Contacts of the helix formed by residues 200 - 213 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A TYR* 2.6 35.8 + - + +
199A ASN* 1.3 80.9 - - + +
201A ILE* 1.3 75.4 + - + +
202A LEU 3.6 1.1 - - - -
203A PRO* 3.5 3.2 - - - +
204A MET* 3.2 26.9 + - + +
237A PHE* 3.9 19.9 - - + -
240A LEU* 3.5 26.2 - - + -
241A VAL* 4.1 24.0 - - + -
254A THR* 6.2 3.4 - - + -
242C GLU* 3.4 26.0 - - - +
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Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PRO* 5.8 5.8 - - + -
120A PHE* 5.4 15.0 - - + -
196A TYR* 2.9 27.8 + - + +
197A ILE* 3.9 20.6 - - + -
200A ILE* 1.3 82.9 - - + +
202A LEU* 1.3 70.8 + - + +
204A MET* 3.1 12.5 + - + +
205A LEU* 2.9 40.9 + - + +
254A THR* 5.5 9.0 - - + -
257A ILE* 5.2 14.6 - - + -
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ILE* 3.2 34.6 + - + +
201A ILE* 1.3 83.6 - - + +
203A PRO* 1.3 68.3 - - + +
205A LEU* 3.0 26.7 + - + +
206A PHE* 2.9 46.8 + - + -
259C PHE* 3.4 36.1 - - + -
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Residues in contact with PRO 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ILE 3.4 10.1 - - - +
198A PRO 3.9 9.2 - - - +
199A ASN 3.2 17.0 - - - +
200A ILE 3.5 9.6 - - - +
202A LEU* 1.3 94.8 - - + +
204A MET* 1.3 55.9 + - - +
206A PHE* 3.3 11.4 + - + +
207A ILE* 2.9 35.9 + - - +
237A PHE* 3.7 16.4 - - + -
259C PHE* 5.3 1.6 - - + -
262C TYR* 3.6 40.2 - - + -
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Residues in contact with MET 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ILE* 3.2 16.9 + - + +
201A ILE* 3.1 19.5 + - + +
203A PRO* 1.3 76.5 - - - +
205A LEU* 1.3 62.7 + - + +
207A ILE* 3.1 14.4 - - + +
208A LEU* 2.9 28.9 + - - +
234A HIS* 3.7 33.4 - - + -
237A PHE* 4.5 22.3 - - + -
254A THR* 6.0 2.9 - - + -
257A ILE* 4.6 15.7 - - + -
258A ILE* 4.0 22.4 - - + -
261A ILE* 3.6 23.1 - - + -
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ILE* 2.9 26.3 + - + +
202A LEU* 3.0 34.1 + - + +
204A MET* 1.3 80.7 - - + +
206A PHE* 1.3 60.0 + - + +
208A LEU* 3.1 9.0 + - + +
209A PHE* 2.9 50.9 + - + -
257A ILE* 6.5 1.6 - - + -
261A ILE* 5.6 5.2 - - + -
302A PHE* 4.0 31.6 - - + -
306A ASN* 6.2 0.4 - - - +
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Residues in contact with PHE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LEU* 2.9 43.3 + - + -
203A PRO* 3.5 11.7 - - + +
205A LEU* 1.3 79.5 - - + +
207A ILE* 1.3 60.1 + - + +
209A PHE* 3.1 11.4 + + - +
210A ILE* 2.9 37.4 + - + +
231C LEU* 6.2 1.1 - - + -
259C PHE* 3.9 13.2 - + - -
262C TYR* 4.6 22.0 - + + -
263C LEU* 3.6 32.1 - - + -
266C PHE* 4.1 36.6 - + + -
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A PRO* 2.9 17.0 + - + +
204A MET* 3.1 27.1 - - + +
206A PHE* 1.3 75.8 - - + +
208A LEU* 1.3 56.8 + - - +
210A ILE* 4.2 8.1 - - - -
211A SER 2.9 20.4 + - - -
230A THR* 3.2 26.7 - - + +
233A ALA* 3.7 10.3 - - + +
234A HIS* 3.3 38.1 - - + +
237A PHE* 4.6 2.9 - - + -
265A TYR* 3.0 14.5 + - - +
231C LEU* 4.0 24.2 - - + -
235C ILE* 4.2 16.6 - - + -
262C TYR* 5.7 1.8 - - + -
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Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A MET 2.9 15.8 + - - +
205A LEU* 3.3 11.4 - - + +
207A ILE* 1.3 75.6 - - - +
209A PHE* 1.3 69.0 + - + +
211A SER* 3.1 17.2 - - - +
212A TRP* 3.5 32.9 + - + -
261A ILE* 3.9 20.0 - - + -
264A PHE* 4.4 10.1 - - + -
265A TYR* 3.2 37.5 - - + +
302A PHE* 3.4 43.5 - - + -
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Residues in contact with PHE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 2.9 42.3 + - + -
206A PHE* 3.1 13.2 + + - +
208A LEU* 1.3 75.2 - - + +
210A ILE* 1.3 67.8 + - - +
211A SER 3.0 0.9 - - - -
212A TRP* 2.9 57.9 + + - +
213A THR* 3.0 8.5 + - - -
299A PRO* 6.2 1.1 - - + -
302A PHE* 4.5 16.2 - + - -
266C PHE* 3.7 27.8 - + + -
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Residues in contact with ILE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PHE* 2.9 25.2 + - + +
207A ILE* 3.9 5.6 - - - +
209A PHE* 1.3 74.9 - - - +
211A SER* 1.3 64.1 + - - +
213A THR* 3.1 28.9 - - - +
226A LEU* 3.2 22.1 - - + +
230A THR* 4.0 8.1 - - + -
228C VAL* 5.0 5.4 - - + -
231C LEU* 4.2 24.2 - - + -
265C TYR 4.7 0.7 - - - +
266C PHE* 3.5 32.3 - - + +
269C VAL* 3.5 39.5 - - + -
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Residues in contact with SER 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ILE 2.9 13.5 + - - -
208A LEU* 3.1 15.4 + - - +
209A PHE 3.0 0.2 - - - -
210A ILE* 1.3 78.3 - - - +
212A TRP* 1.3 62.8 + - - +
213A THR 3.6 0.2 + - - -
214A ALA* 4.0 9.4 + - - +
226A LEU* 4.1 4.4 - - - +
227A VAL* 3.8 26.4 - - - +
230A THR* 3.1 27.6 + - - +
264A PHE 5.8 0.2 - - - -
265A TYR* 3.5 24.7 - - - -
268A ALA* 4.5 5.9 - - - +
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Residues in contact with TRP 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU* 3.7 26.0 - - + -
209A PHE* 2.9 62.9 + + - +
211A SER* 1.3 78.0 - - - +
213A THR* 1.3 61.5 + - - +
214A ALA* 2.9 7.7 + - - +
215A PHE* 3.1 52.6 + + + +
216A TRP* 4.4 5.0 - + - -
264A PHE* 3.7 28.0 - + + -
268A ALA* 5.4 3.4 - - + -
298A PHE* 3.4 42.0 - + + -
299A PRO* 4.2 26.9 - - + +
302A PHE* 3.8 20.0 - + + -
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Residues in contact with THR 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A PHE 3.0 10.8 + - - -
210A ILE* 3.1 24.5 + - - +
212A TRP* 1.3 73.3 - - - +
214A ALA* 1.3 60.0 + - - +
215A PHE 2.9 11.1 + - - -
216A TRP* 3.2 19.3 + - - +
217A SER 4.6 0.5 + - - -
226A LEU* 4.2 11.9 - - + -
220C TYR* 4.6 5.7 + - - +
269C VAL* 4.0 15.3 - - + +
270C ILE* 4.3 10.6 - - - +
273C THR* 3.1 44.8 + - - +
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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