Contacts of the helix formed by residues 237 - 244 (chain C) in PDB entry 1A81
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 237 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160C THR 5.5 2.6 + - - +
163C HIS* 3.2 37.6 - - + +
168C TRP* 3.8 17.2 - - + -
169C PHE* 5.6 0.9 - - + -
194C ILE* 4.8 9.0 - - + -
203C TYR* 3.4 36.8 - - + -
218C ILE* 4.5 19.7 - - + -
226C LEU* 3.3 22.2 - - + -
236C THR* 1.3 72.4 + - - +
238C TRP* 1.3 65.0 + - - +
239C GLN 2.7 7.2 + - - -
240C LEU* 3.7 15.9 - - + -
241C VAL* 2.9 25.8 + - - +
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Residues in contact with TRP 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 5.5 7.6 - - + +
120C PHE* 2.9 78.5 - + + -
121C GLU* 4.7 6.3 - - - -
123C LEU* 3.7 20.2 - - + -
124C LYS* 4.1 12.3 - - + -
127C LEU* 6.0 0.4 - - + -
158C ILE* 6.0 0.2 - - + -
159C ALA* 5.0 19.3 - - + +
162C ALA* 4.3 17.7 - - + -
163C HIS* 4.5 16.0 - - - +
166C MET* 5.4 7.4 - - - -
168C TRP* 3.8 21.0 - - + -
236C THR* 2.7 21.7 + - + +
237C LEU* 1.3 77.4 - - - +
239C GLN* 1.3 97.8 + - + +
241C VAL* 4.2 2.3 - - - +
242C GLU* 3.3 23.9 + - - +
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Residues in contact with GLN 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C SER 5.6 0.2 + - - -
45C ARG* 3.8 19.7 + - - +
46C ASN 3.2 21.7 - - - +
47C TYR 3.6 14.5 + - - +
48C LEU* 3.9 8.2 - - - +
120C PHE* 5.2 4.5 - - + -
234C PHE* 4.1 8.1 - - + -
235C ASP* 3.0 15.9 + - - +
236C THR* 2.9 40.7 + - - +
237C LEU 2.7 0.2 - - - -
238C TRP* 1.3 107.7 - - + +
240C LEU* 1.3 72.7 + - - +
241C VAL 3.1 1.1 - - - -
242C GLU* 2.9 16.1 + - - +
243C HIS* 2.9 11.6 + - - +
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ILE* 5.6 3.6 - - + -
205C LEU* 5.5 7.2 - - + -
218C ILE* 4.0 34.8 - - + -
226C LEU* 5.6 4.3 - - + +
227C SER* 5.6 1.8 - - - -
228C ILE* 5.3 4.3 - - + -
234C PHE* 3.2 39.9 - - + -
236C THR 3.2 11.7 + - - +
237C LEU* 3.1 21.3 + - + +
239C GLN* 1.3 80.1 - - - +
241C VAL* 1.3 78.6 + - + +
243C HIS* 3.0 3.8 + - - +
244C TYR* 2.8 44.9 + - + +
255C LEU* 5.3 1.1 - - + -
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Residues in contact with VAL 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C TRP* 4.3 31.9 - - + +
192C PHE* 3.6 32.5 - - + -
194C ILE* 4.3 11.0 - - + -
205C LEU* 6.1 1.1 - - + -
237C LEU 2.9 10.5 + - - +
238C TRP 4.2 6.3 - - - +
240C LEU* 1.3 80.4 - - + +
242C GLU* 1.3 73.5 + - + +
243C HIS 2.4 17.2 + - - -
244C TYR 2.7 12.3 + - - -
245C SER* 2.9 17.5 + - - +
255C LEU* 3.7 14.1 - - + -
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Residues in contact with GLU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ASN* 5.1 2.2 + - - -
45C ARG* 3.4 29.5 + - - +
119C PRO* 2.8 38.5 - - + +
120C PHE* 3.2 26.0 - - + -
238C TRP 3.3 17.1 + - - +
239C GLN 2.9 8.1 + - - +
241C VAL* 1.3 84.1 - - + +
243C HIS* 1.3 61.3 + - - +
245C SER* 3.3 12.7 + - - +
246C TYR* 4.0 9.9 - - - +
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Residues in contact with HIS 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ARG* 4.0 27.4 - - + +
46C ASN* 6.4 0.4 - - + -
232C LYS* 3.7 29.5 + - + +
234C PHE* 3.7 15.9 - + + -
239C GLN 2.9 9.2 + - - +
240C LEU 3.6 4.5 - - - +
241C VAL 2.4 11.5 + - - -
242C GLU* 1.3 69.7 + - - +
244C TYR* 1.3 101.4 + + - +
245C SER 2.7 11.7 + - - -
246C TYR* 2.8 37.8 + + - +
247C LYS* 3.3 15.7 + - - +
249C ASP* 3.6 25.5 + - + +
181D PTR 5.3 4.0 + - - -
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Residues in contact with TYR 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C LEU* 5.6 2.0 - - + -
228C ILE* 3.7 28.8 - - + +
231C GLY* 4.0 8.8 - - - -
232C LYS* 3.7 18.6 + - + -
234C PHE* 4.1 17.3 - + - -
240C LEU* 2.8 36.2 + - + +
241C VAL 2.7 6.5 + - - +
243C HIS* 1.3 98.9 + + - +
245C SER* 1.3 55.4 + - - +
246C TYR 3.1 2.0 - - - -
247C LYS 3.5 8.9 - - - +
248C ALA 3.3 19.3 - - - -
249C ASP* 3.5 17.7 + - + -
250C GLY* 5.3 0.2 - - - -
251C LEU* 3.1 29.9 - - + +
254C VAL* 3.3 15.9 - - - +
255C LEU* 3.5 17.0 + - + +
173D ILE* 4.4 5.5 - - - +
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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