Contacts of the helix formed by residues 224 - 241 (chain B) in PDB entry 6GES
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 LYS 224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B HIS* 2.8 68.9 + - + +
159B SER* 5.0 0.6 - - - +
161B ASN* 3.1 29.1 + - - +
163B LEU* 3.4 21.8 - - + -
191B ALA* 4.4 11.9 - - + -
223B THR* 1.3 70.5 - - - +
225B SER* 1.3 65.0 + - - +
226B ILE 3.1 2.5 - - - -
227B ASP 3.0 13.2 + - - +
228B ILE* 3.4 8.1 + - + +
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Residues in contact with SER 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLU* 4.1 2.3 + - - -
223B THR* 3.1 19.0 + - - -
224B LYS* 1.3 79.0 - - - +
226B ILE* 1.3 62.1 + - - +
227B ASP 3.2 0.2 - - - -
228B ILE* 3.4 9.8 + - - -
229B TRP 3.2 12.6 + - - -
315B PRO* 3.5 36.2 - - - +
318B ARG* 3.0 33.3 + - - -
319B ILE 5.8 0.2 - - - -
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Residues in contact with ILE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 5.1 1.6 - - + -
165B ARG* 3.6 37.0 - - + -
204B TYR* 4.3 7.4 - - - +
210B TYR 4.9 0.3 - - - +
212B ALA* 4.2 9.4 + - + +
214B GLU* 3.7 21.1 - - + +
215B ILE* 4.0 15.9 - - + -
219B SER* 4.7 2.0 - - - +
221B GLY* 3.8 29.8 - - - +
223B THR* 3.1 19.9 + - - +
224B LYS 3.1 0.4 - - - -
225B SER* 1.3 80.7 + - - +
227B ASP* 1.3 74.3 + - - +
229B TRP* 3.6 4.9 + - - +
230B SER* 3.2 24.8 + - - +
318B ARG* 4.4 2.2 - - - +
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Residues in contact with ASP 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 3.9 5.3 - - + +
158B HIS* 2.9 28.0 + - + +
163B LEU* 3.5 5.7 - - - +
164B HIS* 2.9 22.9 + - - -
165B ARG* 2.9 29.6 + - - -
167B LEU* 3.9 23.3 - - + +
224B LYS 3.0 9.4 + - - +
226B ILE* 1.3 81.4 - - - +
228B ILE* 1.3 65.4 - - - +
230B SER* 3.3 6.9 + - - -
231B VAL* 3.0 26.8 + - - +
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Residues in contact with ILE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 4.8 8.7 - - + -
154B LEU* 4.1 17.0 - - + -
158B HIS* 4.8 2.7 - - + -
224B LYS* 3.8 13.5 - - + +
225B SER* 3.4 10.7 + - - +
226B ILE 3.4 0.2 - - - -
227B ASP* 1.3 74.7 - - - +
229B TRP* 1.3 66.8 + - - +
231B VAL* 3.1 5.9 + - + +
232B GLY* 2.9 19.2 + - - -
310B MET* 4.0 13.2 - - + +
318B ARG* 3.9 16.8 - - + -
319B ILE* 3.3 38.1 - - + +
320B THR* 4.0 2.9 - - - +
321B VAL* 3.7 33.4 - - + +
324B ALA* 5.4 1.6 - - + -
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Residues in contact with TRP 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B TRP 5.2 0.2 + - - -
210B TYR 3.5 14.1 - - - -
211B ARG 3.4 11.7 + - - -
212B ALA* 3.4 26.9 - - + -
213B PRO* 3.6 32.3 - - + -
225B SER 3.2 3.8 + - - -
226B ILE 3.7 4.5 - - - +
227B ASP 3.3 0.2 - - - -
228B ILE* 1.3 79.6 - - - +
230B SER* 1.3 65.1 + - - +
232B GLY* 3.0 4.3 + - - -
233B CYS* 3.0 32.5 + - - -
245B PHE* 3.5 25.4 - + - -
257B ILE* 3.7 26.0 - - + -
261B LEU* 3.8 9.6 - - + -
310B MET 3.9 8.5 - - - -
311B LEU* 3.6 46.9 - - + +
312B THR 3.7 6.7 - - - -
318B ARG* 3.7 23.1 - - - +
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Residues in contact with SER 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ARG 5.6 3.3 - - - -
167B LEU* 3.5 35.2 + - - -
210B TYR* 2.9 26.2 + - - +
226B ILE* 3.2 12.9 + - - +
227B ASP* 3.3 11.1 + - - -
228B ILE 3.3 0.4 - - - -
229B TRP* 1.3 79.6 - - - +
231B VAL* 1.3 61.3 + - - +
233B CYS* 3.1 7.5 + - - +
234B ILE* 3.0 27.3 + - - +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 3.8 18.6 - - + +
150B ILE* 3.9 21.5 - - + -
151B LEU* 4.1 8.7 - - + -
154B LEU* 3.9 22.2 - - + -
167B LEU* 4.0 10.3 - - + -
227B ASP 3.0 19.1 + - - +
228B ILE* 3.1 9.2 + - - +
230B SER* 1.3 72.3 - - - +
232B GLY* 1.3 61.5 + - - +
234B ILE* 3.1 11.2 + - + +
235B LEU* 2.9 27.5 + - - +
310B MET* 3.7 24.9 - - + -
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Residues in contact with GLY 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ILE 2.9 11.3 + - - -
229B TRP 3.0 4.9 + - - -
231B VAL* 1.3 76.5 - - - +
233B CYS* 1.4 61.3 + - - +
235B LEU* 3.2 2.1 + - - -
236B ALA* 3.0 19.4 + - - +
307B LEU* 3.2 13.8 - - - +
310B MET* 3.8 27.7 - - - -
311B LEU* 3.8 14.4 - - - -
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Residues in contact with CYS 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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209B TRP 4.0 11.2 - - - +
210B TYR* 3.7 22.9 - - + -
229B TRP* 3.0 46.0 + - - -
230B SER 3.1 7.1 + - - +
232B GLY* 1.4 76.7 - - - +
234B ILE* 1.3 58.2 + - - +
236B ALA* 3.5 3.5 + - - +
237B GLU* 3.0 29.0 + - - +
244B ILE* 4.1 16.7 + - + +
245B PHE* 3.9 22.7 - - - -
311B LEU* 3.9 1.3 - - - +
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Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 3.8 27.8 - - + -
147B LEU* 6.3 0.2 - - + -
150B ILE* 4.1 20.6 - - + -
167B LEU* 3.8 13.7 - - + -
168B LYS* 3.7 36.6 - - - +
169B PRO* 4.1 9.2 - - + -
172B LEU* 4.0 13.5 - - + -
210B TYR* 4.6 3.8 - - + -
230B SER 3.0 19.3 + - - +
231B VAL* 3.1 14.6 + - + +
233B CYS* 1.3 75.0 - - - +
235B LEU* 1.3 60.7 + - - +
237B GLU* 3.1 8.7 + - - +
238B MET* 2.9 31.6 + - + +
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Residues in contact with LEU 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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143B ILE* 3.8 27.4 - - + -
147B LEU* 4.2 33.0 - - + -
231B VAL 2.9 12.7 + - - +
232B GLY* 3.2 8.3 + - - +
234B ILE* 1.3 76.2 - - - +
236B ALA* 1.3 63.6 + - - +
238B MET* 3.0 12.4 + - + +
239B LEU* 3.0 37.0 + - + +
303B ALA* 3.9 24.2 - - + +
306B LEU* 4.7 2.7 - - + -
307B LEU* 4.0 23.6 - - + +
310B MET* 4.4 9.2 - - - -
329B TYR* 4.8 3.6 - - + -
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Residues in contact with ALA 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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232B GLY 3.0 12.7 + - - +
233B CYS 3.6 8.3 - - - +
235B LEU* 1.3 76.7 - - - +
237B GLU* 1.3 61.5 + - - +
239B LEU* 3.1 20.8 + - - +
240B SER* 3.0 21.7 + - - -
242B ARG 4.5 0.7 - - - -
244B ILE* 3.8 33.9 - - + -
296B PHE* 3.7 15.7 - - + -
307B LEU* 3.9 7.6 - - + +
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Residues in contact with GLU 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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130B TYR* 5.2 9.0 - - - -
133B LEU* 3.8 17.6 - - + +
169B PRO* 3.9 13.8 - - + +
209B TRP* 5.7 0.9 - - - -
210B TYR* 2.6 39.4 + - - -
233B CYS 3.0 15.1 + - - +
234B ILE* 3.1 8.2 + - - +
236B ALA* 1.3 78.9 - - - +
238B MET* 1.3 54.8 + - - +
241B ASN* 2.7 35.0 + - - -
242B ARG* 3.4 23.4 + - - +
243B PRO* 3.7 28.4 - - + +
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Residues in contact with MET 238 (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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129B LEU* 3.9 24.7 - - + -
133B LEU* 3.9 14.2 - - + +
138B LEU* 4.2 22.5 + - + +
143B ILE* 3.4 49.9 - - + +
146B PHE* 3.8 22.2 - - + -
147B LEU* 4.1 21.8 - - + +
150B ILE* 4.5 4.0 - - + -
234B ILE* 2.9 22.7 + - + +
235B LEU* 3.5 21.5 - - + +
237B GLU* 1.3 76.9 - - - +
239B LEU* 1.3 61.5 + - - +
241B ASN* 4.4 7.8 - - - +
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Residues in contact with LEU 239 (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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137B GLN* 5.4 6.4 + - - +
140B ASN* 5.4 3.4 - - - +
143B ILE* 3.8 26.7 - - + -
235B LEU* 3.0 33.0 + - + +
236B ALA* 3.1 14.0 + - - +
238B MET* 1.3 77.0 - - - +
240B SER* 1.3 58.4 + - - +
241B ASN* 4.8 2.3 - - - +
296B PHE* 3.8 19.0 - - + -
299B SER* 3.6 26.0 + - - +
300B ASP 5.5 0.4 - - - +
303B ALA* 4.7 12.1 - - + -
304B LEU* 4.0 26.0 - - + -
307B LEU* 4.4 6.1 - - + -
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Residues in contact with SER 240 (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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236B ALA 3.0 13.5 + - - -
239B LEU* 1.3 78.6 - - - +
241B ASN* 1.3 75.1 + - - +
242B ARG* 3.3 33.4 + - - +
295B LEU 5.6 1.6 - - - -
296B PHE* 3.7 23.0 - - - -
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Residues in contact with ASN 241 (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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133B LEU* 2.8 44.6 + - - +
134B LYS* 5.5 4.7 + - - -
136B GLN 2.9 24.0 + - - -
137B GLN* 3.8 24.2 + - - +
138B LEU 4.5 0.7 + - - -
237B GLU* 2.7 24.3 + - - -
238B MET 4.4 7.3 - - - +
239B LEU 4.8 1.0 - - - +
240B SER* 1.3 77.7 + - - +
242B ARG* 1.3 58.3 + - - +
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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
------------------------------------------------------------
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