Contacts of the helix formed by residues 221 - 236 (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 GLY 221 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A SER* 4.2 12.6 - - - -
219A THR 3.6 3.2 - - - +
220A GLU* 1.3 79.6 + - - +
222A ASN* 1.3 64.1 + - - -
223A TYR* 3.3 3.4 - - - -
225A GLU* 3.1 28.0 + - - +
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Residues in contact with ASN 222 (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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152A SER* 4.0 0.5 - - - -
153A SER* 3.5 28.1 - - - +
156A ILE* 3.4 27.0 - - + +
176A SER* 2.7 34.5 + - - -
178A ASP* 3.0 25.5 + - - -
221A GLY* 1.3 73.2 - - - -
223A TYR* 1.3 57.0 + - - +
225A GLU* 4.8 2.4 - - - +
226A SER* 2.9 39.1 + - - +
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Residues in contact with TYR 223 (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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151A SER* 5.6 1.1 - - - +
152A SER* 4.0 13.8 - - - +
153A SER 4.7 1.1 - - - +
175A THR* 3.4 1.3 - - - -
176A SER* 4.5 3.7 - - - -
195A ASP* 3.3 27.2 - - - +
219A THR* 5.4 2.0 - - - -
221A GLY* 3.3 0.8 - - - -
222A ASN* 1.3 79.5 - - - +
224A GLY* 1.3 65.2 + - - +
226A SER* 4.3 0.5 - - - -
227A GLY* 3.0 27.0 + - - -
277A PHE* 3.6 12.2 - + - -
278A CYS 3.6 27.4 - - - -
279A GLU* 4.0 21.1 - - + +
304A SER* 2.6 25.5 + - - -
305A ASP* 2.7 28.0 + - - -
306A GLY 3.3 6.4 + - - -
506A GLU* 3.3 43.1 - - + +
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Residues in contact with GLY 224 (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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218A HIS* 3.2 8.6 - - - +
219A THR 3.5 16.7 + - - -
221A GLY 3.6 2.8 + - - -
222A ASN 3.5 0.2 - - - -
223A TYR* 1.3 80.6 - - - +
225A GLU* 1.3 56.3 + - - +
228A MET* 2.8 38.1 + - - +
277A PHE* 3.5 23.0 - - - +
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Residues in contact with GLU 225 (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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218A HIS* 3.1 28.1 - - + +
220A GLU* 6.1 0.7 - - - +
221A GLY 3.1 21.5 + - - +
222A ASN* 4.4 2.7 - - - +
224A GLY* 1.3 74.4 - - - +
226A SER* 1.3 59.2 + - - +
228A MET* 4.2 0.7 - - - +
229A GLU* 3.0 33.7 + - - +
247A LYS* 6.0 3.1 - - + +
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Residues in contact with SER 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER* 3.4 12.9 + - - -
177A MET* 3.9 17.9 + - - +
178A ASP* 2.8 29.8 + - - -
195A ASP* 5.9 0.4 - - - -
222A ASN* 2.9 23.5 + - - +
223A TYR 4.3 0.7 - - - -
225A GLU* 1.3 77.4 - - - +
227A GLY* 1.3 61.1 + - - +
229A GLU* 3.9 4.4 - - - +
230A ALA* 3.2 22.0 + - - +
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Residues in contact with GLY 227 (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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176A SER* 6.1 0.4 - - - +
177A MET* 6.1 0.2 - - - -
195A ASP* 4.7 8.0 + - - +
199A ALA* 4.1 0.2 - - - +
223A TYR 3.0 17.9 + - - -
226A SER* 1.3 76.2 - - - +
228A MET* 1.3 59.5 + - - +
230A ALA* 3.3 8.5 + - - +
231A PHE* 3.0 26.3 + - - +
277A PHE* 3.7 31.1 - - - -
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Residues in contact with MET 228 (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* 6.0 0.4 - - - -
216A ALA* 3.6 22.9 - - + -
217A VAL 3.5 28.7 - - - +
218A HIS* 3.8 20.2 - - + +
224A GLY 2.8 23.0 + - - +
225A GLU 4.2 1.6 - - - +
227A GLY* 1.3 69.2 - - - +
229A GLU* 1.3 56.1 + - - +
231A PHE* 3.0 31.5 + - + +
232A LYS* 2.7 50.6 + - + +
245A SER* 4.7 4.0 - - - +
275A ALA* 3.6 18.2 - - + +
277A PHE* 3.8 16.6 - - + +
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Residues in contact with GLU 229 (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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225A GLU* 3.0 22.6 + - + +
226A SER* 3.9 6.5 - - - +
228A MET* 1.3 76.5 - - - +
230A ALA* 1.3 61.4 + - - +
232A LYS* 3.3 17.4 + - - +
233A ASP* 3.0 58.4 + - - +
247B LYS* 5.5 9.2 - - - +
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Residues in contact with ALA 230 (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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177A MET* 3.7 26.0 - - + -
195A ASP 4.6 0.7 - - - +
196A ALA* 5.4 0.2 - - - -
199A ALA* 3.6 18.8 - - + -
226A SER 3.2 12.8 + - - +
227A GLY* 3.5 10.8 - - - +
228A MET 3.2 0.2 - - - -
229A GLU* 1.3 78.6 - - - +
231A PHE* 1.3 57.4 + - - +
233A ASP* 4.0 3.9 - - - +
234A MET* 3.0 36.1 + - + +
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Residues in contact with PHE 231 (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* 4.1 9.2 - - + +
202A MET* 3.8 33.2 - - + -
203A VAL* 3.6 32.5 - - + -
206A VAL* 4.1 15.3 - - + -
214A VAL* 4.6 5.8 - - + -
216A ALA* 5.0 0.7 - - + -
227A GLY 3.0 13.4 + - - +
228A MET* 3.0 30.9 + - + +
230A ALA* 1.3 75.9 - - - +
232A LYS* 1.3 60.3 + - + +
234A MET* 3.4 3.7 + - - +
235A SER* 2.8 39.3 + - - -
240A ILE* 6.1 0.4 - - + -
242A ILE* 4.0 22.0 - - + -
275A ALA* 3.5 29.4 - - + -
277A PHE* 4.8 5.2 - - + -
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Residues in contact with LYS 232 (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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228A MET* 2.7 44.6 + - + +
229A GLU* 3.9 21.3 - - - +
231A PHE* 1.3 69.5 - - + +
233A ASP* 1.3 59.2 + - - +
234A MET 3.0 4.9 - - - -
235A SER* 3.3 6.3 + - - -
236A ALA* 3.1 34.8 + - - +
242A ILE* 4.7 19.6 - - + +
245A SER* 4.4 20.2 - - - +
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Residues in contact with ASP 233 (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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229A GLU* 3.0 44.2 + - - +
230A ALA* 4.0 4.0 - - - +
232A LYS* 1.3 75.7 - - - +
234A MET* 1.3 58.4 + - - +
236A ALA* 4.7 4.2 - - - +
237A LYS* 3.0 38.6 + - - +
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Residues in contact with MET 234 (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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177A MET* 6.4 0.4 - - - -
196A ALA* 3.8 22.0 - - + +
199A ALA* 4.1 6.3 - - + -
200A ARG* 3.4 70.2 - - + +
203A VAL* 3.8 8.7 - - + -
230A ALA* 3.0 24.5 - - + +
231A PHE 3.7 4.0 - - - +
233A ASP* 1.3 78.2 - - - +
235A SER* 1.3 63.1 + - - +
236A ALA 3.4 0.9 - - - -
237A LYS* 3.6 8.9 + - - +
238A GLU* 3.1 31.7 + - + +
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Residues in contact with SER 235 (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* 3.9 10.9 - - - +
231A PHE* 2.8 31.1 + - - -
232A LYS* 3.3 8.7 + - - -
234A MET* 1.3 76.3 - - - +
236A ALA* 1.3 56.1 + - - +
237A LYS 3.3 0.2 - - - -
238A GLU* 3.2 8.4 + - - -
239A GLY 3.0 8.3 + - - -
240A ILE* 2.7 57.3 + - - +
242A ILE* 4.0 15.9 - - - +
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Residues in contact with ALA 236 (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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232A LYS 3.1 19.1 + - - +
233A ASP* 4.9 5.2 - - - +
235A SER* 1.3 77.2 + - - +
237A LYS* 1.3 64.1 + - + +
239A GLY* 3.4 10.7 + - - -
240A ILE 3.8 10.8 - - - +
242A ILE* 6.5 0.4 - - + -
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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