Contacts of the helix formed by residues 225 - 237 (chain B) in PDB entry 4GKH
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 ARG 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B HIS* 3.5 25.4 + - + +
191B ASP* 2.8 52.5 + - + +
193B VAL* 3.5 50.2 - - + +
223B ALA 3.6 0.8 + - - -
224B ASP* 1.3 73.2 + - - +
226B TYR* 1.3 78.6 + - + +
227B GLN 3.1 1.2 + - - -
228B ASP 3.1 10.9 + - - -
229B LEU* 3.3 16.0 + - + +
251B TYR* 2.8 44.5 + - - +
253B ILE* 4.5 8.1 - - - -
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Residues in contact with TYR 226 (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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191B ASP* 6.1 0.2 - - - -
224B ASP* 2.9 20.5 + - - +
225B ARG* 1.3 86.8 - - + +
227B GLN* 1.3 65.9 + - - +
228B ASP 3.2 0.2 - - - -
229B LEU* 3.8 8.3 - - + -
230B ALA* 2.9 26.9 + - - +
248B PHE* 3.7 28.9 - + - -
253B ILE* 3.7 25.0 - - + +
255B ASN 4.8 0.2 + - - -
256B PRO* 3.5 7.4 - - - +
257B ASP* 2.8 44.9 + - + +
260B LYS* 3.9 21.8 - - + +
261B LEU* 3.7 24.0 - - + -
264B HIS* 3.6 18.2 - - + +
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Residues in contact with GLN 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B SER* 6.5 0.7 - - - -
148B ARG* 5.8 4.6 - - - +
195B THR* 4.3 9.2 - - + +
197B GLY* 3.1 33.7 + - - -
219B ARG* 5.7 1.2 - - - +
223B ALA* 4.3 14.1 - - + -
224B ASP 2.9 16.5 + - - +
226B TYR* 1.3 79.0 - - - +
228B ASP* 1.3 68.4 + - - +
230B ALA* 4.4 0.7 - - - +
231B ILE* 3.5 36.2 + - - +
264B HIS* 3.4 31.6 + - + +
267B LEU* 4.4 12.3 - - - +
268B ASP* 4.8 5.9 + - - +
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Residues in contact with ASP 228 (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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128B LEU* 3.7 15.0 - - + -
131B LEU* 3.5 6.2 - - - +
132B HIS* 2.9 32.2 + - + +
195B THR* 3.3 8.5 - - - -
196B HIS* 2.9 23.3 + - - +
197B GLY* 3.0 26.9 + - - -
199B PHE* 3.7 22.5 + - + +
225B ARG 3.1 2.2 + - - -
227B GLN* 1.3 79.7 - - - +
229B LEU* 1.3 65.3 + - - +
230B ALA 3.2 0.2 - - - -
231B ILE* 3.4 1.8 + - - -
232B LEU* 3.2 24.3 + - - +
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Residues in contact with LEU 229 (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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128B LEU* 3.7 24.2 - - + -
225B ARG* 3.3 19.8 + - + +
226B TYR* 3.5 17.7 + - + -
228B ASP* 1.3 76.7 - - - +
230B ALA* 1.3 57.5 + - - +
233B TRP* 2.8 34.0 + - - +
247B LEU* 3.9 17.1 - - + +
248B PHE* 3.8 27.4 - - + -
251B TYR* 3.9 33.7 - - + -
253B ILE* 3.7 28.7 - - + -
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Residues in contact with ALA 230 (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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226B TYR 2.9 20.7 + - - +
227B GLN 4.4 1.3 - - - +
229B LEU* 1.3 78.4 - - - +
231B ILE* 1.3 59.6 + - + +
233B TRP* 3.7 1.2 - - - +
234B ASN* 2.9 29.8 + - - +
261B LEU* 3.7 32.3 - - + +
264B HIS* 3.7 21.8 - - + -
265B LEU* 3.4 13.8 - - + +
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Residues in contact with ILE 231 (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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197B GLY 3.6 12.6 - - - +
198B ASP* 3.9 20.2 - - - +
199B PHE 3.7 23.1 - - - +
200B SER* 3.9 8.5 - - - -
227B GLN* 3.5 38.0 + - - +
228B ASP 3.4 4.1 + - - +
229B LEU 3.4 0.2 - - - -
230B ALA* 1.3 78.0 - - + +
232B LEU* 1.3 62.8 + - - +
234B ASN* 3.3 8.1 + - - +
235B CYS* 3.1 23.2 + - - -
264B HIS* 5.5 2.0 - - + +
265B LEU* 5.1 1.8 - - + -
268B ASP* 3.6 36.6 - - + +
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Residues in contact with LEU 232 (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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124B LEU* 4.1 21.1 - - + -
128B LEU* 5.0 2.5 - - + -
199B PHE* 3.4 44.3 + - + +
200B SER 4.6 1.1 - - - -
201B LEU* 3.7 38.8 - - + +
204B LEU* 4.9 1.8 - - + -
228B ASP 3.2 15.2 + - - +
229B LEU* 5.0 0.2 - - - -
231B ILE* 1.3 74.8 - - - +
233B TRP* 1.3 68.0 + - - +
235B CYS* 3.1 2.6 + - + -
236B LEU* 3.0 28.2 + - + +
247B LEU* 3.8 32.8 - - + -
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Residues in contact with TRP 233 (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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169B GLU* 5.6 3.4 - - - -
229B LEU 2.8 22.0 + - - +
230B ALA* 3.7 4.0 - - - +
232B LEU* 1.3 75.9 - - - +
234B ASN* 1.3 74.6 + - - +
236B LEU* 3.3 12.0 + - - -
237B GLY 3.4 0.5 + - - -
244B GLN* 2.9 80.4 + - + +
245B LYS* 4.7 2.4 - - - +
247B LEU* 3.7 10.0 - - + +
248B PHE* 3.2 30.0 - + + -
258B MSE 6.1 1.8 - - - -
261B LEU* 4.0 21.6 - - + +
265B LEU* 3.8 28.9 - - + -
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Residues in contact with ASN 234 (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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167B ASP* 3.1 35.3 + - - +
169B GLU* 5.5 1.4 - - - +
230B ALA 2.9 18.1 + - - +
231B ILE* 3.4 7.9 - - - +
232B LEU 3.1 0.2 - - - -
233B TRP* 1.3 89.6 - - - +
235B CYS* 1.3 64.2 + - - +
237B GLY* 3.0 13.9 + - - -
238B GLU* 3.2 9.4 - - - +
244B GLN* 4.4 1.2 + - - +
265B LEU* 3.7 18.0 - - + +
268B ASP* 5.9 1.2 + - - -
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Residues in contact with CYS 235 (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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200B SER* 3.6 30.3 - - - -
201B LEU* 3.7 30.4 - - + +
202B ASP* 6.4 0.9 - - - -
231B ILE* 3.1 17.5 + - - -
232B LEU* 3.1 8.7 + - - +
234B ASN* 1.3 79.7 - - - +
236B LEU* 1.3 61.2 + - - +
238B GLU* 2.8 29.1 + - - +
239B PHE* 3.7 7.4 - - - -
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Residues in contact with LEU 236 (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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110B LEU* 4.1 23.6 - - + -
121B VAL* 3.7 26.7 - - + -
124B LEU* 4.7 2.7 - - + -
201B LEU* 4.4 11.4 - - + -
232B LEU* 3.0 28.9 + - + +
233B TRP 3.7 5.4 - - - +
234B ASN 3.2 0.4 - - - -
235B CYS* 1.3 72.3 - - - +
237B GLY* 1.3 59.7 + - - +
238B GLU 3.1 0.2 - - - -
239B PHE* 2.9 22.7 + - + +
240B SER 3.1 15.2 + - - +
243B LEU* 3.7 24.9 - - + +
244B GLN* 3.7 15.7 - - + +
247B LEU* 3.8 27.4 - - + -
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Residues in contact with GLY 237 (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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233B TRP 3.4 4.8 + - - -
234B ASN 3.0 11.5 + - - -
236B LEU* 1.3 73.5 - - - +
238B GLU* 1.3 62.6 + - - +
239B PHE 3.0 7.0 + - - -
240B SER* 4.3 6.9 + - - -
244B GLN* 3.4 24.7 - - - -
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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