Contacts of the helix formed by residues 236 - 244 (chain B) in PDB entry 4YCV
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 GLN 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538A ALA* 6.4 1.6 - - + -
541A THR* 4.5 7.5 - - + +
545A TYR* 3.8 10.8 + - - -
232B ILE* 2.6 53.1 + - + +
233B ARG* 3.5 4.4 - - - +
235B ARG* 1.3 80.5 - - + +
237B ARG* 1.3 61.0 + - - +
238B TYR* 3.0 39.1 + - + +
239B LEU* 3.3 33.3 + - + +
240B ASP 3.9 1.6 + - - -
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Residues in contact with ARG 237 (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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313A MET* 5.0 0.2 - - - +
314A LEU* 4.8 1.6 - - + -
233B ARG 3.8 14.5 + - - -
234B TYR* 3.5 23.3 + - - +
235B ARG 3.7 3.8 + - - -
236B GLN* 1.3 71.1 - - - +
238B TYR* 1.3 64.7 + - - +
239B LEU 3.1 2.2 - - - -
240B ASP* 2.7 54.0 + - - +
241B LEU* 2.9 31.9 + - + +
247B SER* 4.9 0.2 - - - -
251B PHE* 3.5 26.2 - - - -
571B LYS 3.4 14.6 + - - -
572B ASP* 4.3 3.6 + - - +
574B ILE 3.0 22.6 + - - -
575B LEU* 2.7 26.9 + - + +
576B PHE* 3.7 31.0 - - + -
577B PRO* 3.7 4.4 - - - +
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Residues in contact with TYR 238 (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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313A MET* 3.5 38.7 + - + +
314A LEU* 6.3 0.2 - - - +
316A VAL* 3.9 16.4 - - + +
317A GLY* 3.5 20.9 - - - +
538A ALA* 4.5 2.0 + - + -
541A THR* 3.5 12.1 - - - +
542A SER* 3.5 24.4 + - - -
545A TYR* 3.2 40.5 - + + -
236B GLN* 3.0 38.0 + - + +
237B ARG* 1.3 81.7 - - - +
239B LEU* 1.3 85.4 + - + +
241B LEU* 3.3 3.3 + - - +
242B LEU* 2.9 37.6 + - + +
576B PHE* 5.9 0.2 - - - -
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Residues in contact with LEU 239 (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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545A TYR* 3.6 34.5 - - + +
221B LEU* 4.6 5.6 - - + -
222B PRO* 4.0 14.4 - - + -
227B LEU* 3.4 11.0 - - + +
232B ILE* 3.4 22.0 - - + -
236B GLN* 3.3 33.1 + - + +
237B ARG 3.1 0.2 - - - -
238B TYR* 1.3 95.9 - - + +
240B ASP* 1.3 56.3 + - - +
242B LEU* 4.6 4.9 - - + -
243B ILE* 2.9 54.4 + - + +
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Residues in contact with ASP 240 (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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227B LEU* 3.4 8.9 - - - +
233B ARG* 3.4 34.5 - - + +
236B GLN 3.9 1.2 + - - -
237B ARG* 2.7 42.2 + - - +
239B LEU* 1.3 78.1 - - - +
241B LEU* 1.3 55.9 + - - +
244B ASN* 2.5 50.6 + - - +
247B SER* 2.6 33.3 + - - -
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Residues in contact with LEU 241 (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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314A LEU* 4.1 19.5 - - + +
317A GLY* 3.1 29.2 - - - +
319A ILE* 4.6 15.0 - - + -
237B ARG* 2.9 32.2 + - + +
238B TYR* 3.8 4.5 - - - +
239B LEU 3.2 0.2 - - - -
240B ASP* 1.3 80.1 - - - +
242B LEU* 1.3 60.5 + - - +
245B GLU* 4.2 11.3 + - - -
247B SER* 3.2 20.1 + - - +
248B ARG* 3.6 37.5 - - + +
251B PHE* 3.9 17.3 - - + -
575B LEU* 4.8 4.7 - - + -
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Residues in contact with LEU 242 (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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316A VAL* 3.8 18.8 - - + +
317A GLY 3.8 14.4 - - - +
318A GLY* 4.2 6.3 - - - +
545A TYR* 5.9 1.8 - - + +
138B ARG* 3.7 43.7 - - - +
140B MET* 4.4 16.3 - - + +
155B VAL* 5.5 7.1 - - + +
221B LEU* 4.8 13.2 - - + -
238B TYR* 2.9 24.9 + - + +
239B LEU* 3.8 12.3 - - + +
241B LEU* 1.3 79.8 - - - +
243B ILE* 1.3 68.5 + - + +
245B GLU* 4.3 6.1 + - - +
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Residues in contact with ILE 243 (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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140B MET* 4.6 16.2 - - + -
186B ARG* 5.6 3.1 - - - +
221B LEU* 4.6 5.6 - - + -
222B PRO* 3.4 43.7 - - + +
223B MET* 3.4 33.2 - - - +
224B LYS* 4.0 10.7 - - + +
227B LEU* 4.1 6.1 - - + -
239B LEU* 2.9 45.9 + - + +
242B LEU* 1.3 80.1 - - + +
244B ASN* 1.3 70.4 + - - +
245B GLU* 3.4 4.5 + - - +
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Residues in contact with ASN 244 (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 LYS* 5.0 6.4 - - - +
227B LEU* 3.8 25.6 + - - +
228B LYS* 4.5 8.4 - - - +
233B ARG* 3.8 19.4 - - - +
240B ASP* 2.5 38.9 + - - +
243B ILE* 1.3 83.1 - - - +
245B GLU* 1.3 58.3 + - - +
246B SER* 2.8 23.3 + - - +
247B SER* 4.0 6.7 - - - +
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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