Contacts of the helix formed by residues 219 - 234 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A PHE* 3.6 30.3 - - - -
175A PHE* 6.2 0.4 - - - -
177A MET* 4.2 11.4 - - - -
217A ASN 3.5 3.0 + - - -
218A GLU* 1.3 80.7 + - - +
220A TRP* 1.3 66.0 + - - -
221A SER 3.4 2.5 - - - -
222A THR* 2.9 20.0 + - - -
223A LEU* 3.0 9.4 + - - +
253A HIS* 3.9 1.6 - - - -
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Residues in contact with TRP 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A MET* 4.5 3.0 - - + +
181A ASP* 6.0 0.2 - - - +
185A LEU* 4.8 8.9 - - + +
218A GLU 4.4 0.4 - - - -
219A GLY* 1.3 69.8 - - - -
221A SER* 1.3 69.9 + - - +
223A LEU* 3.0 7.9 + - + +
224A MET* 2.9 48.3 + - + +
253A HIS* 3.2 45.8 - - + +
254A LEU* 5.2 4.5 - - + -
257A LYS* 3.3 52.1 - - + +
258A LEU* 3.9 20.0 - - + -
261A TYR* 3.5 49.5 - + + -
494D ASP* 5.6 1.0 + - - -
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Residues in contact with SER 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A MET* 3.1 7.6 - - - +
180A SER* 2.7 34.2 + - - -
181A ASP* 2.8 27.4 + - - -
183A ILE 5.8 0.2 - - - -
185A LEU* 3.6 16.0 - - - +
219A GLY 3.4 0.4 - - - -
220A TRP* 1.3 89.9 - - - +
222A THR* 1.3 56.8 + - - +
224A MET* 4.9 0.2 - - - -
225A ARG* 3.1 33.0 + - - +
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Residues in contact with THR 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PHE* 4.6 6.5 - - + -
177A MET* 4.2 11.9 - - - -
180A SER* 3.6 23.8 - - - +
218A GLU* 2.9 24.8 + - - -
219A GLY* 2.9 18.1 + - - -
221A SER* 1.3 77.0 + - - +
223A LEU* 1.3 59.7 + - - +
225A ARG* 4.2 7.3 - - - +
226A THR* 2.9 27.9 + - - -
302A ALA 3.4 2.6 - - - +
303A HIS* 4.3 3.5 - - - -
338A TYR* 4.5 2.9 - - - +
441A ILE* 3.7 30.7 - - + +
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ILE* 4.2 24.9 - - + -
215A PHE* 4.2 26.0 - - + -
218A GLU* 3.8 10.5 - - + -
219A GLY 3.0 16.9 + - - +
220A TRP* 3.7 5.8 - - + +
222A THR* 1.3 78.4 + - - +
224A MET* 1.3 76.2 + - - +
226A THR* 3.2 17.7 + - - -
227A VAL* 3.3 9.3 + - + +
244A LEU* 4.6 13.0 - - + -
254A LEU* 3.9 25.1 - - + -
258A LEU* 4.5 11.9 - - + -
302A ALA* 3.4 16.4 - - + +
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Residues in contact with MET 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 3.9 19.3 - - + -
220A TRP* 2.9 44.6 + - + +
223A LEU* 1.3 84.3 - - - +
225A ARG* 1.3 63.0 + - - +
226A THR 3.1 1.6 - - - -
227A VAL* 3.1 16.0 + - + +
228A HIS* 2.7 36.8 + - + -
244A LEU* 5.4 1.8 - - + -
258A LEU* 3.9 25.4 - - - -
261A TYR* 3.8 9.6 - - + -
262A ILE* 3.6 11.2 - - + -
265A TRP* 3.4 39.3 - - + -
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Residues in contact with ARG 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A SER* 2.5 44.4 + - - +
183A ILE* 3.0 35.8 + - - +
184A SER 3.1 18.7 + - - -
185A LEU* 3.7 30.5 - - + +
187A ARG* 4.2 7.6 - - - +
221A SER 3.1 23.1 + - - +
222A THR* 4.2 8.8 - - - +
224A MET* 1.3 76.6 - - - +
226A THR* 1.3 53.0 + - - +
228A HIS* 3.6 0.7 - - - +
229A SER* 2.7 33.5 + - - -
304A CYS 5.3 0.2 - - - +
305A GLU* 3.5 40.6 + - + -
338A TYR* 4.6 9.1 - - - -
441A ILE* 5.9 1.0 - - - +
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Residues in contact with THR 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ILE* 3.9 24.2 - - + -
222A THR 2.9 17.3 + - - -
223A LEU 3.2 10.7 + - - -
224A MET 3.1 0.2 - - - -
225A ARG* 1.3 77.6 - - - +
227A VAL* 1.3 61.3 + - - +
229A SER* 3.1 6.3 + - - +
230A VAL* 3.0 31.6 + - + +
300A LEU* 5.1 2.9 - - + -
301A ASP 4.0 15.5 - - - +
302A ALA* 3.1 8.4 + - - +
304A CYS* 2.8 42.2 + - + +
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ILE* 4.0 20.9 - - + -
223A LEU* 3.3 12.1 + - + +
224A MET* 3.1 18.9 + - + +
226A THR* 1.3 75.4 - - - +
228A HIS* 1.3 67.5 + - - +
230A VAL* 3.0 8.4 + - - +
231A ILE* 2.9 24.0 + - + +
242A ILE* 4.3 12.1 - - + -
244A LEU* 4.0 19.7 - - + -
265A TRP* 3.7 30.5 - - + -
269A VAL* 4.2 16.2 - - + -
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Residues in contact with HIS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 3.1 43.0 - - + +
186A ASP* 2.7 27.6 + - - +
224A MET* 2.7 31.5 + - + +
227A VAL* 1.3 72.0 - - - +
229A SER* 1.3 63.1 + - - +
231A ILE* 3.3 6.0 + - - +
232A LYS* 2.9 27.6 + - - +
261A TYR* 2.6 29.6 + - - -
264A LEU* 4.5 3.1 - - + -
265A TRP* 3.7 26.8 + + - -
494D ASP* 4.8 0.9 - - - -
496D SER* 3.8 17.5 - - - -
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Residues in contact with SER 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU 4.5 1.7 + - - -
225A ARG* 2.7 23.5 + - - -
226A THR 3.1 7.4 + - - -
228A HIS* 1.3 75.7 - - - +
230A VAL* 1.3 64.5 + - - +
232A LYS* 3.4 3.0 + - - +
233A ARG* 3.2 41.1 + - - +
304A CYS 4.6 0.2 + - - -
305A GLU* 3.8 12.9 - - - -
306A VAL* 3.0 36.4 + - - +
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Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A VAL* 4.3 19.1 - - + -
213A ILE* 5.2 2.0 - - + -
226A THR* 3.0 22.1 + - + +
227A VAL* 3.0 6.7 + - - +
229A SER* 1.3 80.5 - - - +
231A ILE* 1.3 61.5 + - - +
234A THR* 2.7 42.2 + - - +
239A LEU* 4.6 6.1 - - + -
242A ILE* 3.8 21.8 - - + -
300A LEU* 4.0 24.5 - - + -
306A VAL* 4.4 10.1 - - + -
310A TRP* 4.2 9.6 - - + -
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Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A VAL* 2.9 18.2 + - + +
228A HIS* 3.9 5.2 - - - +
230A VAL* 1.3 75.4 - - - +
232A LYS* 1.3 63.0 + - - +
233A ARG 3.3 0.9 + - - -
234A THR 3.8 12.4 - - - +
236A ARG* 5.9 1.6 - - - +
239A LEU* 4.7 7.2 - - + -
242A ILE* 3.7 22.0 - - + -
265A TRP* 3.1 50.3 - - + +
268A LEU* 4.4 11.7 - - + -
269A VAL* 4.3 5.4 - - + -
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Residues in contact with LYS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLU* 2.5 37.4 + - + +
142A PRO* 2.9 31.5 + - - -
144A GLY* 4.6 0.8 - - - +
186A ASP* 3.0 42.2 + - + +
187A ARG 4.0 3.0 + - - +
228A HIS 2.9 18.0 + - - +
229A SER* 3.8 5.2 - - - +
231A ILE* 1.3 78.4 - - - +
233A ARG* 1.3 70.2 + - + +
234A THR 3.7 0.8 + - - -
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Residues in contact with ARG 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLU* 3.0 30.8 + - - +
187A ARG 3.0 26.9 + - - -
189A VAL* 3.5 31.8 - - - +
229A SER* 3.2 32.7 + - - +
232A LYS* 1.3 90.5 - - + +
234A THR* 1.3 63.9 + - - +
235A PRO* 3.9 5.4 - - - +
305A GLU* 5.0 2.8 - - - +
306A VAL* 2.8 39.8 + - + +
307A ALA 3.7 22.7 - - - +
308A VAL* 3.8 13.0 - - + +
309A ASN* 4.5 8.5 + - - -
310A TRP* 3.5 12.3 + - - -
311A TYR* 5.2 0.2 - - - +
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Residues in contact with THR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A VAL* 2.7 19.9 + - - +
231A ILE 3.8 10.8 - - - +
232A LYS 5.0 0.7 - - - +
233A ARG* 1.3 79.8 - - - +
235A PRO* 1.3 85.7 - - + +
236A ARG* 3.3 7.3 + - - +
239A LEU* 4.1 26.6 - - + +
310A TRP* 2.9 27.7 + - + +
311A TYR* 3.9 29.2 - - + -
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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