Contacts of the helix formed by residues 220 - 233 (chain B) in PDB entry 4TNV
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 LEU 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B TYR* 5.8 0.9 - - + -
138B PRO* 5.4 4.0 - - + -
215B PHE* 5.3 0.4 - - + -
216B TYR* 3.3 42.9 + - + +
219B GLN* 1.3 99.5 - - + +
221B TYR* 1.3 67.1 + - + +
223B PRO* 3.5 9.0 - - - +
224B SER* 3.5 16.1 + - - -
259B GLN* 5.3 1.6 + - - +
263B ILE* 3.6 37.9 - - + +
267B LEU* 4.6 8.7 - - + -
276B ILE* 3.5 39.5 - - + -
279B TRP* 4.0 3.5 - - - -
280B ILE* 5.6 2.4 - - + +
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Residues in contact with TYR 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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137B TYR 3.8 7.1 + - - -
138B PRO* 3.9 8.6 - - + +
139B MET* 3.2 32.7 - - + +
213B PHE* 5.3 1.3 - + - -
216B TYR 3.3 25.1 - - - -
217B LEU* 3.3 23.3 + - + +
220B LEU* 1.3 80.5 - - + +
222B ILE* 1.3 67.8 + - + +
224B SER 3.1 7.6 + - - -
225B CYS* 3.2 6.3 + - - -
276B ILE* 3.8 17.6 - - + +
279B TRP* 3.1 65.6 - + + -
334B TYR* 2.6 23.8 + + - -
335B TRP* 3.5 26.0 - + + -
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Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU* 3.0 44.7 + - + +
218B LEU* 4.2 18.2 - - + +
221B TYR* 1.3 72.4 - - + +
223B PRO* 1.4 69.6 - - + +
225B CYS* 3.4 14.0 + - + +
226B MET* 3.3 40.7 + - + +
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Residues in contact with PRO 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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284A MET* 4.1 19.2 - - + +
218B LEU 3.4 20.4 - - - +
219B GLN* 3.4 19.3 - - - +
220B LEU 3.5 9.6 - - - +
221B TYR 3.4 3.8 - - - -
222B ILE* 1.4 89.6 - - + +
224B SER* 1.3 60.3 + - - +
226B MET* 3.3 17.2 + - - +
227B LEU* 3.2 22.5 + - - +
259B GLN* 3.3 26.0 - - - +
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Residues in contact with SER 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU 3.5 11.3 + - - -
221B TYR 3.1 1.8 + - - -
223B PRO* 1.3 74.8 - - - +
225B CYS* 1.3 60.8 + - - +
227B LEU* 2.9 12.2 + - - +
228B VAL* 2.9 34.0 + - - +
256B MET* 4.2 11.3 - - - +
259B GLN* 3.9 17.2 - - - +
279B TRP* 3.4 27.6 - - - -
280B ILE* 4.7 3.6 - - - +
283B CYS* 4.0 13.5 - - - -
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Residues in contact with CYS 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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221B TYR* 3.2 13.4 + - - -
222B ILE* 3.6 19.3 - - + +
224B SER* 1.3 75.2 - - - +
226B MET* 1.3 62.8 + - + +
228B VAL* 4.0 7.4 - - - +
229B ILE* 3.2 34.6 + - + +
279B TRP* 3.8 24.9 - - - -
327B PHE* 4.4 17.0 - - - -
331B ASN* 5.6 3.4 - - - -
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Residues in contact with MET 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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253A LEU* 5.8 2.2 - - + -
281A GLY 5.2 0.9 - - - +
284A MET* 4.1 24.9 - - + +
285A THR* 3.7 35.2 - - + +
288A PHE* 3.6 48.4 - - + -
222B ILE* 3.6 31.0 - - + +
223B PRO* 3.3 10.0 + - - +
224B SER 3.1 0.6 - - - -
225B CYS* 1.3 77.9 - - + +
227B LEU* 1.3 60.7 + - + +
229B ILE* 3.6 1.5 + - + -
230B VAL* 3.1 34.5 + - + +
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Residues in contact with LEU 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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253A LEU* 4.6 13.9 - - + -
257A THR* 4.6 0.7 - - - +
284A MET* 4.1 19.5 - - + -
223B PRO 3.2 22.2 + - - +
224B SER* 2.9 11.3 + - - +
226B MET* 1.3 80.7 - - + +
228B VAL* 1.3 64.8 + - + +
230B VAL* 3.3 6.0 + - - +
231B SER* 3.1 17.5 + - - -
252B THR* 3.4 19.0 - - + +
255B THR* 3.7 32.3 - - + +
256B MET* 3.8 35.7 - - + +
259B GLN* 4.3 10.5 - - + +
287B ILE* 4.4 9.4 - - + -
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Residues in contact with VAL 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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224B SER 2.9 20.2 + - - +
225B CYS 4.0 4.0 - - - +
226B MET 3.4 0.2 - - - -
227B LEU* 1.3 75.3 - - - +
229B ILE* 1.3 62.0 + - + +
231B SER* 2.3 29.4 + - - +
232B TRP* 3.4 37.9 - - + +
283B CYS* 3.9 33.9 - - + +
286B PHE* 4.2 11.9 - - + -
287B ILE* 4.6 5.2 - - + -
327B PHE* 3.8 30.3 - - + -
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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
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288A PHE* 4.1 26.9 - - + -
292A LEU* 5.4 7.0 - - + -
225B CYS* 3.2 24.8 + - + +
226B MET* 3.7 4.7 - - + +
228B VAL* 1.3 74.3 - - + +
230B VAL* 1.3 65.7 + - - +
232B TRP* 3.0 46.1 + - + +
233B VAL* 3.6 12.7 - - + +
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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
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250A VAL* 5.4 1.3 - - + -
253A LEU* 3.9 25.6 - - + -
288A PHE* 4.1 14.6 - - + +
291A LEU* 3.9 26.5 - - + -
226B MET 3.1 23.7 + - - +
227B LEU* 3.5 9.2 - - - +
228B VAL 3.3 0.2 - - - -
229B ILE* 1.3 75.6 - - - +
231B SER* 1.3 63.5 + - - +
232B TRP 3.0 1.6 + - - -
233B VAL* 3.1 29.1 - - + +
234B SER* 4.3 0.5 + - - -
248B LEU* 4.0 13.7 - - + +
252B THR* 3.7 20.2 - - + +
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Residues in contact with SER 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 LEU 3.1 11.7 + - - -
228B VAL* 2.3 31.9 + - - +
230B VAL* 1.3 75.5 - - - +
232B TRP* 1.3 65.6 + - - +
234B SER* 3.1 21.8 + - - -
235B PHE* 4.2 2.4 - - - -
248B LEU* 5.7 2.2 - - - -
249B GLY* 6.4 1.6 - - - -
252B THR* 4.0 18.8 - - - +
286B PHE 4.2 1.7 + - - -
287B ILE* 4.2 12.1 - - - +
290B ALA* 3.7 28.6 - - - +
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Residues in contact with TRP 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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228B VAL* 3.4 36.6 + - + +
229B ILE* 3.3 39.5 - - + +
230B VAL 3.0 0.8 - - - -
231B SER* 1.3 83.2 + - - +
233B VAL* 1.3 56.9 + - + +
234B SER 3.1 5.6 - - - -
235B PHE* 3.0 42.0 + + + +
236B TRP* 3.5 11.0 + - - +
286B PHE* 4.8 1.8 + + - -
290B ALA* 5.3 0.2 - - + -
320B ARG 6.1 0.4 - - - +
323B PHE* 3.3 50.7 + + + +
324B PRO* 3.5 37.0 - - + -
327B PHE* 3.7 22.0 - + + -
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Residues in contact with VAL 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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291A LEU* 5.9 5.6 - - + +
292A LEU* 5.0 12.8 - - + -
295A ALA* 4.5 23.3 - - + -
229B ILE* 3.6 18.4 - - + +
230B VAL* 3.1 20.9 - - + +
232B TRP* 1.3 76.6 - - + +
234B SER* 1.3 61.6 + - - +
235B PHE 3.2 1.3 + - - -
236B TRP* 3.5 22.0 + - + +
237B PHE* 3.7 22.1 - - + -
248B LEU* 3.8 21.3 - - + -
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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
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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