Contacts of the helix formed by residues 223 - 234 (chain B) in PDB entry 3A7H
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 HIS 223 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B GLU 4.2 0.4 + - - -
222B LEU* 1.3 75.4 - - - +
224B PRO* 1.3 84.1 - - + +
225B MET* 2.9 58.3 + - + +
226B LYS* 2.9 32.2 + - + +
227B VAL* 3.3 8.0 + - - +
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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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183B PRO* 4.1 27.7 - - + +
184B PHE* 4.5 14.6 - - + -
222B LEU 3.4 5.8 - - - +
223B HIS* 1.3 101.5 - - + +
225B MET* 1.3 61.2 + - - +
227B VAL* 3.0 23.7 + - + +
228B LEU* 3.1 11.7 + - - +
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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
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223B HIS* 2.9 34.8 + - + +
224B PRO* 1.3 73.2 - - - +
226B LYS* 1.3 60.0 + - + +
228B LEU* 3.3 29.6 - - + +
229B PHE* 3.9 6.4 + - - +
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Residues in contact with LYS 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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222B LEU* 4.5 24.5 - - + +
223B HIS* 2.9 25.2 + - + +
225B MET* 1.3 75.2 - - - +
227B VAL* 1.3 65.9 + - - +
229B PHE* 3.1 42.9 + - + -
230B LEU* 3.1 19.5 + - + +
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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
----------------------------------------------------------
183B PRO* 4.1 8.1 - - + +
184B PHE* 3.2 44.4 - - + -
219B HIS* 4.0 22.7 - - + +
222B LEU* 4.2 5.4 - - + -
223B HIS 3.4 13.9 - - - +
224B PRO* 3.0 9.4 + - + +
226B LYS* 1.3 78.6 - - - +
228B LEU* 1.3 61.8 + - - +
229B PHE 3.0 1.2 + - - -
230B LEU* 3.1 7.3 + - - -
231B ILE* 3.1 54.1 + - + +
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Residues in contact with LEU 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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179B PHE* 3.5 43.1 - - + -
183B PRO* 4.1 28.3 - - + -
186B MET* 4.8 1.1 - - - -
191B ILE* 3.3 28.1 - - + +
224B PRO 3.1 7.4 + - - +
225B MET* 3.3 25.4 - - + +
226B LYS 3.2 0.4 - - - -
227B VAL* 1.3 76.9 - - - +
229B PHE* 1.3 56.5 + - + +
232B PRO* 3.1 19.8 - - - +
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Residues in contact with PHE 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 4.1 3.6 - - - -
226B LYS* 3.1 47.3 + - + -
228B LEU* 1.3 77.4 - - - +
230B LEU* 1.3 94.4 + - + +
231B ILE 3.5 0.2 - - - -
232B PRO* 3.5 5.2 - - - +
233B LYS* 3.2 45.6 + - - +
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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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219B HIS* 4.4 18.2 - - + +
222B LEU* 3.4 33.7 - - + -
226B LYS* 3.1 26.8 + - + +
227B VAL* 3.1 8.4 + - - +
229B PHE* 1.3 102.4 - - + +
231B ILE* 1.3 60.6 + - - +
233B LYS* 3.0 5.0 + - + -
234B ASN* 2.6 59.4 + - - +
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Residues in contact with ILE 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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183B PRO 3.2 28.0 - - - +
184B PHE 4.6 6.3 - - - +
186B MET 3.7 20.2 - - - +
188B PRO* 3.9 14.8 - - + -
191B ILE* 3.6 18.2 - - + -
203B TRP* 3.9 20.1 - - + +
219B HIS* 4.5 12.1 - - + +
227B VAL* 3.1 33.3 + - + +
228B LEU 5.0 0.2 - - - +
230B LEU* 1.3 76.1 - - - +
232B PRO* 1.3 70.7 - - + +
234B ASN* 3.7 5.2 - - - +
237B PRO* 6.5 0.7 - - + -
257B LYS* 3.4 15.6 + - - +
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Residues in contact with PRO 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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188B PRO* 4.2 15.7 - - + +
191B ILE* 3.5 29.6 - - + -
192B LYS* 4.1 23.6 - - + -
228B LEU 3.1 22.2 - - - +
229B PHE* 3.5 8.7 - - - +
231B ILE* 1.3 90.1 - - + +
233B LYS* 1.3 54.6 + - - +
257B LYS* 2.7 22.7 + - - -
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Residues in contact with LYS 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 PHE* 3.2 43.8 + - + +
230B LEU* 3.0 3.5 + - + +
232B PRO* 1.3 81.6 - - - +
234B ASN* 1.3 77.4 + - - +
257B LYS* 4.1 2.1 + - - -
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Residues in contact with ASN 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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219B HIS* 4.3 16.4 - - + +
230B LEU* 2.6 49.2 + - - +
231B ILE* 3.7 3.4 - - - +
233B LYS* 1.3 92.7 - - - +
235B ASN* 1.3 72.3 + - - +
236B PRO* 4.4 0.2 - - - +
257B LYS* 2.9 28.7 + - - +
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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