1 19.3 - - + +
260B ALA 3.1 20.3 + - - +
261B GLN* 3.4 9.0 - - - +
262B TYR 3.1 0.6 - - - -
263B GLU* 1.3 74.0 - - - +
265B GLU* 1.3 66.5 + - + +
267B ARG* 3.2 4.3 + - - +
268B PHE 3.1 18.4 + - - -
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Residues in contact with GLU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B PHE 4.8 2.0 - - - +
169B LEU* 5.6 0.3 - - - +
235B ALA 5.3 0.5 - - - -
236B GLY 4.2 8.8 - - - +
238B PRO* 4.2 18.7 - - + +
244B PHE* 3.2 30.2 - - + -
261B GLN* 3.0 39.4 + - - +
262B TYR 3.7 4.7 - - - +
264B ALA* 1.3 74.9 - - + +
266B LEU* 1.3 63.2 + - - +
268B PHE* 3.4 7.9 + - - +
269B PHE* 3.0 24.6 + - - +
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ASP* 5.3 1.6 - - - +
238B PRO* 4.0 26.6 - - + +
262B TYR* 2.8 41.8 + - + +
263B GLU* 3.6 12.3 - - + +
265B GLU* 1.3 77.5 - - - +
267B ARG* 1.3 61.4 + - - +
269B PHE* 3.2 10.1 + - + +
270B LYS* 3.0 53.5 + - + +
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Residues in contact with ARG 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLU* 2.8 43.6 + - + +
162B GLU* 3.9 23.3 - - + +
163B PHE* 4.3 6.3 - - + -
263B GLU 2.9 19.0 + - - +
264B ALA 3.4 5.4 - - - +
266B LEU* 1.3 75.8 - - - +
268B PHE* 1.3 52.0 + - - +
270B LYS* 3.2 10.4 + - - +
271B ALA* 2.7 47.5 + - + +
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Residues in contact with PHE 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B MSE 6.3 2.2 - - + -
153B TYR* 4.1 20.6 - + - -
155B LEU* 4.3 16.4 - - + -
163B PHE* 3.5 53.6 - + + +
164B ILE* 4.9 5.2 - - + -
234B ILE* 3.9 22.2 - - + -
235B ALA* 3.6 29.4 - - + -
264B ALA 3.1 8.3 + - - +
265B GLU* 3.7 9.6 - - - +
267B ARG* 1.3 76.2 - - - +
269B PHE* 1.3 63.5 + - - +
271B ALA* 4.4 1.8 - - - -
272B LEU* 2.9 45.2 + - + +
278B LEU* 4.5 4.5 - - + -
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Residues in contact with PHE 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B LYS* 4.9 7.1 + - - -
235B ALA* 3.1 27.6 + - - +
236B GLY* 3.7 6.5 - - - +
237B ASP* 3.2 50.9 - - + -
238B PRO* 4.3 5.2 - - + -
265B GLU 3.0 13.9 + - - +
266B LEU* 3.4 14.1 - - + +
268B PHE* 1.3 79.2 - - - +
270B LYS* 1.3 73.9 + - + +
272B LEU* 4.0 11.1 - - - +
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Residues in contact with LYS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B LEU* 3.0 44.1 + - + +
267B ARG* 3.8 11.4 - - - +
269B PHE* 1.3 90.7 - - + +
271B ALA* 1.3 59.7 + - - +
272B LEU 5.0 0.7 - - - -
273B HIS* 4.7 6.8 - - - -
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Residues in contact with ALA 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU* 3.8 24.3 - - + +
158B GLU* 4.2 16.2 - - + -
163B PHE* 6.1 0.7 - - + -
267B ARG* 2.7 34.5 + - + +
268B PHE* 3.1 2.9 + - - +
270B LYS* 1.3 75.2 - - - +
272B LEU* 1.3 59.6 + - - +
273B HIS* 3.0 23.0 + - - -
276B SER* 3.4 5.0 + - - -
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU* 4.5 4.9 - - + +
213B LEU* 4.1 17.0 - - + -
226B TYR* 3.7 15.6 + - + +
229B LEU* 5.3 3.6 - - + -
230B LYS* 4.4 16.3 + - + +
234B ILE* 4.2 18.6 - - + +
235B ALA* 3.7 22.7 - - + -
268B PHE* 2.9 32.2 + - + +
269B PHE 4.0 9.4 - - - +
270B LYS 5.0 0.7 - - - -
271B ALA* 1.3 75.9 - - - +
273B HIS* 1.3 70.0 + - - +
276B SER* 3.8 17.3 - - - -
278B LEU* 4.2 21.5 - - + -
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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