Contacts of the helix formed by residues 219 - 234 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173D PHE* 4.0 26.6 - - - +
177D MET* 4.4 12.8 - - - -
217D ASN 3.5 3.2 + - - -
218D GLU* 1.3 80.3 + - - +
220D TRP* 1.3 66.2 + - - -
221D SER 3.4 2.5 - - - -
222D THR* 2.9 19.9 + - - -
223D LEU* 3.0 10.4 + - - +
253D HIS* 3.9 4.0 - - - -
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Residues in contact with TRP 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D MET* 4.9 1.4 - - - +
185D LEU* 4.8 6.9 - - + +
219D GLY* 1.3 71.8 - - - +
221D SER* 1.3 69.8 + - - +
223D LEU* 3.7 3.6 - - - +
224D MET* 2.7 53.2 + - + +
253D HIS* 3.2 45.1 - - + +
254D LEU* 5.2 4.3 - - + -
257D LYS* 3.4 48.5 - - + +
258D LEU* 3.9 17.3 - - + -
261D TYR* 3.0 62.0 - + + -
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Residues in contact with SER 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D MET* 3.3 5.0 - - - +
180D SER* 2.7 33.5 + - - -
181D ASP* 2.8 30.4 + - - -
183D ILE 5.8 0.2 - - - -
185D LEU* 3.6 17.6 - - - +
219D GLY 3.4 0.4 - - - -
220D TRP* 1.3 89.6 - - - +
222D THR* 1.3 60.4 + - - +
224D MET* 4.4 0.2 - - - -
225D ARG* 3.0 30.7 + - - +
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Residues in contact with THR 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D PHE* 4.9 4.0 - - + -
177D MET* 4.2 13.8 - - - +
180D SER* 3.6 23.6 - - - +
218D GLU* 2.9 27.0 + - - +
219D GLY* 2.9 17.6 + - - -
221D SER* 1.3 79.1 + - - +
223D LEU* 1.3 61.6 + - - +
225D ARG* 3.4 12.2 + - - +
226D THR* 3.1 25.5 + - - -
302D ALA 3.4 2.3 - - - +
303D HIS* 4.3 3.9 - - - -
338D TYR* 4.5 3.1 - - - +
441D ILE* 3.9 26.0 - - + -
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Residues in contact with LEU 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ILE* 4.7 4.0 - - + -
215D PHE* 3.9 32.1 - - + -
218D GLU* 3.5 16.8 - - + -
219D GLY 3.0 11.7 + - - +
220D TRP* 3.8 3.1 - - - +
222D THR* 1.3 76.8 + - - +
224D MET* 1.3 84.0 + - + +
226D THR* 3.4 14.9 + - - -
227D VAL* 3.5 8.9 + - + +
244D LEU* 4.5 22.9 - - + -
254D LEU* 4.1 21.5 - - + -
258D LEU* 4.4 3.1 - - + -
302D ALA* 3.3 25.1 + - + +
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Residues in contact with MET 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D LEU* 4.1 18.8 - - + -
220D TRP* 2.7 51.6 + - + +
221D SER 4.3 0.4 - - - +
223D LEU* 1.3 104.3 - - + +
225D ARG* 1.3 64.7 + - - +
227D VAL* 3.2 9.8 + - - +
228D HIS* 3.0 28.5 + - - -
244D LEU* 4.8 4.0 - - + -
258D LEU* 3.0 37.7 - - + -
261D TYR* 3.9 21.1 - - + +
262D ILE* 3.9 7.0 - - + -
265D TRP* 4.6 7.6 - - - -
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Residues in contact with ARG 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D SER* 2.2 57.0 + - - +
183D ILE* 3.3 30.6 + - - +
184D SER 3.6 12.3 + - - -
185D LEU* 3.8 26.8 - - + +
187D ARG* 4.5 5.4 - - + +
221D SER 3.0 20.5 + - - +
222D THR* 3.8 18.5 - - - +
223D LEU 3.4 0.2 - - - -
224D MET* 1.3 76.1 - - - +
226D THR* 1.3 53.8 + - - +
228D HIS* 3.7 0.3 - - - +
229D SER* 2.7 36.8 + - - -
304D CYS 4.4 0.7 - - - +
305D GLU* 3.7 39.1 + - + +
338D TYR* 4.1 11.3 - - - -
441D ILE* 5.4 2.2 - - - +
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Residues in contact with THR 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ILE* 3.6 27.6 - - + -
222D THR 3.1 11.9 + - - -
223D LEU* 3.4 10.5 - - - -
224D MET 3.1 0.4 - - - -
225D ARG* 1.3 79.3 - - - +
227D VAL* 1.3 60.5 + - - +
229D SER* 3.3 3.1 + - - -
230D VAL* 3.1 33.1 + - + +
300D LEU* 4.9 2.5 - - + -
301D ASP 3.9 13.0 - - - +
302D ALA 3.2 6.9 + - - +
304D CYS* 2.7 46.4 + - + +
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Residues in contact with VAL 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ILE* 4.4 7.4 - - + -
223D LEU* 3.5 13.0 + - + +
224D MET* 3.2 13.1 + - - +
226D THR* 1.3 75.2 - - - +
228D HIS* 1.3 66.8 + - - +
230D VAL* 3.0 8.4 + - - +
231D ILE* 2.9 24.1 + - + +
242D ILE* 4.2 13.9 - - + -
244D LEU* 3.9 31.9 - - + -
262D ILE* 6.6 0.2 - - + -
265D TRP* 3.6 32.1 - - + -
269D VAL* 4.1 17.9 - - + -
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Residues in contact with HIS 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D LEU* 3.1 39.2 - - + +
186D ASP* 2.7 30.6 + - - +
224D MET* 3.0 25.3 + - + +
225D ARG 3.7 0.4 - - - +
227D VAL* 1.3 74.8 - - - +
229D SER* 1.3 63.3 + - - +
231D ILE* 3.8 4.5 - - - +
232D LYS* 2.9 27.8 + - - +
261D TYR* 2.7 29.5 + + - -
264D LEU* 4.5 11.2 - - + -
265D TRP* 3.5 31.2 + + - -
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Residues in contact with SER 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D LEU 4.5 2.0 + - - -
225D ARG* 2.7 22.1 + - - -
226D THR* 3.3 7.5 + - - +
227D VAL 3.1 0.2 - - - -
228D HIS* 1.3 75.6 - - - +
230D VAL* 1.3 63.8 + - - +
232D LYS* 3.8 2.6 - - - +
233D ARG* 3.2 41.9 + - - +
305D GLU* 3.8 13.4 - - - -
306D VAL* 3.0 35.5 + - - +
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Residues in contact with VAL 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D VAL* 4.2 21.8 - - + -
213D ILE* 5.2 1.6 - - + -
226D THR* 3.1 21.5 - - + +
227D VAL* 3.0 7.3 + - - +
229D SER* 1.3 80.3 - - - +
231D ILE* 1.3 62.3 + - - +
234D THR* 2.7 42.7 + - - +
239D LEU* 4.3 7.8 - - + +
242D ILE* 3.6 24.9 - - + -
300D LEU* 4.0 24.0 - - + -
306D VAL* 4.4 10.8 - - + -
310D TRP* 4.4 4.3 - - + -
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Residues in contact with ILE 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D VAL 2.9 17.1 + - - +
228D HIS* 3.9 4.3 - - - +
230D VAL* 1.3 77.3 - - - +
232D LYS* 1.3 62.6 + - - +
233D ARG 3.3 0.7 + - - -
234D THR 3.8 12.6 - - - +
236D ARG* 5.6 3.1 - - - +
239D LEU* 4.6 9.4 - - + -
242D ILE* 4.2 11.4 - - + -
265D TRP* 3.1 52.5 - - + +
268D LEU* 4.3 13.5 - - + -
269D VAL* 4.2 12.8 - - + -
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Residues in contact with LYS 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D GLU* 2.5 36.5 + - + +
142D PRO* 2.9 31.1 + - - -
143D PRO 4.8 0.2 - - - -
144D GLY 4.6 0.4 - - - +
186D ASP* 3.0 43.0 + - + +
187D ARG 4.6 1.0 - - - -
228D HIS 2.9 19.3 + - - +
229D SER* 3.8 5.8 - - - +
231D ILE* 1.3 79.1 - - - +
233D ARG* 1.3 71.6 + - + +
234D THR 3.7 0.8 + - - +
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Residues in contact with ARG 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D GLU* 3.0 33.8 + - - +
187D ARG 3.0 26.3 + - - -
189D VAL* 3.7 29.9 - - - +
229D SER* 3.2 32.5 + - - +
232D LYS* 1.3 91.0 - - + +
234D THR* 1.3 65.7 + - - +
235D PRO* 3.9 5.6 - - - +
305D GLU* 5.0 3.2 - - - +
306D VAL* 2.8 40.7 + - + +
307D ALA 3.7 22.2 - - - +
308D VAL* 3.9 11.9 - - + +
309D ASN* 4.7 8.4 + - - +
310D TRP* 3.8 10.8 + - - -
311D TYR* 5.1 0.9 - - - +
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Residues in contact with THR 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D VAL* 2.7 20.5 + - - +
231D ILE* 3.8 10.4 - - - +
232D LYS 3.7 1.0 - - - -
233D ARG* 1.3 80.4 - - - +
235D PRO* 1.3 85.3 - - + +
236D ARG* 3.2 9.0 + - - +
239D LEU* 3.9 26.7 - - + +
310D TRP* 3.1 25.8 + - + +
311D TYR* 3.7 31.0 - - + -
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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
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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