Contacts of the helix formed by residues 214 - 231 (chain A) in PDB entry 3LM0
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 THR 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A HIS* 3.4 50.4 - - + +
155A VAL* 3.7 13.9 - - + +
186A ILE* 3.5 37.5 - - + +
213A THR* 1.3 73.9 + - - +
215A ALA* 1.3 65.5 + - - +
216A THR 3.0 1.4 + - - -
217A ASP* 3.1 12.4 + - - +
218A MET* 3.6 4.5 + - - +
283A THR* 5.8 4.3 - - - +
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Residues in contact with ALA 215 (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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213A THR* 3.0 15.3 + - - +
214A THR* 1.3 81.3 + - - +
216A THR* 1.3 60.8 + - - +
218A MET* 3.0 21.7 + - - +
219A TRP 3.1 6.8 + - - -
278A PRO* 3.3 40.6 - - + +
281A ARG* 3.1 21.1 + - + +
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Residues in contact with THR 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 4.0 21.3 - - + +
203A ALA* 3.7 11.7 - - + -
205A GLU* 2.9 22.2 + - - +
206A ILE* 3.4 33.0 - - + +
212A ILE* 5.0 1.4 - - - -
213A THR* 3.1 24.3 + - - +
214A THR 3.0 1.0 + - - -
215A ALA* 1.3 78.0 - - - +
217A ASP* 1.3 62.4 + - - +
219A TRP* 3.5 5.4 - - - +
220A ASN* 3.2 26.3 + - - +
281A ARG* 3.9 1.6 - - - +
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Residues in contact with ASP 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL* 4.3 4.9 - - + +
149A LEU* 5.6 0.7 - - - +
150A HIS* 2.8 34.9 + - + +
155A VAL* 3.5 6.0 - - - -
156A HIS* 2.9 27.3 + - - +
157A LEU* 3.0 29.1 + - - +
159A LEU* 4.0 23.8 + - + +
214A THR 3.1 4.8 + - - +
216A THR* 1.3 79.5 - - - +
218A MET* 1.3 58.2 + - - +
220A ASN* 3.2 7.6 + - - +
221A ILE* 3.0 29.7 + - - +
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Residues in contact with MET 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 3.8 11.2 - - + -
146A VAL* 4.3 0.7 - - - -
150A HIS* 4.2 13.5 - - + -
214A THR* 3.7 13.9 - - - +
215A ALA* 3.0 13.1 + - - +
217A ASP* 1.3 75.4 - - - +
219A TRP* 1.3 64.8 + - - +
221A ILE* 3.1 17.3 + - + +
222A GLY 3.0 17.7 + - - -
273A LEU* 3.5 26.9 - - + +
281A ARG* 4.7 4.3 - - + -
282A PRO 3.8 14.1 - - - +
283A THR* 4.7 1.8 - - - -
284A ALA* 3.7 34.1 - - - +
287A CYS* 3.5 31.6 - - - -
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Residues in contact with TRP 219 (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 GLU 5.3 0.2 + - - -
202A LEU 3.9 3.8 + - - -
203A ALA* 3.5 26.8 - - + +
204A PRO* 3.7 30.3 - - + -
215A ALA 3.1 5.7 + - - -
216A THR 3.5 9.0 - - - +
218A MET* 1.3 73.3 - - - +
220A ASN* 1.3 69.8 + - - +
222A GLY 3.1 10.4 + - - -
223A ILE* 3.2 29.0 + - + +
235A PHE* 3.3 40.8 - + - -
247A ILE* 4.0 15.0 - - + -
250A VAL* 4.1 10.5 - - + -
273A LEU 3.8 23.8 - - - -
274A LEU* 3.5 25.6 - - + +
275A VAL 3.9 13.9 - - - -
281A ARG* 3.6 30.9 - - - +
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Residues in contact with ASN 220 (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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157A LEU 5.3 4.3 - - - -
158A ASP* 5.8 0.4 - - - -
159A LEU* 3.6 35.1 + - + +
201A TYR* 2.8 43.7 + - - +
203A ALA 5.1 0.3 + - - -
206A ILE* 5.8 0.2 - - - +
216A THR* 3.2 25.7 + - - +
217A ASP* 3.2 11.8 + - - +
219A TRP* 1.3 80.5 - - - +
221A ILE* 1.3 56.3 + - - +
223A ILE* 3.3 14.9 + - - +
224A ILE* 3.1 33.3 + - - +
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Residues in contact with ILE 221 (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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139A ILE* 4.5 14.0 - - + +
142A ILE* 4.2 19.7 - - + -
143A LEU* 3.5 34.3 - - + -
146A VAL* 4.1 24.2 - - + -
159A LEU* 4.6 6.7 - - + -
217A ASP 3.0 17.3 + - - +
218A MET* 3.1 21.5 + - - +
220A ASN* 1.3 72.5 - - - +
222A GLY* 1.3 65.3 + - - +
224A ILE* 3.3 8.5 + - + +
225A ALA* 3.1 21.8 + - - +
269A PHE* 4.2 10.3 - - + -
273A LEU* 4.0 13.9 - - + -
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Residues in contact with GLY 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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218A MET 3.0 10.9 + - - -
219A TRP 3.1 5.7 + - - -
221A ILE* 1.3 76.4 - - - +
223A ILE* 1.3 55.7 + - - +
225A ALA* 3.4 5.8 + - - +
226A TYR* 2.9 30.0 + - - +
270A ILE* 4.1 9.7 - - - +
273A LEU* 3.8 24.3 - - - +
274A LEU* 4.0 12.3 - - - -
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Residues in contact with ILE 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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161A PRO* 5.3 0.2 - - + -
200A GLU 4.0 20.2 - - - +
201A TYR* 4.0 17.3 - - + -
219A TRP* 3.2 37.6 + - + +
220A ASN* 3.6 20.2 - - - +
221A ILE 3.3 0.4 - - - -
222A GLY* 1.3 76.2 - - - +
224A ILE* 1.3 60.7 + - + +
226A TYR* 3.2 6.8 + - - +
227A MET* 2.8 51.0 + - - +
234A PRO* 3.9 20.2 - - + -
235A PHE* 4.2 7.2 - - + -
274A LEU* 4.1 10.8 - - + -
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Residues in contact with ILE 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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118A ILE* 3.3 28.7 - - + -
122A CYS* 5.6 0.2 - - - -
139A ILE* 4.1 3.4 - - + -
142A ILE* 4.1 13.9 - - + -
159A LEU* 3.4 24.9 - - + +
161A PRO* 4.2 20.4 - - + -
164A ILE* 3.7 23.8 - - + -
220A ASN 3.1 21.3 + - - +
221A ILE* 3.8 12.8 - - + +
222A GLY 3.3 0.4 - - - -
223A ILE* 1.3 79.5 - - + +
225A ALA* 1.3 56.7 + - - +
227A MET* 3.2 6.1 + - - +
228A LEU* 2.9 43.1 + - + +
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Residues in contact with ALA 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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135A VAL* 5.3 0.2 - - - -
139A ILE* 4.0 21.7 - - + +
221A ILE 3.1 16.1 + - - +
222A GLY 3.7 4.5 - - - +
224A ILE* 1.3 77.8 - - - +
226A TYR* 1.3 62.8 + - - +
228A LEU* 3.9 3.4 - - - +
229A LEU* 3.1 30.7 + - - +
269A PHE* 4.2 16.6 - - + -
270A ILE* 3.8 18.2 - - + -
292A TRP* 4.5 8.1 - - + -
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Residues in contact with TYR 226 (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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222A GLY 2.9 18.7 + - - +
223A ILE* 3.5 5.2 - - - +
225A ALA* 1.3 75.8 - - - +
227A MET* 1.3 53.9 + - - +
229A LEU* 3.9 0.8 - - - -
230A THR* 2.6 58.0 + - + +
232A THR* 3.3 26.4 + - - -
233A SER 4.2 0.9 + - - -
234A PRO* 3.7 31.2 - - + +
252A VAL* 3.3 30.1 - - + -
253A ASP* 2.6 41.8 + - - +
254A TYR* 4.4 0.2 - + - -
258A THR* 4.1 2.4 - - - +
259A PHE* 3.7 22.4 - + - -
270A ILE* 3.8 23.5 - - + +
274A LEU* 4.7 1.1 - - + -
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Residues in contact with MET 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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119A PHE* 3.9 26.2 - - + -
122A CYS* 3.6 26.5 - - + +
161A PRO* 4.0 10.3 - - + -
200A GLU* 5.6 0.2 - - - +
201A TYR* 3.6 27.4 - - - +
223A ILE* 2.8 38.9 + - - +
224A ILE* 3.8 2.7 - - - +
226A TYR* 1.3 75.8 - - - +
228A LEU* 1.3 60.1 + - - +
231A HIS* 2.9 27.0 + - - -
232A THR 3.4 23.6 - - - +
233A SER* 4.8 11.4 - - - +
234A PRO* 3.7 11.2 - - + -
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Residues in contact with LEU 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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118A ILE* 4.2 10.3 - - + +
121A LEU* 4.1 31.4 - - + +
122A CYS* 3.8 18.4 - - - +
130A VAL* 5.4 5.9 - - + +
135A VAL* 4.0 32.3 - - + +
138A LEU* 4.6 19.5 - - + -
139A ILE* 4.1 16.8 - - + -
142A ILE* 5.4 1.1 - - + -
224A ILE* 2.9 39.4 + - + +
225A ALA 3.9 2.9 - - - +
227A MET* 1.3 76.3 - - - +
229A LEU* 1.3 59.1 + - - +
231A HIS* 3.1 24.5 + - - -
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Residues in contact with LEU 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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132A GLU* 5.6 9.4 - - + +
135A VAL* 4.0 26.5 - - + -
225A ALA* 3.1 20.3 + - + +
226A TYR* 4.1 2.0 - - - +
228A LEU* 1.3 79.9 - - - +
230A THR* 1.3 62.3 + - + +
231A HIS* 4.1 10.1 + - - -
258A THR 5.2 0.2 - - - +
261A SER* 5.0 4.4 + - - +
262A VAL* 3.6 33.4 - - + +
266A ALA* 3.7 27.6 - - + -
270A ILE* 4.0 15.5 - - + -
292A TRP* 3.9 20.2 - - + -
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Residues in contact with THR 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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226A TYR* 2.6 32.8 + - + +
229A LEU* 1.3 76.9 - - + +
231A HIS* 1.3 77.8 + - - +
232A THR* 2.9 32.9 + - - +
258A THR* 3.7 33.1 - - + +
259A PHE* 3.7 28.0 - - + -
262A VAL* 4.6 2.9 - - + -
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Residues in contact with HIS 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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121A LEU 3.7 15.5 + - - -
122A CYS* 3.2 25.5 - - - +
124A PRO* 3.8 30.1 - - + +
127A ALA* 3.1 43.2 + - + +
130A VAL* 5.6 5.0 + - - +
227A MET 2.9 13.5 + - - -
228A LEU 3.1 25.3 + - - -
229A LEU 4.1 10.7 + - - -
230A THR* 1.3 81.7 + - - +
232A THR* 1.3 62.7 + - - +
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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
------------------------------------------------------------
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