Contacts of the helix formed by residues 221 - 232 (chain B) in PDB entry 5XVO
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 PHE 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B LEU* 3.7 23.5 - - + +
187B PHE* 3.5 33.0 - + + -
217B LEU 4.0 4.7 - - - -
218B MET 2.9 13.0 + - - +
220B PRO* 1.3 83.6 - - + +
222B ARG* 1.3 65.3 + - - +
223B PRO* 3.2 3.6 - - - -
224B LEU* 2.9 24.4 + - + +
261B LEU* 3.9 22.7 - - + -
264B ILE* 3.9 21.8 - - + -
265B ALA* 5.2 0.2 - - - -
268B TYR* 4.0 32.5 - + + -
286B PHE* 3.6 48.0 - + + -
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Residues in contact with ARG 222 (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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112B LYS* 4.4 14.1 - - + +
116B GLN* 6.3 0.9 - - - +
180B TYR* 3.5 33.9 + - + +
183B LEU* 4.0 4.9 - - - +
215B SER* 4.1 6.1 + - - +
218B MET* 3.5 41.7 + - + +
219B GLU* 3.0 44.5 + - - +
221B PHE* 1.3 77.7 - - - +
223B PRO* 1.3 69.8 - - + +
225B VAL* 2.9 17.3 + - - +
226B ASP* 3.1 15.9 + - - +
5H G 5.7 3.0 + - - -
5R C 2.7 51.3 + - - +
6R G 4.6 6.1 + - - -
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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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112B LYS* 4.3 3.4 - - + +
115B ASN* 3.7 39.7 - - + +
116B GLN* 3.9 13.7 - - + +
119B HIS* 4.7 1.7 + - + -
155B TYR* 4.3 5.2 - - - +
219B GLU 4.0 2.7 - - - +
220B PRO 3.4 11.9 - - - +
221B PHE 3.4 4.3 - - - -
222B ARG* 1.3 94.6 - - + +
224B LEU* 1.3 52.4 + - - +
226B ASP* 3.4 17.6 - - + +
227B GLN* 2.7 39.0 + - - +
288B ILE* 4.2 13.9 - - + -
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Residues in contact with LEU 224 (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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183B LEU* 5.5 1.6 - - + -
221B PHE* 2.9 19.8 + - + +
223B PRO* 1.3 78.2 - - - +
225B VAL* 1.3 61.1 + - + +
227B GLN* 3.7 15.9 - - - +
228B ILE* 3.5 25.8 + - - +
247B LEU* 3.9 17.7 - - + -
252B TYR* 3.8 36.3 - - + -
261B LEU* 3.9 26.0 - - + -
286B PHE* 3.8 27.4 - - + -
288B ILE* 3.6 23.8 - - + -
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Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 3.9 16.6 - - + +
179B GLY* 3.7 36.3 - - - +
180B TYR* 4.0 9.2 - - + +
183B LEU* 3.7 30.1 - - + -
222B ARG 2.9 7.8 + - - +
224B LEU* 1.3 76.5 - - - +
226B ASP* 1.3 65.0 + - - +
228B ILE* 3.1 3.9 + - - +
229B ILE* 3.0 32.1 + - + +
244B LEU* 4.0 13.7 - - + -
247B LEU* 4.1 14.6 - - + -
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Residues in contact with ASP 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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116B GLN* 5.0 2.4 + - - -
119B HIS* 3.8 6.1 - - + -
155B TYR* 2.8 43.6 + - + +
156B PHE* 4.5 3.1 - - + -
159B LEU* 5.0 2.5 - - + -
160B PHE* 5.1 2.9 - - + -
176B LEU* 3.3 18.4 - - + +
180B TYR* 2.5 28.8 + - - -
222B ARG* 3.1 11.3 + - - +
223B PRO* 3.0 18.8 + - - +
225B VAL* 1.3 76.2 - - - +
227B GLN* 1.3 57.3 + - - +
229B ILE* 3.3 0.9 + - - +
230B TYR* 2.8 33.6 + - - +
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Residues in contact with GLN 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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119B HIS* 3.5 28.2 - - + -
122B GLN* 3.0 30.4 + - - +
123B ARG* 3.5 7.4 + - - +
223B PRO 2.7 20.7 + - - +
224B LEU* 3.7 28.0 - - - +
226B ASP* 1.3 72.6 - - - +
228B ILE* 1.3 66.4 + - + +
230B TYR* 3.5 1.2 - - - +
231B GLU* 3.0 34.8 + - - +
252B TYR* 5.4 2.3 - - - -
288B ILE* 3.7 25.9 + - + +
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Residues in contact with ILE 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 LEU 3.5 14.8 + - - +
225B VAL 3.1 7.2 + - - +
227B GLN* 1.3 83.7 - - + +
229B ILE* 1.3 63.8 + - + +
231B GLU* 3.4 10.8 + - - +
232B ASN* 2.9 32.3 + - - +
240B MET* 4.9 1.1 - - - +
243B LYS* 3.8 41.3 - - + +
244B LEU* 4.0 19.1 - - + +
246B ALA* 4.1 15.5 - - + -
247B LEU* 4.2 23.6 - - + +
250B ASN* 5.7 1.6 - - - +
252B TYR* 5.0 3.1 - - - +
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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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160B PHE* 4.5 5.6 - - + -
172B ILE* 3.9 38.6 - - + +
175B GLY* 3.6 38.8 - - - +
176B LEU* 3.9 10.3 - - + +
225B VAL* 3.0 25.1 + - + +
226B ASP 4.0 2.2 - - - +
228B ILE* 1.3 76.4 - - + +
230B TYR* 1.3 64.6 + - - +
232B ASN* 3.1 5.7 + - - +
233B ARG* 2.9 21.5 + - - -
240B MET* 3.9 26.5 - - + +
244B LEU* 4.0 15.3 - - + -
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Residues in contact with TYR 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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119B HIS* 4.2 8.5 - - + -
123B ARG* 3.2 52.1 - - + +
125B TYR* 4.3 13.5 + - - -
159B LEU* 3.4 39.2 + - + -
160B PHE* 3.9 23.1 - + + -
226B ASP 2.8 18.1 + - - +
227B GLN 3.5 4.0 - - - +
229B ILE* 1.3 77.4 - - - +
231B GLU* 1.3 62.7 + - - +
233B ARG* 3.1 69.3 + - - +
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Residues in contact with GLU 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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122B GLN* 4.4 3.3 - - - +
123B ARG* 3.1 33.6 + - - +
227B GLN* 3.0 27.6 + - - +
228B ILE* 3.7 13.2 - - - +
229B ILE 3.3 0.2 - - - -
230B TYR* 1.3 77.5 - - + +
232B ASN* 1.3 67.2 + - - +
233B ARG* 3.5 2.9 + - - +
235B GLU* 5.5 0.2 - - - +
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Residues in contact with ASN 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ILE* 2.9 27.7 + - + +
229B ILE* 3.1 6.7 + - - +
231B GLU* 1.3 87.6 + - - +
233B ARG* 1.3 63.7 + - - +
234B LYS 3.1 3.8 - - - -
235B GLU* 3.0 38.7 + - + +
240B MET* 3.7 24.4 - - + +
243B LYS* 3.3 50.0 + - - +
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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