Contacts of the helix formed by residues 225 - 236 (chain B) in PDB entry 4LGD
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 HIS 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A LEU* 3.7 17.4 + - - +
172A THR* 4.6 0.7 - - + -
178A ARG* 3.2 47.5 + - - +
182A ILE* 3.7 21.8 - - + +
196A ILE* 3.5 47.0 - - + +
223B ASP 4.2 0.4 + - - -
224B ILE* 1.3 78.8 - - + +
226B PRO* 1.3 76.0 - - + +
227B MET* 3.2 33.9 + - + -
228B ARG* 3.3 5.9 + - - +
229B ALA 3.1 12.6 + - - -
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Residues in contact with PRO 226 (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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178A ARG* 4.2 12.8 - - + +
182A ILE* 4.6 9.4 - - + -
182B ILE 4.0 13.9 - - - +
183B GLY* 3.4 28.3 - - - +
185B PRO* 4.2 8.7 - - + -
186B PHE* 4.7 6.3 - - + -
224B ILE 3.4 4.0 - - - +
225B HIS* 1.3 99.9 - - + +
227B MET* 1.3 51.5 + - - +
229B ALA* 2.5 32.8 + - + +
230B ILE* 2.7 20.2 + - + +
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Residues in contact with MET 227 (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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171A LEU* 5.0 8.3 - - - -
181A VAL 5.6 0.2 - - - -
182A ILE* 4.1 24.2 - - + +
185A PRO* 4.6 0.2 - - + -
188A MET* 3.8 39.3 - - + -
192A VAL 4.7 0.9 - - - +
193A ILE* 3.9 20.8 - - + +
196A ILE* 3.8 13.9 - - + -
230A ILE* 3.2 49.3 - - + +
225B HIS* 3.2 25.3 + - + +
226B PRO* 1.3 78.6 - - - +
228B ARG* 1.3 62.3 + - - +
230B ILE* 3.8 12.8 - - - +
231B PHE* 3.3 12.5 + - - +
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Residues in contact with ARG 228 (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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193A ILE 3.5 17.9 - - - +
194A GLN* 3.0 47.9 + - - +
196A ILE* 3.8 15.7 - - + -
224B ILE* 3.6 27.1 - - + +
225B HIS* 3.3 9.1 + - - +
226B PRO 2.9 0.8 + - - -
227B MET* 1.3 80.2 - - - +
229B ALA* 1.3 60.3 + - - +
231B PHE* 3.3 14.5 + - + +
232B MET* 3.0 59.9 + - - +
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Residues in contact with ALA 229 (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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185B PRO* 4.8 2.0 - - + -
186B PHE* 3.8 31.9 - - + -
221B TYR* 4.1 18.6 - - + +
224B ILE* 4.7 2.5 - - + +
225B HIS 3.1 9.3 + - - +
226B PRO* 2.5 17.2 + - + +
228B ARG* 1.3 69.5 - - - +
230B ILE* 1.3 63.1 + - - +
231B PHE 3.0 1.8 - - - -
232B MET* 3.6 8.2 - - - +
233B ILE* 2.9 36.2 + - + +
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Residues in contact with ILE 230 (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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182A ILE* 5.3 0.7 - - + -
227A MET* 3.6 42.2 - - + +
230A ILE* 4.3 14.4 - - + -
231A PHE* 4.4 2.1 - - + +
182B ILE* 3.6 39.3 - - + +
185B PRO* 3.2 26.7 - - + -
193B ILE* 3.4 18.8 - - + +
226B PRO* 2.7 12.0 + - + +
227B MET* 3.7 23.1 - - - +
228B ARG 3.4 0.2 - - - -
229B ALA* 1.3 71.6 - - - +
231B PHE* 1.3 57.0 + - - +
233B ILE* 4.3 1.3 - - - -
234B PRO* 3.1 22.9 - - - +
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Residues in contact with PHE 231 (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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193A ILE* 4.3 5.2 - - + -
194A GLN* 3.9 38.1 - - + -
230A ILE 4.0 11.4 - - - +
231A PHE* 3.9 18.6 - + - +
234A PRO* 3.8 22.2 - - + -
235A THR* 3.5 23.8 - - - -
227B MET 3.3 11.2 + - - +
228B ARG* 3.6 19.5 - - + +
229B ALA 3.0 0.8 - - - -
230B ILE* 1.3 79.8 - - - +
232B MET* 1.3 69.6 - - + +
234B PRO* 3.5 5.3 - - - +
235B THR* 2.7 51.3 + - + -
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Residues in contact with MET 232 (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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221B TYR* 3.8 31.0 - - + -
224B ILE* 4.5 13.9 - - + -
228B ARG* 3.0 60.1 + - + +
229B ALA* 3.0 6.5 + - - +
231B PHE* 1.3 88.2 - - + +
233B ILE* 1.3 59.5 + - - +
235B THR* 2.9 5.8 + - - -
236B ASN* 2.7 58.7 + - - +
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Residues in contact with ILE 233 (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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185B PRO 3.3 30.1 - - - +
186B PHE* 4.5 9.4 - - - +
188B MET 3.8 18.4 - - - +
190B PRO* 4.1 22.8 - - + +
193B ILE* 3.9 14.6 - - + -
205B TRP* 4.4 13.2 - - + -
221B TYR* 3.7 26.7 - - + -
229B ALA* 2.9 29.3 + - + +
230B ILE* 4.3 0.9 - - - -
232B MET* 1.3 75.8 - - - +
234B PRO* 1.3 68.8 - - + +
235B THR 3.5 0.2 + - - -
236B ASN 4.0 9.2 - - - +
261B LYS* 4.0 6.4 - - - +
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Residues in contact with PRO 234 (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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231A PHE* 3.7 23.4 - - + -
190B PRO* 4.0 14.6 - - + +
193B ILE* 3.8 26.2 - - + -
194B GLN* 3.4 26.2 - - + +
230B ILE 3.1 23.1 - - - +
231B PHE 3.5 6.3 - - - +
233B ILE* 1.3 93.4 - - + +
235B THR* 1.3 55.4 + - - +
261B LYS* 2.7 22.8 + - - -
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Residues in contact with THR 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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231A PHE* 3.5 15.3 - - - -
235A THR* 4.2 2.0 + - - +
231B PHE* 2.7 47.2 + - + -
232B MET* 2.9 6.6 + - - -
234B PRO* 1.3 75.9 - - - +
236B ASN* 1.3 78.3 - - - +
261B LYS* 3.3 8.1 + - - -
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Residues in contact with ASN 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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221B TYR* 3.6 19.0 + - - +
232B MET* 2.7 59.2 + - - +
233B ILE 4.0 5.1 - - - +
235B THR* 1.3 85.2 - - - +
237B PRO* 1.3 75.9 - - + +
261B LYS* 3.0 23.5 + - - +
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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