Contacts of the helix formed by residues 222 - 233 (chain J) in PDB entry 6QY3
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 222 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184J LEU* 5.9 7.4 - - + -
218J ILE 5.5 0.4 + - - +
219J MET* 3.5 13.5 + - + +
220J GLU 3.2 1.4 - - - -
221J PRO* 1.3 75.9 - - - +
223J ARG* 1.3 63.8 + - - +
224J PRO 3.3 2.9 - - - -
225J ILE* 3.3 22.9 + - + +
226J ILE* 3.9 3.5 + - - +
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Residues in contact with ARG 223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219J MET 3.9 6.0 + - - +
220J GLU* 3.5 14.1 + - - +
221J PRO 3.4 1.4 - - - -
222J PHE* 1.3 77.6 - - - +
224J PRO* 1.3 58.8 - - - +
226J ILE* 2.9 13.0 + - - +
227J ASP* 2.9 23.6 + - - +
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Residues in contact with PRO 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J LYS 5.8 0.7 - - - +
116J ASN* 4.4 30.1 - - + +
117J GLN* 4.9 5.8 - - + +
120J TYR* 4.6 15.2 - - + +
221J PRO 4.4 3.7 - - - +
222J PHE 3.3 0.4 - - - -
223J ARG* 1.3 78.6 - - - +
225J ILE* 1.3 58.8 + - - +
227J ASP* 3.5 12.2 - - + +
228J ARG* 2.9 29.3 + - - +
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Residues in contact with ILE 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222J PHE* 3.3 16.6 + - + +
223J ARG 3.1 0.8 - - - -
224J PRO* 1.3 78.7 - - - +
226J ILE* 1.3 61.0 + - - +
228J ARG* 3.6 11.5 + - - +
229J ILE* 3.7 12.5 + - - +
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Residues in contact with ILE 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J ALA 6.1 0.4 - - - +
177J LEU* 5.9 4.7 - - - +
180J GLY* 5.0 18.8 - - - -
181J TYR 5.7 0.4 - - - +
222J PHE 3.9 3.2 + - - +
223J ARG* 2.9 12.0 + - - +
225J ILE* 1.3 77.2 - - - +
227J ASP* 1.3 61.4 + - - +
229J ILE* 3.5 4.1 + - - +
230J VAL* 2.9 31.4 + - - +
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Residues in contact with ASP 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223J ARG 2.9 12.9 + - - +
224J PRO* 3.2 15.4 + - + +
226J ILE* 1.3 78.0 - - - +
228J ARG* 1.3 57.0 - - - +
230J VAL* 3.8 5.9 - - - +
231J TYR* 2.9 29.5 + - - +
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Residues in contact with ARG 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120J TYR* 6.4 2.0 - - + -
224J PRO 2.9 15.6 + - - +
225J ILE* 3.8 8.1 - - - +
226J ILE 3.2 0.6 - - - -
227J ASP* 1.3 74.5 - - - +
229J ILE* 1.3 62.2 + - - +
231J TYR* 3.0 7.2 + - - +
232J GLN* 2.9 28.2 + - - +
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Residues in contact with ILE 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225J ILE 3.7 8.5 + - - +
226J ILE* 3.5 7.2 + - - +
228J ARG* 1.3 78.5 - - - +
230J VAL* 1.3 57.6 + - - +
232J GLN* 3.9 6.3 - - - +
233J ASN* 2.9 34.1 + - - +
244J GLU* 4.9 21.1 - - + +
245J LEU* 5.5 3.6 - - - +
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Residues in contact with VAL 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173J ILE* 5.5 7.6 - - + +
176J ALA* 5.3 13.2 - - + -
177J LEU* 5.7 7.0 - - + +
226J ILE 2.9 19.7 + - - +
227J ASP* 3.9 7.6 - - - +
229J ILE* 1.3 76.9 - - - +
231J TYR* 1.3 58.4 + - - +
233J ASN* 5.2 1.8 - - - -
234J ARG* 3.1 29.8 + - - +
241J ILE* 6.3 2.2 - - - -
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Residues in contact with TYR 231 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160J LEU* 5.5 11.9 - - + -
227J ASP 2.9 19.9 + - - +
228J ARG* 3.0 6.9 + - - +
230J VAL* 1.3 79.3 - - - +
232J GLN* 1.3 61.3 + - - +
234J ARG* 3.9 12.0 + - - +
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Residues in contact with GLN 232 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228J ARG 2.9 15.0 + - - +
229J ILE* 3.3 6.5 + - - +
231J TYR* 1.3 80.7 - - - +
233J ASN* 1.3 59.5 + - + +
234J ARG 3.3 1.3 + - - -
235J HIS* 4.6 4.9 + - - +
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Residues in contact with ASN 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229J ILE 2.9 17.7 + - - +
230J VAL* 4.0 2.2 - - - +
232J GLN* 1.3 73.5 - - + +
234J ARG* 1.3 58.1 + - - +
235J HIS 3.1 3.4 - - - -
236J ASN* 2.8 37.3 + - + +
240J LYS 5.3 0.7 - - - +
241J ILE* 4.4 28.7 - - + +
244J GLU* 4.8 12.1 - - + -
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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