Contacts of the helix formed by residues 200 - 212 (chain C) in PDB entry 4LML
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 ILE 200 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242B GLU* 3.6 26.7 - - - +
196C TYR* 2.8 31.1 + - + +
199C ASN* 1.3 78.7 - - + +
201C ILE* 1.3 72.4 + - + +
202C LEU 3.6 0.4 - - - -
203C PRO* 3.5 1.0 - - - +
204C MET* 2.9 37.0 + - + +
237C PHE* 3.4 36.5 - - + -
240C LEU* 3.8 15.7 - - + -
241C VAL* 3.9 26.9 - - + -
258C ILE* 6.2 0.7 - - + -
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Residues in contact with ILE 201 (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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119C PRO* 5.2 7.6 - - + -
120C PHE* 4.8 20.2 - - + -
196C TYR* 2.6 36.5 + - + +
197C ILE* 3.8 14.4 - - + +
200C ILE* 1.3 80.7 - - + +
202C LEU* 1.3 73.4 + - + +
204C MET* 3.1 11.7 + - + +
205C LEU* 2.9 39.6 + - + +
254C THR* 5.6 7.6 - - + -
257C ILE* 5.3 13.7 - - + -
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Residues in contact with LEU 202 (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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259B PHE* 3.7 21.8 - - + -
197C ILE* 3.0 44.9 + - + +
201C ILE* 1.3 90.1 - - + +
203C PRO* 1.4 60.4 - - + +
205C LEU* 3.1 17.1 + - + +
206C PHE* 2.8 61.4 + - + -
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Residues in contact with PRO 203 (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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259B PHE* 4.9 2.0 - - + -
262B TYR* 3.7 36.3 - - + -
197C ILE 3.4 8.7 - - - +
198C PRO 3.4 14.8 - - - +
199C ASN 3.1 24.5 - - - +
200C ILE 3.5 7.0 - - - +
202C LEU* 1.4 93.5 - - + +
204C MET* 1.3 60.8 + - - +
206C PHE* 3.5 10.9 - - + +
207C ILE* 2.9 30.9 + - - +
237C PHE* 3.7 10.1 - - + -
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Residues in contact with MET 204 (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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200C ILE* 2.9 28.3 + - + +
201C ILE* 3.3 14.6 - - + +
203C PRO* 1.3 76.2 - - - +
205C LEU* 1.3 61.5 + - + +
207C ILE* 3.1 12.4 - - + +
208C LEU* 2.9 29.2 + - - +
234C HIS* 3.6 37.4 - - + -
237C PHE* 4.5 23.0 - - + -
254C THR* 6.0 3.4 - - + -
257C ILE* 4.4 16.4 - - + -
258C ILE* 3.9 20.9 - - + -
261C ILE* 3.7 23.6 - - + -
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Residues in contact with LEU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C ILE* 2.9 33.3 + - + +
202C LEU* 3.1 22.0 + - + +
204C MET* 1.3 80.4 - - + +
206C PHE* 1.3 57.6 + - + +
208C LEU* 3.1 11.2 + - + +
209C PHE* 2.9 50.2 + - + -
257C ILE* 6.1 3.4 - - + -
261C ILE* 5.2 6.1 - - + -
302C PHE* 3.5 37.7 - - + -
306C ASN* 5.7 0.4 - - - +
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Residues in contact with PHE 206 (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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231B LEU* 6.3 0.4 - - + -
259B PHE* 3.7 16.2 - + - -
262B TYR* 4.2 26.2 - + + +
263B LEU* 3.4 35.7 - - + -
266B PHE* 4.0 37.9 - + + -
202C LEU* 2.8 44.3 + - + -
203C PRO* 3.2 14.8 + - + +
205C LEU* 1.3 74.3 - - + +
207C ILE* 1.3 60.8 + - + +
209C PHE* 3.0 8.7 + + - +
210C ILE* 2.9 39.5 + - + +
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Residues in contact with ILE 207 (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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231B LEU* 3.9 23.6 - - + -
235B ILE* 4.0 17.5 - - + -
262B TYR* 5.1 3.1 - - + -
203C PRO* 2.9 18.5 + - + +
204C MET* 3.1 19.1 - - + +
206C PHE* 1.3 74.6 - - + +
208C LEU* 1.3 56.4 + - - +
210C ILE* 4.3 7.4 - - - -
211C SER* 2.9 28.4 + - - -
230C THR* 3.4 18.9 - - + +
233C ALA* 3.7 11.0 - - + +
234C HIS* 3.5 34.1 - - + +
237C PHE* 4.4 8.7 - - + -
265C TYR* 3.5 15.7 + - - +
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Residues in contact with LEU 208 (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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204C MET 2.9 15.0 + - - +
205C LEU* 3.2 13.5 - - + +
206C PHE 3.0 0.4 - - - -
207C ILE* 1.3 79.1 - - - +
209C PHE* 1.3 71.9 + - + +
211C SER* 3.2 18.6 + - - +
212C TRP* 3.5 28.8 + - + -
261C ILE* 3.6 30.5 - - + -
264C PHE* 4.8 9.2 - - + -
265C TYR* 3.9 16.8 - - + +
302C PHE* 3.3 45.1 - - + -
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Residues in contact with PHE 209 (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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266B PHE* 3.9 28.3 - + + -
205C LEU* 2.9 44.6 + - + +
206C PHE* 3.7 9.6 - + - +
208C LEU* 1.3 85.6 - - + +
210C ILE* 1.3 66.5 + - - +
211C SER 3.0 1.3 - - - -
212C TRP* 2.9 55.3 + + - +
213C THR* 3.0 8.8 + - - -
302C PHE* 4.3 11.9 - + - -
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Residues in contact with ILE 210 (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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228B VAL* 5.0 7.4 - - + -
231B LEU* 4.4 21.8 - - + -
265B TYR* 4.3 0.7 - - + +
266B PHE* 3.5 39.9 - - + +
269B VAL* 3.6 42.8 - - + -
206C PHE* 2.9 23.9 + - + +
207C ILE* 4.1 4.3 - - - +
209C PHE* 1.3 74.9 - - - +
211C SER* 1.3 63.3 + - - +
213C THR* 3.2 25.9 - - - +
226C LEU* 3.3 14.9 - - + +
230C THR* 4.7 7.4 - - + -
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Residues in contact with SER 211 (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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207C ILE 2.9 23.2 + - - -
208C LEU* 3.2 14.0 + - - +
209C PHE 3.0 0.2 - - - -
210C ILE* 1.3 77.7 - - - +
212C TRP* 1.3 62.0 + - - +
213C THR 3.5 0.7 + - - -
214C ALA* 4.0 5.9 + - - +
226C LEU* 4.0 9.8 - - - +
227C VAL* 4.2 24.1 - - - +
230C THR* 3.3 28.5 + - - -
265C TYR* 3.8 16.6 - - - -
268C ALA* 5.5 3.5 - - - +
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Residues in contact with TRP 212 (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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208C LEU* 3.7 20.6 - - + -
209C PHE* 2.9 62.8 + + - +
211C SER* 1.3 78.6 - - - +
213C THR* 1.3 61.3 + - - +
214C ALA* 3.0 8.3 + - - +
215C PHE* 3.5 41.6 + + + +
216C TRP* 4.5 4.6 - + - -
227C VAL* 6.0 0.4 - - - -
264C PHE* 3.8 27.6 - + + -
268C ALA* 5.8 5.4 - - + -
298C PHE* 3.9 29.8 - + + -
299C PRO* 4.0 30.6 - - + +
302C PHE* 3.8 29.2 - + + -
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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