Contacts of the helix formed by residues 217 - 234 (chain B) in PDB entry 1Q6X
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 SER 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B SER* 5.5 0.2 - - - -
214B ARG* 4.4 0.4 - - - +
215B ARG 3.5 2.8 + - - -
216B LEU* 1.3 76.3 - - - +
218B GLU* 1.3 68.8 + - - +
219B GLY* 3.7 2.7 + - - -
220B ASP* 2.6 36.7 + - - -
221B LEU* 3.0 23.3 + - - +
363B ALA* 3.7 26.7 + - - -
364B ASP* 4.0 9.4 - - - -
365B SER* 4.1 9.4 + - - -
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Residues in contact with GLU 218 (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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125B ARG* 4.1 4.2 - - - +
128B ALA* 3.7 6.7 - - + +
129B CYS* 3.1 52.8 + - - +
132B SER* 4.6 15.8 + - - +
217B SER* 1.3 74.1 - - - +
219B GLY* 1.3 62.2 + - - +
221B LEU* 3.4 13.4 + - - +
222B PHE* 3.1 21.8 + - - +
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Residues in contact with GLY 219 (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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217B SER* 3.1 6.7 + - - -
218B GLU* 1.3 79.3 - - - +
220B ASP* 1.3 61.3 + - - +
222B PHE* 3.1 11.1 + - - +
223B THR* 3.0 24.6 + - - -
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Residues in contact with ASP 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ARG* 3.6 15.0 + - - -
216B LEU* 4.0 7.4 - - + -
217B SER* 2.6 37.0 + - - +
219B GLY* 1.3 72.3 - - - +
221B LEU* 1.3 61.9 + - - +
223B THR* 3.0 9.8 + - - -
224B GLN* 2.8 33.6 + - - +
365B SER* 3.6 21.5 + - - -
369B LEU* 3.7 27.8 - - + +
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Residues in contact with LEU 221 (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 ALA* 3.7 30.1 - - + +
131B ILE* 4.0 29.2 - - + -
132B SER* 4.1 11.7 - - - +
135B LEU* 4.9 4.0 - - + -
207B LEU* 4.2 19.1 - - + -
209B VAL* 4.8 7.4 - - + -
216B LEU* 4.0 30.3 - - + +
217B SER 3.0 19.5 + - - +
218B GLU* 3.7 11.4 - - - +
220B ASP* 1.3 75.8 - - - +
222B PHE* 1.3 57.2 + - - +
224B GLN* 3.3 6.1 + - - +
225B LEU* 2.9 39.7 + - + +
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Residues in contact with PHE 222 (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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121B ASN* 3.7 41.5 - - + -
124B LEU* 3.7 38.5 - - + +
125B ARG* 3.9 22.9 - - + -
128B ALA* 3.9 9.8 - - + +
218B GLU* 3.1 13.2 + - + +
219B GLY* 3.3 13.5 - - - +
220B ASP 3.1 0.2 - - - -
221B LEU* 1.3 77.7 - - - +
223B THR* 1.3 68.4 + - - +
225B LEU* 3.3 4.6 + - - +
226B ARG* 3.1 47.4 + - - +
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Residues in contact with THR 223 (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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219B GLY 3.0 13.6 + - - -
220B ASP* 3.0 13.0 + - - +
222B PHE* 1.3 83.5 - - - +
224B GLN* 1.3 64.0 + - + +
226B ARG* 3.3 18.7 + - - +
227B LYS* 3.4 35.6 + - + +
369B LEU* 6.1 3.4 - - + -
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Residues in contact with GLN 224 (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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207B LEU* 3.5 29.5 - - + +
208B ASP 5.6 1.6 + - - +
211B ILE* 5.6 2.6 - - - +
216B LEU* 4.4 12.2 - - + +
220B ASP 2.8 24.0 + - - +
221B LEU* 3.7 4.3 - - - +
223B THR* 1.3 75.0 - - - +
225B LEU* 1.3 62.1 + - - +
227B LYS* 3.1 38.2 + - - +
228B ILE* 3.2 25.2 + - - +
369B LEU* 3.9 20.3 - - + +
370B PRO 2.9 24.5 + - - -
372B PRO* 3.6 15.5 - - + +
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Residues in contact with LEU 225 (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* 3.8 38.8 - - + +
127B ALA* 4.0 10.8 - - + -
128B ALA* 3.8 19.7 - - + +
131B ILE* 4.6 9.2 - - + -
198B VAL* 4.0 33.9 - - + -
207B LEU* 4.3 10.3 - - + -
221B LEU 2.9 21.9 + - - +
222B PHE* 3.8 4.0 - - - +
224B GLN* 1.3 73.2 - - - +
226B ARG* 1.3 59.3 + - - +
228B ILE* 3.2 11.7 + - + +
229B VAL* 2.9 32.9 + - - +
280B VAL* 5.5 0.9 - - + -
282B LEU* 4.7 11.9 - - + -
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Residues in contact with ARG 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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121B ASN* 3.8 29.4 + - - +
124B LEU* 3.9 20.4 - - + +
222B PHE* 3.1 33.7 + - + +
223B THR* 3.4 14.1 + - - +
224B GLN 3.2 0.2 - - - -
225B LEU* 1.3 78.4 - - - +
227B LYS* 1.3 62.7 + - + +
229B VAL* 3.5 3.4 + - - +
230B LYS* 3.1 22.5 + - - +
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Residues in contact with LYS 227 (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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223B THR* 3.4 26.2 + - - +
224B GLN* 3.1 33.8 + - - +
225B LEU 3.2 0.4 - - - -
226B ARG* 1.3 75.3 - - + +
228B ILE* 1.3 61.7 + - - +
230B LYS* 3.2 9.5 + - - +
231B MET* 2.9 46.4 + - + +
368B GLU* 3.7 12.2 + - - -
369B LEU* 3.4 24.4 + - - +
371B ALA* 4.4 13.0 - - + +
372B PRO* 4.0 8.3 - - + -
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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
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198B VAL* 3.8 46.2 - - + -
200B CYS* 4.4 10.1 - - + -
205B PHE* 3.9 30.4 - - + -
207B LEU* 4.7 7.6 - - + -
224B GLN 3.2 15.4 + - - +
225B LEU* 3.2 16.3 + - + +
227B LYS* 1.3 75.0 - - - +
229B VAL* 1.3 61.6 + - - +
231B MET* 3.3 7.2 + - + +
232B ALA* 2.9 29.5 + - - +
282B LEU* 4.8 3.1 - - + -
372B PRO* 3.7 28.5 - - + -
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR* 4.7 15.5 - - + -
123B GLN* 5.7 1.6 - - - +
124B LEU* 3.9 18.2 - - + -
200B CYS* 4.3 13.5 - - - -
225B LEU 2.9 19.6 + - - +
226B ARG* 3.9 6.1 - - - +
228B ILE* 1.3 75.9 - - - +
230B LYS* 1.3 59.5 + - - +
232B ALA* 4.2 0.5 - - - +
233B SER* 2.6 43.1 + - - +
282B LEU* 3.7 27.6 - - + -
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Residues in contact with LYS 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 ARG 3.1 14.6 + - - +
227B LYS* 3.4 11.9 - - - +
228B ILE 3.2 0.2 - - - -
229B VAL* 1.3 80.2 - - - +
231B MET* 1.3 65.2 + - + +
233B SER* 3.5 10.7 + - - -
234B ASN* 3.6 10.7 + - - +
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Residues in contact with MET 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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205B PHE* 3.9 27.1 - - + -
227B LYS* 2.9 41.1 + - + +
228B ILE* 4.1 2.9 - - - +
230B LYS* 1.3 76.4 - - + +
232B ALA* 1.3 66.7 + - - +
234B ASN* 3.3 17.9 + - - +
371B ALA* 4.8 8.5 - - + -
372B PRO* 3.5 30.5 - - + +
374B ARG* 3.4 26.0 + - - +
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Residues in contact with ALA 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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200B CYS* 3.6 44.0 - - + +
201B CYS* 3.8 15.9 - - - +
203B GLN* 4.5 4.9 - - + +
205B PHE* 3.9 15.2 - - + -
228B ILE 2.9 18.0 + - - +
229B VAL 4.2 0.7 - - - +
231B MET* 1.3 77.6 - - - +
233B SER* 1.3 61.3 + - - +
234B ASN 3.3 6.2 + - - +
235B GLU* 4.8 2.6 - - - +
238B ARG* 4.9 3.3 + - - +
374B ARG* 4.4 6.5 + - - +
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Residues in contact with SER 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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200B CYS* 5.8 0.3 - - - -
201B CYS* 4.4 11.7 - - - -
229B VAL* 2.6 32.4 + - - +
230B LYS* 3.8 7.2 - - - -
231B MET 3.3 0.4 - - - -
232B ALA* 1.3 75.8 - - - +
234B ASN* 1.3 62.2 + - - +
235B GLU* 3.2 18.0 + - - +
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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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230B LYS 3.6 8.3 + - - +
231B MET* 3.3 17.6 + - - +
232B ALA 3.1 6.6 - - - +
233B SER* 1.3 76.1 - - - +
235B GLU* 1.3 68.4 + - - +
236B ASP* 3.4 32.2 + - - +
237B GLU* 3.6 23.9 + - - +
238B ARG* 4.1 7.1 + - - +
374B ARG* 4.4 4.0 + - - +
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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