Contacts of the helix formed by residues 219 - 233 (chain B) in PDB entry 6IWQ
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 GLY 219 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B PHE* 3.6 28.8 - - - +
175B PHE* 6.3 0.2 - - - -
177B MET* 4.2 11.4 - - - -
217B ASN 3.5 3.6 + - - -
218B GLU* 1.3 81.1 + - - +
220B TRP* 1.3 67.3 + - - -
221B SER 3.4 2.5 - - - -
222B THR* 2.9 20.3 + - - -
223B LEU* 3.0 9.5 + - - +
253B HIS* 3.8 1.8 - - - -
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Residues in contact with TRP 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B MET* 4.5 2.6 - - + +
185B LEU* 4.8 9.3 - - + +
218B GLU 4.4 0.4 - - - -
219B GLY* 1.3 69.8 - - - -
221B SER* 1.3 70.4 + - - +
223B LEU* 3.0 6.6 + - + +
224B MET* 2.9 44.0 + - + +
253B HIS* 3.3 52.3 - - + +
254B LEU* 4.9 5.4 - - + -
257B LYS* 3.5 43.6 - - + +
258B LEU* 3.9 19.5 - - + -
261B TYR* 3.5 52.7 - + + -
494C ASP* 5.4 2.0 + - - +
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Residues in contact with SER 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B MET* 3.2 6.6 - - - +
180B SER* 2.7 34.3 + - - -
181B ASP* 2.8 29.8 + - - -
183B ILE 5.8 0.2 - - - -
185B LEU* 3.6 17.0 - - - +
219B GLY 3.4 0.4 - - - -
220B TRP* 1.3 89.6 - - - +
222B THR* 1.3 59.1 + - - +
225B ARG* 3.1 31.9 + - - +
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Residues in contact with THR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PHE* 4.6 11.7 - - + -
177B MET* 4.1 14.9 - - - +
180B SER* 3.6 21.3 - - - +
218B GLU* 2.9 24.8 + - - -
219B GLY* 2.9 17.9 + - - -
221B SER* 1.3 78.2 + - - +
223B LEU* 1.3 59.6 + - - +
225B ARG* 4.2 8.0 - - - +
226B THR* 2.9 27.2 + - - -
302B ALA 3.5 2.7 - - - +
303B HIS* 4.5 10.5 - - + -
338B TYR* 4.5 11.2 - - + +
441B ILE* 5.3 4.7 - - + -
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ILE* 4.2 24.0 - - + -
215B PHE* 4.2 26.2 - - + -
218B GLU* 3.8 11.0 - - + +
219B GLY 3.0 16.1 + - - +
220B TRP* 3.7 3.8 - - + +
222B THR* 1.3 78.2 + - - +
224B MET* 1.3 76.1 + - - +
226B THR* 3.2 18.2 - - - -
227B VAL* 3.3 14.9 + - + +
244B LEU* 4.6 7.4 - - + -
254B LEU* 3.8 26.7 - - + -
258B LEU* 4.3 13.0 - - + -
302B ALA* 3.6 14.4 - - + +
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Residues in contact with MET 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 3.9 18.8 - - + -
220B TRP* 2.9 36.7 + - + +
223B LEU* 1.3 83.3 - - - +
225B ARG* 1.3 61.6 + - - +
226B THR 3.1 1.6 - - - -
227B VAL* 3.2 14.3 + - + +
228B HIS* 2.7 37.6 + - + -
244B LEU* 5.4 1.3 - - + -
258B LEU* 4.0 25.1 - - - -
261B TYR* 3.6 20.9 - - + -
262B ILE* 3.8 7.6 - - + -
265B TRP* 3.2 43.1 - - + -
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Residues in contact with ARG 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B SER* 2.5 45.0 + - - +
183B ILE* 3.0 35.8 + - - +
184B SER 3.1 18.8 + - - -
185B LEU* 3.7 29.1 - - + +
187B ARG* 4.3 10.8 - - - +
221B SER 3.1 22.3 + - - +
222B THR* 4.2 9.4 - - - +
224B MET* 1.3 77.3 - - - +
226B THR* 1.3 56.7 + - - +
228B HIS* 3.5 1.1 - - - +
229B SER* 2.8 30.0 + - - +
305B GLU* 3.6 37.8 + - + +
338B TYR* 4.6 7.5 - - - -
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Residues in contact with THR 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ILE* 3.9 23.6 - - + -
222B THR 2.9 16.9 + - - -
223B LEU 3.2 10.7 + - - -
224B MET 3.1 0.2 - - - -
225B ARG* 1.3 78.9 - - - +
227B VAL* 1.3 63.3 + - - +
229B SER* 3.0 14.3 + - - -
230B VAL* 3.1 19.5 + - + +
300B LEU* 5.1 7.4 - - + -
301B ASP 4.0 14.8 - - - +
302B ALA* 2.9 14.3 + - - +
304B CYS* 3.1 32.9 + - - +
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ILE* 4.1 20.2 - - + -
223B LEU* 3.5 16.8 - - + +
224B MET* 3.2 19.8 + - + +
226B THR* 1.3 75.4 - - - +
228B HIS* 1.3 51.3 + - - +
230B VAL* 2.6 31.4 - - - +
231B ILE* 2.9 16.6 - - + +
242B ILE* 4.1 20.0 - - + -
244B LEU* 4.2 16.6 - - + -
265B TRP* 3.7 27.1 - - + -
269B VAL* 4.2 9.9 - - + -
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Residues in contact with HIS 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 3.0 39.4 - - + +
186B ASP* 2.6 27.6 + - - +
224B MET* 2.7 31.9 + - + +
225B ARG 3.5 0.9 - - - +
227B VAL* 1.3 72.7 - - - +
229B SER* 1.3 53.3 + - - +
230B VAL 2.6 18.7 - - - +
231B ILE* 3.7 8.4 - - - +
232B LYS* 3.1 21.0 + - - +
261B TYR* 2.9 23.8 + - - -
264B LEU* 4.9 0.7 - - + -
265B TRP* 3.5 27.7 + + - -
494C ASP* 4.7 0.9 - - - -
496C SER* 3.6 24.7 - - - -
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Residues in contact with SER 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU 4.6 1.6 + - - -
225B ARG* 2.8 18.6 + - - +
226B THR 3.0 11.0 + - - -
228B HIS* 1.3 69.4 - - - +
230B VAL* 1.3 62.8 + - - +
232B LYS* 3.7 4.5 - - - +
233B ARG* 3.0 49.6 + - - +
304B CYS 4.7 0.2 - - - -
305B GLU* 3.5 26.8 + - - +
306B VAL* 3.8 21.6 - - - +
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Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B VAL* 4.7 8.5 - - + -
213B ILE* 5.2 1.8 - - + -
226B THR* 3.1 19.5 - - + +
227B VAL* 2.6 20.6 - - - +
228B HIS 2.6 19.8 - - - +
229B SER* 1.3 74.0 - - - +
231B ILE* 1.3 72.9 + - + +
232B LYS 3.0 2.0 - - - -
234B THR* 3.5 17.7 - - - +
239B LEU* 3.8 13.0 - - + -
242B ILE* 3.6 24.7 - - + -
300B LEU* 4.6 18.6 - - + -
306B VAL* 4.3 7.8 - - + +
310B TRP* 4.5 14.1 - - + -
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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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227B VAL* 2.9 17.5 - - + +
228B HIS* 3.7 11.0 - - - +
230B VAL* 1.3 87.8 - - - +
232B LYS* 1.3 66.0 + - + +
233B ARG 3.3 0.4 - - - -
234B THR* 3.3 21.4 + - - +
236B ARG* 4.3 26.9 + - - +
239B LEU* 3.9 13.2 - - + +
242B ILE* 3.3 26.9 - - + -
265B TRP* 2.8 44.4 - - + +
268B LEU* 5.3 4.0 - - + -
269B VAL* 5.5 0.7 - - + -
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Residues in contact with LYS 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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141B GLU* 3.8 27.3 - - + +
142B PRO* 3.4 29.4 + - - -
143B PRO 6.0 0.2 - - - -
186B ASP* 3.3 42.4 + - + +
187B ARG 3.8 9.3 + - - -
188B SER* 4.2 2.0 - - - +
228B HIS 3.1 17.3 - - - +
229B SER* 3.7 4.0 - - - +
230B VAL 2.7 9.9 + - - -
231B ILE* 1.3 77.1 - - + +
233B ARG* 1.3 76.1 + - + +
234B THR 3.6 1.1 + - - +
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Residues in contact with ARG 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLU* 4.1 22.3 - - - +
187B ARG 2.8 29.5 + - - -
188B SER* 4.0 6.1 - - - +
189B VAL* 3.9 28.2 - - - +
229B SER* 3.0 37.9 + - - +
232B LYS* 1.3 94.2 - - + +
234B THR* 1.3 61.8 + - - +
235B PRO* 3.9 6.5 - - - +
305B GLU* 4.6 1.8 + - - +
306B VAL* 2.4 48.8 + - + +
307B ALA* 3.8 17.5 - - - +
308B VAL* 3.9 16.5 - - - +
309B ASN* 4.4 9.2 + - - -
310B TRP* 3.7 11.6 + - - -
311B TYR* 5.5 0.3 - - - +
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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
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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