Contacts of the helix formed by residues 227 - 237 (chain F) in PDB entry 3J7Y
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 PRO 227 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193F LEU* 3.0 33.9 - - + +
194F GLU* 4.6 12.1 - - + +
220F ASP* 3.9 17.9 - - - +
225F GLU 4.0 2.5 - - - +
226F MET* 1.3 86.0 - - + +
228F GLN* 1.3 65.3 + - - +
229F SER* 3.3 3.1 - - - +
230F ILE* 3.0 39.6 - - + +
231F VAL* 3.2 9.6 + - - +
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Residues in contact with GLN 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F MET 3.6 3.9 + - - -
227F PRO* 1.3 72.4 - - - +
229F SER* 1.3 58.3 + - - +
231F VAL* 3.2 19.5 + - - +
232F GLU* 2.9 44.4 + - - +
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Residues in contact with SER 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F GLU* 5.6 1.6 - - - -
195F LEU* 2.7 34.7 + - - +
196F PRO 5.5 0.2 - - - -
197F THR 3.6 2.9 - - - -
198F GLY* 3.0 28.2 + - - -
227F PRO* 5.1 3.1 - - - -
228F GLN* 1.3 79.4 - - - +
230F ILE* 1.3 56.9 + - - +
232F GLU* 3.2 8.5 + - - +
233F ALA* 2.9 25.1 + - - +
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Residues in contact with ILE 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F LEU* 4.6 12.3 - - + -
193F LEU* 4.3 23.6 - - + -
194F GLU 5.1 0.4 - - - +
195F LEU* 3.5 33.5 - - + +
203F LEU* 4.0 15.5 - - + -
218F LEU* 4.2 8.1 - - + -
227F PRO* 3.0 51.0 + - + +
229F SER* 1.3 78.9 - - - +
231F VAL* 1.3 57.4 + - + +
233F ALA* 3.2 1.9 + - - +
234F THR* 2.9 35.8 + - + +
242F LEU* 3.9 22.4 - - + -
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Residues in contact with VAL 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F MET* 3.8 13.5 - - + -
227F PRO 3.2 13.7 + - - +
228F GLN* 3.2 21.7 + - - +
230F ILE* 1.3 77.9 - - - +
232F GLU* 1.3 63.0 - - - +
234F THR* 3.1 7.3 + - - -
235F SER* 3.0 27.1 + - - -
242F LEU* 4.1 11.4 - - + -
26q ARG* 3.3 51.5 - - - +
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Residues in contact with GLU 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F GLY* 3.8 13.7 - - - +
200F PRO* 4.9 0.9 - - - +
228F GLN* 2.9 34.8 + - - +
229F SER* 3.3 12.3 - - - +
231F VAL* 1.3 77.4 - - - +
233F ALA* 1.3 62.8 + - - +
235F SER* 2.8 22.7 + - - -
236F ARG* 3.5 35.7 + - - +
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Residues in contact with ALA 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F LEU* 3.3 33.9 - - + -
198F GLY 3.8 9.6 - - - -
199F ASP 3.6 16.2 - - - +
200F PRO* 3.7 12.8 - - + +
203F LEU* 4.2 6.7 - - + -
229F SER 2.9 9.9 + - - +
230F ILE 3.2 2.2 + - - +
232F GLU* 1.3 81.9 - - - +
234F THR* 1.3 63.7 + - - +
236F ARG 3.9 0.7 + - - -
237F LEU* 3.4 21.8 + - - +
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Residues in contact with THR 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F LEU* 4.2 4.9 - - + -
218F LEU* 3.6 31.6 - - + -
230F ILE* 2.9 21.5 + - + +
231F VAL* 3.1 9.7 + - - -
233F ALA* 1.3 74.9 - - - +
235F SER* 1.3 58.8 + - - +
237F LEU* 2.8 30.3 + - - +
240F PHE 3.5 18.2 - - - +
242F LEU* 3.6 26.1 - - + +
25q TYR 3.0 20.1 + - - -
26q ARG* 4.8 3.8 + - - +
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Residues in contact with SER 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231F VAL* 3.0 13.3 + - - -
232F GLU* 2.8 27.1 + - - +
234F THR* 1.3 81.3 + - - +
236F ARG* 1.3 66.8 + - - +
25q TYR* 3.8 21.1 + - - -
26q ARG* 4.2 21.5 + - - +
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Residues in contact with ARG 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F PRO* 3.8 35.4 - - + +
232F GLU* 3.5 36.5 + - - +
233F ALA 3.9 0.8 + - - -
234F THR 3.2 0.6 - - - -
235F SER* 1.3 83.4 + - - +
237F LEU* 1.3 64.4 + - - +
238F LYS* 3.3 8.7 + - - +
25q TYR* 5.5 1.7 - - - -
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Residues in contact with LEU 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F PRO* 3.5 35.7 - - + +
203F LEU* 3.9 15.7 - - + -
204F THR* 3.5 24.0 - - + -
233F ALA 3.4 20.6 - - - +
234F THR* 2.8 11.7 + - - +
235F SER 4.7 0.2 - - - -
236F ARG* 1.3 69.3 - - - +
238F LYS* 1.3 59.3 + - - +
239F THR* 3.3 1.3 + - - +
240F PHE* 3.4 40.2 - - + +
25q TYR 2.6 30.1 + - - -
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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