Contacts of the helix formed by residues 230 - 238 (chain B) in PDB entry 4LDR
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 MET 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A PRO* 4.7 2.5 - - + -
260A VAL* 3.8 26.9 - - + -
305A LEU* 3.8 1.3 - - + -
321A TRP* 3.2 30.7 - - + +
322A ASN* 3.3 31.0 - - - +
323A PRO* 3.7 20.9 - - + +
226B ILE* 3.8 15.0 - - + -
227B THR* 3.1 47.8 + - + +
229B SER* 1.3 78.0 - - - +
231B VAL* 1.3 57.7 + - - +
232B ALA 3.3 2.9 - - - -
233B ALA* 3.1 5.4 + - - +
234B ALA* 2.8 28.9 + - - +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A GLN* 3.2 11.7 - - - +
165B LEU* 4.4 8.7 - - + -
200B THR* 3.6 30.7 - - + -
226B ILE* 4.1 9.4 - - + -
227B THR 4.3 1.1 - - - +
228B ASP 3.3 16.2 - - - +
229B SER 3.4 1.8 - - - -
230B MET* 1.3 77.9 - - - +
232B ALA* 1.3 64.0 + - - +
234B ALA* 3.2 3.4 + - - +
235B MET* 3.0 49.2 + - + +
265B LEU* 3.8 27.4 - - + -
268B VAL* 4.4 8.1 - - + -
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A TYR* 3.6 25.9 - - + -
264A GLN* 2.9 37.7 + - + +
267A ILE* 3.8 2.2 - - + -
326A ASP* 5.6 0.2 - - - +
229B SER 5.4 0.7 - - - +
230B MET 3.3 0.4 - - - -
231B VAL* 1.3 74.4 - - - +
233B ALA* 1.3 65.3 + - - +
235B MET* 3.2 3.5 + - - +
236B ALA* 3.1 23.4 + - - +
268B VAL* 3.5 23.3 - - + -
272B HIS* 3.7 1.7 + - - -
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 4.5 11.0 - - + -
263A TYR* 4.1 8.1 - - - -
321A TRP* 3.9 17.7 - - + -
323A PRO* 5.2 0.7 - - + -
325A PHE 5.7 0.7 - - - +
326A ASP* 4.2 24.6 + - + +
229B SER 5.2 0.6 + - - -
230B MET* 3.1 11.7 + - - +
232B ALA* 1.3 78.4 - - - +
234B ALA* 1.3 57.7 + - - +
236B ALA* 3.2 2.2 + - - -
237B HIS* 2.8 44.8 + - - +
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A TRP* 3.6 18.1 - - + -
165B LEU* 4.4 2.9 - - + -
198B PHE* 4.8 5.6 - - + -
226B ILE* 4.1 16.8 - - + -
230B MET 2.8 16.6 + - - +
231B VAL* 3.5 5.6 - - - +
232B ALA 3.2 0.2 - - - -
233B ALA* 1.3 78.9 - - - +
235B MET* 1.3 59.2 + - - +
238B ARG* 2.8 40.8 + - + +
240B VAL* 3.6 14.9 - - + +
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Residues in contact with MET 235 (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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165B LEU* 4.9 4.7 - - + -
231B VAL* 3.0 32.2 + - + +
232B ALA 3.2 6.5 + - - +
234B ALA* 1.3 77.7 - - - +
236B ALA* 1.3 62.1 + - - +
239B GLY* 4.3 4.0 + - - -
240B VAL* 3.9 30.5 + - + +
243B VAL* 3.5 32.3 - - + -
265B LEU* 4.2 4.0 - - + +
268B VAL* 3.6 29.6 - - - +
269B ALA* 3.7 12.6 - - + +
272B HIS* 3.7 19.3 - - + +
274B ILE* 3.5 22.6 - - + +
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Residues in contact with ALA 236 (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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263A TYR* 4.0 15.5 - - + +
232B ALA 3.1 16.2 + - - +
233B ALA 3.8 3.1 - - - +
235B MET* 1.3 80.0 - - - +
237B HIS* 1.3 78.0 + - + +
238B ARG 3.9 0.2 - - - -
239B GLY 5.1 0.4 + - - -
272B HIS* 3.8 17.5 + - + +
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Residues in contact with HIS 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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263A TYR* 6.0 2.9 - + - -
297A ILE* 5.4 13.9 - - + +
321A TRP* 4.6 9.9 - - + -
326A ASP* 5.4 4.0 - - + -
327A VAL* 5.2 17.7 - - + +
233B ALA* 2.8 28.8 + - + +
236B ALA* 1.3 96.7 - - + +
238B ARG* 1.3 71.4 + - + +
239B GLY 3.6 1.8 - - - -
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Residues in contact with ARG 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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321A TRP* 3.2 77.8 - - + +
163B THR* 4.1 4.3 + - - +
196B HIS* 5.2 5.3 + - - -
198B PHE* 3.6 44.5 - - + -
224B THR* 4.9 7.5 + - - +
234B ALA* 2.8 19.6 + - - +
237B HIS* 1.3 84.0 + - - +
239B GLY* 1.3 62.6 + - - +
240B VAL 3.3 3.5 + - - -
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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