Contacts of the helix formed by residues 194 - 209 (chain B) in PDB entry 3LMK
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 SER 194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175B THR 3.3 7.9 - - - -
177B MET* 4.0 8.8 - - - +
180B SER* 4.0 9.2 + - - -
190B ARG* 3.2 30.6 - - - +
192B VAL 4.1 0.4 + - - -
193B PRO* 1.3 76.7 - - - +
195B ASP* 1.3 59.9 + - - +
196B ALA* 3.0 23.7 + - - +
197B GLN* 3.1 25.3 + - - +
461B ASP* 4.2 8.3 + - - +
466B TYR* 3.7 3.4 + - - -
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Residues in contact with ASP 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B THR* 2.7 48.9 + - - +
176B SER* 3.8 3.0 + - - -
177B MET* 4.0 13.0 - - + +
194B SER* 1.3 70.3 - - - +
196B ALA* 1.3 64.7 + - - +
197B GLN 2.9 1.6 - - - -
198B GLN* 2.7 37.2 + - - +
199B ALA* 2.9 28.4 + - - +
223B TYR* 3.6 8.0 - - - +
227B GLY* 4.8 8.0 - - - +
277B PHE* 3.6 27.6 - - + -
466B TYR* 4.7 1.2 + - - -
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Residues in contact with ALA 196 (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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177B MET* 3.4 27.8 - - + +
194B SER* 3.0 12.9 + - - +
195B ASP* 1.3 78.7 - - - +
197B GLN* 1.3 60.4 + - + +
200B ARG* 3.3 19.4 + - - +
234B MET* 3.4 19.3 - - + +
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Residues in contact with GLN 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PRO* 3.9 21.3 - - - +
194B SER* 3.1 13.5 + - - +
195B ASP 2.9 0.4 - - - -
196B ALA* 1.3 82.7 - - + +
198B GLN* 1.3 59.4 + - - +
200B ARG* 3.2 7.5 + - - +
201B ALA* 2.8 28.8 + - - +
462B SER 5.3 1.2 + - - -
463B PRO* 5.6 3.3 - - - +
464B GLY 4.1 16.4 + - - +
466B TYR* 3.7 10.2 - - + +
487B TRP* 3.7 31.2 - - + -
489B ASN* 4.8 10.2 + - - +
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Residues in contact with GLN 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B THR* 4.4 2.4 + - - +
195B ASP* 2.7 41.9 + - + +
197B GLN* 1.3 77.6 - - - +
199B ALA* 1.3 63.6 + - - +
201B ALA* 3.0 16.1 + - - +
202B MET* 3.0 12.2 + - + +
277B PHE* 3.9 10.1 - - + -
304B SER* 3.3 13.3 - - - -
305B ASP* 2.8 52.6 + - - +
327B ILE* 3.7 27.6 - - + +
329B LEU* 5.3 0.2 - - - +
466B TYR* 3.2 26.8 + - + +
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ASP 2.9 20.5 + - - +
198B GLN* 1.3 72.7 - - - +
200B ARG* 1.3 64.9 + - - +
202B MET* 3.0 6.7 + - - +
203B VAL* 2.9 25.7 + - - +
227B GLY* 3.9 0.4 - - - +
230B ALA* 3.8 25.6 - - + -
231B PHE* 3.9 13.9 - - - +
234B MET* 4.2 4.7 - - - -
277B PHE* 3.8 23.9 - - + -
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Residues in contact with ARG 200 (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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196B ALA 3.3 17.9 + - - +
197B GLN* 3.2 11.3 + - - +
199B ALA* 1.3 78.6 - - - +
201B ALA* 1.3 56.4 + - - +
203B VAL* 3.4 27.3 + - - +
204B ASP* 2.9 49.7 + - - +
207B LYS* 4.9 0.2 - - - +
234B MET* 3.7 30.9 - - - +
238B GLU* 3.2 31.8 + - - +
487B TRP* 3.4 23.1 - - + -
490B GLY* 5.6 0.9 - - - -
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Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLN 2.8 14.6 + - - +
198B GLN* 3.0 12.8 + - - +
200B ARG* 1.3 72.8 - - - +
202B MET* 1.3 57.4 + - - +
204B ASP* 3.2 2.8 + - - +
205B ILE* 2.9 37.5 + - + +
327B ILE* 4.6 10.1 - - + -
466B TYR* 4.7 6.5 - - + -
468B ILE* 5.9 0.7 - - + -
487B TRP* 3.5 42.5 - - + +
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Residues in contact with MET 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B GLN* 3.0 8.8 + - + +
199B ALA* 3.4 9.0 - - - +
201B ALA* 1.3 72.5 - - - +
203B VAL* 1.3 65.3 + - - +
205B ILE* 3.4 6.6 + - - +
206B VAL* 3.2 27.7 + - - +
228B MET* 5.8 0.7 - - - -
231B PHE* 3.6 27.1 - - + -
275B ALA* 4.5 8.7 - - - -
276B CYS 4.7 4.3 - - - +
277B PHE* 3.8 33.4 - - + -
302B LEU* 3.8 31.6 - - + +
303B GLY 4.2 2.2 - - - -
304B SER* 3.9 22.4 - - - +
327B ILE* 3.6 25.9 - - + +
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ALA 2.9 18.2 + - - +
200B ARG* 3.5 31.2 - - - +
202B MET* 1.3 75.9 - - - +
204B ASP* 1.3 62.7 + - - +
206B VAL* 3.4 5.6 + - - +
207B LYS* 3.2 24.5 + - + +
231B PHE* 3.5 31.4 - - + +
234B MET* 3.8 21.3 - - + -
235B SER* 4.0 11.9 - - - +
238B GLU* 4.3 7.2 - - + -
240B ILE* 3.9 18.6 - - + +
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Residues in contact with ASP 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ARG* 2.9 43.1 + - - +
201B ALA 3.2 5.8 + - - +
203B VAL* 1.3 75.0 - - - +
205B ILE* 1.3 59.2 + - - +
207B LYS* 3.8 16.0 - - - +
208B ARG* 3.0 28.6 + - - +
487B TRP* 2.9 30.0 + - + +
490B GLY 4.3 7.4 - - - +
492B LEU* 3.6 18.5 - - + +
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Residues in contact with ILE 205 (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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201B ALA* 2.9 23.2 + - + +
202B MET* 3.8 5.4 - - - +
203B VAL 3.4 0.2 - - - -
204B ASP* 1.3 72.5 - - - +
206B VAL* 1.3 65.8 + - - +
208B ARG* 3.4 3.8 + - + +
209B TYR* 3.2 23.8 + - + +
211B TRP* 4.7 4.2 - - + -
302B LEU* 4.2 25.6 - - + -
325B ILE* 4.4 19.1 - - + -
327B ILE* 4.1 22.9 - - + -
468B ILE* 3.8 32.1 - - + -
492B LEU* 4.1 21.1 - - + -
494B MET* 5.1 11.0 - - + -
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B MET 3.2 17.2 + - - +
203B VAL 3.6 7.4 - - - +
205B ILE* 1.3 78.9 - - - +
207B LYS* 1.3 62.7 + - - +
209B TYR* 3.4 1.2 + - - -
210B ASN 3.3 3.5 + - - -
211B TRP* 3.1 68.3 + - + +
214B VAL* 4.4 9.4 - - + -
231B PHE* 4.4 15.9 - - + -
240B ILE* 3.7 24.7 - - + -
273B VAL* 5.5 0.4 - - + -
275B ALA* 5.9 0.7 - - + -
302B LEU* 3.6 20.6 - - + -
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Residues in contact with LYS 207 (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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200B ARG* 4.9 0.7 - - - +
203B VAL* 3.2 15.2 + - + +
204B ASP* 3.8 21.3 - - - +
205B ILE 3.3 0.2 - - - -
206B VAL* 1.3 76.4 - - - +
208B ARG* 1.3 63.7 + - - +
210B ASN* 3.0 15.3 + - - +
211B TRP 5.0 2.9 - - - -
238B GLU* 3.3 53.8 + - + +
240B ILE* 4.0 13.5 - - + -
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Residues in contact with ARG 208 (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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204B ASP 3.0 17.4 + - - +
205B ILE* 3.8 5.8 - - - +
206B VAL 3.3 0.2 - - - -
207B LYS* 1.3 78.3 - - - +
209B TYR* 1.3 56.6 - - + +
210B ASN* 3.4 4.0 + - - +
492B LEU* 4.0 17.5 - - + -
494B MET* 5.1 9.4 - - + -
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Residues in contact with TYR 209 (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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205B ILE* 3.2 16.5 + - + +
207B LYS 3.3 0.2 - - - -
208B ARG* 1.3 75.0 - - - +
210B ASN* 1.3 69.1 + - - +
211B TRP* 3.4 45.5 + - + +
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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