Contacts of the helix formed by residues 225 - 239 (chain B) in PDB entry 2H3W
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 THR 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B GLU* 3.9 8.5 - - - +
223B PRO 4.8 4.0 - - - +
224B LEU* 1.3 75.1 - - - +
226B SER* 1.3 67.0 + - - +
227B ASP* 3.5 9.8 + - - +
228B GLN* 2.9 42.7 + - - +
229B ILE* 2.8 24.8 + - - +
368B VAL 5.9 2.0 - - - +
369B ARG* 6.1 1.8 - - - -
370B SER* 2.9 40.4 + - - +
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Residues in contact with SER 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ARG* 6.2 0.2 - - - -
140B ALA* 3.4 24.8 - - - +
141B LYS* 4.2 17.7 - - - -
144B GLU* 3.0 29.4 + - - -
225B THR* 1.3 72.0 - - - +
227B ASP* 1.3 60.2 + - - +
229B ILE* 3.1 4.8 + - - -
230B PHE* 2.7 32.7 + - - +
366B GLU* 4.5 1.6 + - - -
369B ARG* 3.2 31.9 + - - -
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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
----------------------------------------------------------
137B ARG* 3.6 20.5 + - - +
225B THR* 3.1 9.9 + - - +
226B SER* 1.3 83.0 + - - +
228B GLN* 1.3 61.7 + - + +
230B PHE* 3.3 8.9 + - - +
231B VAL* 3.1 28.0 + - + +
369B ARG* 3.2 46.1 + - - +
370B SER 4.5 11.0 + - - +
372B MET* 5.1 4.7 - - + -
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Residues in contact with GLN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B HIS* 2.8 37.7 + - - -
224B LEU* 3.3 8.9 - - + +
225B THR* 2.9 42.0 + - - +
227B ASP* 1.3 74.3 - - + +
229B ILE* 1.3 67.2 + - - +
231B VAL* 3.3 4.7 + - - +
232B GLN* 3.1 26.2 + - - +
370B SER* 3.9 5.8 + - - +
371B PRO 3.6 19.8 - - - +
372B MET* 3.8 25.5 - - - -
373B VAL* 4.0 11.0 - - - +
375B LEU* 3.6 15.7 - - + +
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Residues in contact with ILE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ALA* 3.7 22.7 - - + +
143B ILE* 3.6 51.6 - - + -
144B GLU* 4.1 9.4 - - - +
147B LEU* 4.6 4.9 - - + -
214B LEU* 4.7 6.3 - - + -
216B VAL* 4.8 5.2 - - + -
224B LEU* 3.9 30.7 - - + +
225B THR 2.8 20.3 + - - +
226B SER* 3.5 6.5 - - - +
228B GLN* 1.3 76.7 - - - +
230B PHE* 1.3 59.2 + - - +
232B GLN* 3.1 9.2 + - - +
233B LEU* 2.8 32.3 + - + +
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Residues in contact with PHE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 6.3 0.2 - - + -
133B GLN* 3.7 21.8 - - + -
136B LEU* 3.6 31.9 - - + -
137B ARG* 3.0 63.5 - - - +
140B ALA* 3.7 10.2 - - + +
226B SER 2.7 14.0 + - - +
227B ASP 3.4 10.1 - - - +
228B GLN 3.2 0.2 - - - -
229B ILE* 1.3 76.3 - - - +
231B VAL* 1.3 70.0 + - + +
233B LEU* 3.1 6.8 + - - +
234B GLU* 2.9 59.5 + - + +
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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
----------------------------------------------------------
227B ASP* 3.1 15.2 + - + +
228B GLN 3.3 7.2 + - - +
230B PHE* 1.3 83.5 - - + +
232B GLN* 1.3 62.5 + - - +
234B GLU* 3.3 17.2 + - - +
235B LYS* 3.3 39.7 + - - +
372B MET* 3.4 39.5 - - + -
375B LEU* 4.2 4.3 - - + -
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Residues in contact with GLN 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 3.4 31.3 - - + +
215B ASP 5.1 1.2 + - - +
224B LEU* 4.3 11.0 - - + +
228B GLN 3.1 13.7 + - - +
229B ILE 3.1 8.4 + - - +
231B VAL* 1.3 75.4 - - - +
233B LEU* 1.3 64.8 + - - +
235B LYS* 2.8 38.1 + - - +
236B ILE* 3.0 26.8 + - - +
375B LEU* 3.7 23.2 - - + +
376B PRO* 3.0 29.7 + - - +
378B PRO* 3.9 11.6 - - + +
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 3.5 45.2 - - + +
139B ALA* 3.8 13.5 - - + -
140B ALA* 3.7 21.5 - - + +
143B ILE* 4.3 8.3 - - + -
205B VAL* 4.2 25.4 - - + -
214B LEU* 4.1 20.9 - - + -
229B ILE* 2.8 19.4 + - + +
230B PHE* 3.1 7.4 + - - +
232B GLN* 1.3 75.0 - - - +
234B GLU* 1.3 57.6 + - - +
236B ILE* 3.3 5.4 + - + +
237B TRP* 2.9 31.0 + - - +
286B VAL* 5.7 0.7 - - + -
288B LEU* 4.8 6.9 - - + +
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Residues in contact with GLU 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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132B LEU* 5.6 3.9 - - + +
136B LEU* 3.9 15.7 - - + -
230B PHE* 2.9 52.6 + - + +
231B VAL* 3.5 17.0 - - - +
232B GLN 3.2 0.4 - - - -
233B LEU* 1.3 78.4 - - - +
235B LYS* 1.3 61.5 + - + +
237B TRP* 3.4 1.9 + - - +
238B ASN* 3.0 39.4 + - - +
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Residues in contact with LYS 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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231B VAL* 3.3 23.9 + - + +
232B GLN* 2.8 35.3 + - - +
234B GLU* 1.3 77.9 - - + +
236B ILE* 1.3 62.1 + - - +
238B ASN* 3.3 7.8 + - - +
239B SER* 2.8 30.0 + - - -
372B MET* 5.8 0.2 - - - +
375B LEU* 3.2 32.1 + - - +
376B PRO 3.3 5.4 + - - +
377B MET* 3.9 28.7 - - + +
378B PRO* 3.9 11.9 - - + -
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Residues in contact with ILE 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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205B VAL* 4.0 36.8 - - + -
207B HIS* 4.8 5.4 - - + -
212B PHE* 3.4 49.1 - - + -
214B LEU* 4.2 13.7 - - + -
232B GLN 3.0 14.3 + - - +
233B LEU* 3.6 9.2 - - + +
235B LYS* 1.3 75.6 - - - +
237B TRP* 1.3 65.7 + - - +
239B SER* 2.9 13.9 + - - -
240B SER* 3.0 16.0 + - - +
288B LEU* 5.3 1.6 - - + -
377B MET* 6.0 0.4 - - - -
378B PRO* 3.5 32.3 - - + -
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Residues in contact with TRP 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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132B LEU* 3.5 45.1 - - + +
135B GLN* 3.9 19.1 - - - -
136B LEU* 4.0 14.8 - - + -
207B HIS* 3.3 45.8 - + - -
233B LEU 2.9 17.5 + - - +
234B GLU* 3.6 7.4 - - - +
236B ILE* 1.3 78.6 - - - +
238B ASN* 1.3 66.1 + - - +
240B SER* 3.1 19.4 + - - -
241B LEU* 3.5 31.0 + - + +
288B LEU* 4.0 20.6 - - + +
289B ASP 4.8 5.2 - - - -
290B LYS* 5.9 2.0 - - - -
333B GLU* 6.0 2.5 - - + -
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Residues in contact with ASN 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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234B GLU* 3.0 33.1 + - - +
235B LYS* 3.7 5.7 - - - +
237B TRP* 1.3 86.5 - - - +
239B SER* 1.3 60.0 + - - +
240B SER 3.2 1.7 + - - -
241B LEU* 3.6 30.5 + - + +
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Residues in contact with SER 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B PHE* 3.8 17.3 - - - -
235B LYS 2.8 20.0 + - - -
236B ILE 2.9 7.1 + - - -
238B ASN* 1.3 77.2 - - - +
240B SER* 1.3 58.1 + - - +
241B LEU 3.9 0.4 - - - -
377B MET* 4.2 19.8 - - - +
380B LYS* 2.9 30.8 + - - -
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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