Contacts of the helix formed by residues 194 - 209 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A THR 3.3 7.9 - - - -
177A MET* 3.8 9.5 - - - +
180A SER* 4.0 11.0 + - - -
190A ARG* 3.5 27.6 - - - +
192A VAL 3.8 0.6 + - - -
193A PRO* 1.3 77.8 - - - +
195A ASP* 1.3 59.1 + - - +
196A ALA* 2.9 28.6 + - - +
197A GLN* 3.3 16.8 + - - +
461A ASP* 4.5 7.9 - - - +
466A TYR* 3.6 8.1 + - - -
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Residues in contact with ASP 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A THR* 2.5 46.1 + - - +
176A SER* 3.9 6.1 + - - -
177A MET* 4.2 8.6 - - + +
193A PRO 5.0 0.2 - - - +
194A SER* 1.3 70.2 - - - +
196A ALA* 1.3 58.6 + - - +
197A GLN 3.2 1.1 - - - -
198A GLN* 2.5 34.2 + - - +
199A ALA* 2.9 30.0 + - - +
223A TYR* 3.3 19.4 - - - +
226A SER 5.9 0.2 - - - -
227A GLY* 4.7 8.3 - - - +
230A ALA* 4.6 1.2 - - - +
277A PHE* 3.4 22.6 - - + -
466A TYR* 4.9 0.5 + - - -
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A MET* 3.6 27.4 - - + +
194A SER* 2.9 17.0 + - - +
195A ASP* 1.3 76.9 - - - +
197A GLN* 1.3 66.3 + - + +
199A ALA* 4.0 1.5 - - - +
200A ARG* 3.4 22.2 + - - +
234A MET* 3.8 13.5 - - + +
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Residues in contact with GLN 197 (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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193A PRO* 3.4 25.0 - - - +
194A SER* 3.3 8.9 + - - +
195A ASP 3.2 0.2 - - - -
196A ALA* 1.3 80.5 - - + +
198A GLN* 1.3 59.7 + - - +
200A ARG* 3.2 4.2 + - - +
201A ALA* 2.8 30.5 + - - +
462A SER 5.2 0.3 - - - +
463A PRO* 5.5 3.2 - - - +
464A GLY 4.1 19.2 + - - +
466A TYR* 3.7 13.1 - - + +
487A TRP* 3.7 31.7 - - + -
489A ASN* 4.2 20.4 - - - +
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Residues in contact with GLN 198 (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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175A THR* 4.4 3.4 + - - +
195A ASP* 2.5 39.8 + - - +
197A GLN* 1.3 76.7 - - - +
199A ALA* 1.3 57.1 + - - +
201A ALA* 3.4 6.3 + - - +
202A MET* 2.9 28.4 + - - +
277A PHE* 4.1 9.6 - - + -
304A SER* 3.2 14.1 - - - -
305A ASP* 2.7 53.7 + - - +
327A ILE* 3.9 26.1 - - + +
329A LEU* 5.6 0.4 - - - +
466A TYR* 3.3 26.3 + - + +
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Residues in contact with ALA 199 (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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195A ASP 2.9 19.4 + - - +
196A ALA 4.0 3.1 - - - +
198A GLN* 1.3 77.7 - - - +
200A ARG* 1.3 55.9 + - - +
202A MET* 3.0 6.0 + - - +
203A VAL* 3.0 30.8 + - - +
227A GLY 4.1 6.3 - - - +
230A ALA* 3.6 35.7 - - + -
231A PHE* 4.1 5.4 - - - +
234A MET* 4.1 4.9 - - - -
277A PHE* 4.1 12.0 - - + -
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Residues in contact with ARG 200 (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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196A ALA 3.4 16.8 + - - +
197A GLN* 3.2 6.4 + - - +
199A ALA* 1.3 78.3 - - - +
201A ALA* 1.3 56.6 + - - +
203A VAL* 3.4 7.7 + - - +
204A ASP* 3.0 50.1 + - - +
234A MET* 3.4 49.1 - - + +
238A GLU* 5.1 13.4 + - - +
487A TRP* 3.9 19.5 - - + -
490A GLY* 5.9 1.1 - - - -
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Residues in contact with ALA 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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197A GLN 2.8 17.1 + - - +
198A GLN* 3.4 9.2 - - - +
200A ARG* 1.3 75.6 - - - +
202A MET* 1.3 59.2 + - - +
204A ASP* 3.3 2.8 + - - +
205A ILE* 3.0 34.2 + - + +
327A ILE* 4.9 8.5 - - + -
466A TYR* 4.7 5.8 - - + -
487A TRP* 3.4 44.1 - - + +
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Residues in contact with MET 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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198A GLN* 2.9 12.2 + - + +
199A ALA* 3.0 9.4 + - - +
201A ALA* 1.3 72.3 - - - +
203A VAL* 1.3 66.5 + - - +
205A ILE* 3.2 6.8 + - - +
206A VAL* 3.2 24.3 + - - +
228A MET* 6.0 0.2 - - - -
231A PHE* 3.8 23.6 - - + -
275A ALA* 4.4 9.9 - - - -
276A CYS 4.5 4.7 - - - +
277A PHE* 3.7 27.1 - - + -
302A LEU* 3.9 28.2 - - + +
303A GLY 4.3 2.2 - - - -
304A SER* 3.7 36.3 - - - +
327A ILE* 3.8 23.1 - - + +
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Residues in contact with VAL 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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199A ALA 3.0 12.9 + - - +
200A ARG* 3.5 12.8 - - - +
202A MET* 1.3 75.1 - - - +
204A ASP* 1.3 70.6 + - - +
206A VAL* 3.1 7.6 + - - +
207A LYS* 3.1 24.1 + - + +
231A PHE* 3.6 32.1 - - + +
234A MET* 3.8 26.9 - - + +
235A SER* 3.9 6.3 - - - +
238A GLU* 3.8 32.1 - - + -
240A ILE* 4.4 7.4 - - + -
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Residues in contact with ASP 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 ARG* 3.0 34.2 + - - +
201A ALA 3.6 5.8 - - - +
202A MET 3.2 0.2 - - - -
203A VAL* 1.3 79.7 - - - +
205A ILE* 1.3 56.3 + - - +
207A LYS* 3.5 23.9 + - - +
208A ARG* 2.9 29.3 + - - +
238A GLU* 5.8 1.0 - - - -
487A TRP* 3.3 20.9 + - - +
490A GLY 3.9 11.1 - - - +
492A LEU* 3.4 23.0 - - + +
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Residues in contact with ILE 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 ALA* 3.0 19.8 + - + +
202A MET* 3.2 7.4 + - - +
204A ASP* 1.3 74.4 - - - +
206A VAL* 1.3 65.2 + - - +
208A ARG* 3.3 13.1 + - - +
209A TYR* 3.5 31.1 + - + -
211A TRP* 4.6 3.6 - - + -
302A LEU* 3.8 27.8 - - + -
325A ILE* 4.4 9.0 - - + -
327A ILE* 3.8 25.1 - - + -
468A ILE* 3.6 35.0 - - + -
492A LEU* 4.0 16.8 - - + -
494A MET* 5.0 4.0 - - + -
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Residues in contact with VAL 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 MET 3.2 15.3 + - - +
203A VAL* 3.1 8.0 + - - +
205A ILE* 1.3 74.9 - - - +
207A LYS* 1.3 61.4 + - - +
209A TYR 3.3 6.8 + - - -
211A TRP* 3.2 62.1 + - + +
214A VAL* 4.1 17.7 - - + -
231A PHE* 4.1 22.2 - - + -
240A ILE* 3.8 20.9 - - + -
273A VAL* 5.7 0.4 - - + -
275A ALA* 5.6 0.7 - - + -
302A LEU* 3.8 17.0 - - + -
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Residues in contact with LYS 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 VAL* 3.1 14.3 + - + +
204A ASP* 3.8 30.8 + - - +
206A VAL* 1.3 74.2 - - - +
208A ARG* 1.3 61.4 + - - +
210A ASN* 2.9 23.3 + - - +
211A TRP 4.9 2.7 - - - -
238A GLU* 3.5 38.7 + - + +
240A ILE* 3.9 18.8 - - + -
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Residues in contact with ARG 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 ASP 2.9 19.1 + - - +
205A ILE* 3.6 8.3 - - - +
206A VAL 3.3 0.6 - - - -
207A LYS* 1.3 75.7 - - - +
209A TYR* 1.3 70.3 + - + +
210A ASN* 3.3 0.7 + - - +
492A LEU* 3.9 17.3 - - + -
494A MET* 5.0 11.9 - - + -
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Residues in contact with TYR 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 ILE* 3.5 27.9 + - + -
206A VAL 3.3 2.2 + - - -
207A LYS 3.1 1.0 - - - -
208A ARG* 1.3 84.8 - - + +
210A ASN* 1.3 62.9 + - - +
211A TRP* 2.9 60.3 + + + +
325A ILE* 4.4 19.6 - - + +
484A VAL* 4.7 5.7 - - - +
494A MET* 3.4 33.4 - - + +
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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