Contacts of the helix formed by residues 222 - 235 (chain B) in PDB entry 6R7Z
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 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B PHE 3.4 14.5 + - - +
219B THR* 3.6 3.9 + - - +
221B ALA* 1.3 76.5 - - - +
223B ILE* 1.3 58.1 + - - +
224B PRO 3.5 1.3 - - - -
225B MET* 3.3 12.8 + - + +
226B ALA* 2.8 29.9 + - - +
519B ALA* 4.6 17.9 - - + +
522B ALA* 6.0 2.5 - - + -
523B VAL* 4.8 11.0 - - + +
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Residues in contact with ILE 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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219B THR 3.6 14.2 + - - +
220B PHE* 4.6 7.4 - - - +
222B LEU* 1.3 76.6 - - - +
224B PRO* 1.3 67.3 - - + +
226B ALA* 3.8 6.1 - - - +
227B VAL* 2.8 31.5 + - - +
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Residues in contact with PRO 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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220B PHE 4.3 8.1 - - - +
221B ALA* 4.0 16.4 - - - +
223B ILE* 1.3 92.3 - - + +
225B MET* 1.3 57.7 + - - +
227B VAL* 4.1 4.9 - - + +
228B ILE* 3.0 31.4 + - - +
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Residues in contact with MET 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ALA 4.7 2.8 + - - +
222B LEU* 3.3 18.9 + - + +
223B ILE 3.3 0.4 - - - -
224B PRO* 1.3 78.7 - - - +
226B ALA* 1.3 58.8 + - - +
228B ILE* 4.0 3.1 - - - +
229B GLY* 3.0 25.8 + - - -
246B PHE* 6.6 0.4 - - - -
250B ASN* 5.6 9.9 - - + -
516B PRO* 4.5 6.8 - - - +
519B ALA* 4.2 16.8 - - + -
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Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU 2.8 19.8 + - - +
223B ILE* 3.8 7.6 - - - +
224B PRO 3.3 0.2 - - - -
225B MET* 1.3 73.5 - - - +
227B VAL* 1.3 58.0 + - - +
229B GLY* 3.6 1.8 - - - -
230B LEU* 2.9 32.7 + - - +
516B PRO 5.4 0.7 - - - -
517B LEU* 6.4 0.4 - - - +
519B ALA* 4.7 0.9 - - - +
520B ALA* 3.8 38.9 - - + +
523B VAL* 5.0 5.6 - - + -
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ILE 2.8 18.0 + - - +
224B PRO* 4.1 5.2 - - + +
226B ALA* 1.3 75.3 - - - +
228B ILE* 1.3 64.0 + - - +
230B LEU* 4.1 4.0 - - - +
231B PRO* 3.3 20.1 - - - +
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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
----------------------------------------------------------
224B PRO 3.0 18.8 + - - +
225B MET* 4.1 3.4 - - - +
227B VAL* 1.3 76.5 - - - +
229B GLY* 1.3 61.8 + - - +
230B LEU 3.2 1.7 + - - -
231B PRO* 3.5 11.8 - - - +
232B TYR* 3.4 15.2 + - - +
246B PHE* 5.1 14.8 - - + -
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Residues in contact with GLY 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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225B MET 3.0 18.8 + - - -
226B ALA* 3.4 3.3 + - - -
228B ILE* 1.3 76.0 - - - +
230B LEU* 1.3 61.9 + - - +
232B TYR* 3.8 11.1 - - - +
233B TYR* 3.4 23.2 + - - +
516B PRO* 4.4 19.5 - - - +
517B LEU* 4.1 12.5 + - - +
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Residues in contact with LEU 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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226B ALA 2.9 15.8 + - - +
227B VAL* 4.1 4.9 - - - +
228B ILE 3.2 1.6 - - - -
229B GLY* 1.3 76.2 - - - +
231B PRO* 1.3 68.7 - - + +
233B TYR* 3.6 3.0 + - - +
234B LEU* 3.5 20.3 + - - +
517B LEU* 6.0 0.4 - - - -
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Residues in contact with PRO 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B VAL 3.3 17.7 - - - +
228B ILE* 3.5 7.9 - - - +
230B LEU* 1.3 88.5 - - + +
232B TYR* 1.3 58.8 + - - +
233B TYR 3.2 1.1 - - - -
234B LEU* 4.1 3.1 - - + +
235B PHE* 2.9 38.0 + - + +
237B TRP* 4.5 3.8 - - - +
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Residues in contact with TYR 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 ILE 3.4 16.8 - - - +
229B GLY* 3.8 11.0 - - - -
230B LEU 3.3 0.6 - - - -
231B PRO* 1.3 82.8 - - - +
233B TYR* 1.3 56.8 + - - +
235B PHE 3.1 11.4 - - - +
236B VAL* 4.4 1.4 - - - -
237B TRP* 3.8 22.2 + - + +
238B GLU* 4.2 10.4 + - - +
516B PRO* 4.7 12.7 - - + +
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Residues in contact with TYR 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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229B GLY 3.4 16.0 + - - +
230B LEU* 4.3 2.9 - - - +
231B PRO 3.2 0.6 - - - -
232B TYR* 1.3 80.9 - - - +
234B LEU* 1.3 66.6 + - - +
235B PHE 4.0 1.4 - - - +
236B VAL* 5.0 2.3 + - - +
515B TYR* 5.0 8.1 - - + +
516B PRO* 6.0 2.7 - - + -
517B LEU* 3.7 24.0 - - + +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU 3.5 12.9 + - - +
231B PRO* 4.9 1.8 - - + +
233B TYR* 1.3 78.0 - - - +
235B PHE* 1.3 65.2 + - + +
236B VAL* 3.7 2.6 + - - +
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Residues in contact with PHE 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 PRO* 2.9 26.4 + - + +
232B TYR 3.1 9.2 - - - +
233B TYR 3.8 0.2 - - - -
234B LEU* 1.3 78.2 - - - +
236B VAL* 1.3 62.0 + - - +
237B TRP* 2.7 13.4 + - + +
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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