Contacts of the helix formed by residues 236 - 251 (chain A) in PDB entry 3BMW
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 PRO 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A HIS* 6.3 1.8 - - + -
191A ILE* 3.6 19.3 - - + -
192A TYR* 3.9 5.2 - - + +
203A GLN* 3.9 16.2 - - + +
235A MET* 1.3 90.4 - - + +
237A PHE* 1.3 65.2 + - - +
239A TRP* 3.9 21.1 - - + +
240A GLN* 3.1 21.7 + - - +
636A ASP* 3.7 22.2 - - + +
706A GOL 3.5 28.5 - - - +
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Residues in contact with PHE 237 (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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187A TYR* 3.8 11.6 + - + +
235A MET 3.4 2.8 + - - -
236A PRO* 1.3 70.9 - - - +
238A GLY* 1.3 64.2 + - - +
240A GLN* 3.1 9.5 + - - +
241A LYS* 2.9 49.5 + - + +
272A TYR* 3.6 41.3 - + + -
273A PHE* 3.8 22.0 - + + -
276A GLU* 3.5 32.5 - - + -
277A SER* 3.5 28.0 - - - -
619A ILE* 6.0 2.5 - - + -
635A TYR* 6.2 2.9 - + - -
636A ASP 5.5 0.2 - - - -
638A SER* 5.8 0.7 - - - -
706A GOL 2.8 25.4 + - - +
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Residues in contact with GLY 238 (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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237A PHE* 1.3 86.5 - - - +
239A TRP* 1.3 63.0 + - - +
242A ASN* 3.1 19.9 + - - +
585A CYS* 4.0 6.5 - - - -
636A ASP 3.2 18.8 - - - -
637A VAL* 4.1 0.4 - - - -
638A SER* 3.4 25.1 + - - -
706A GOL 3.0 9.7 + - - -
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Residues in contact with TRP 239 (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 PRO* 4.3 7.0 - - + -
203A GLN* 3.5 42.7 + - + +
204A GLN* 5.2 1.3 - - - +
209A ASP* 2.7 27.5 + - - -
212A LEU* 3.7 34.5 - - + -
229A LEU* 5.6 0.4 - - + -
235A MET* 4.0 21.3 - - + -
236A PRO* 3.3 25.5 + - + +
237A PHE 3.3 0.8 - - - -
238A GLY* 1.3 75.6 - - - +
240A GLN* 1.3 73.0 + - + +
242A ASN* 3.2 17.4 + - - +
243A PHE* 2.8 64.7 + + + -
585A CYS* 3.6 25.7 - - + -
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Residues in contact with GLN 240 (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 LEU* 3.6 11.5 - - + +
232A VAL* 2.9 54.0 + - - +
235A MET* 3.1 31.7 + - + +
236A PRO 3.1 8.6 + - - +
237A PHE 3.1 5.3 + - - +
239A TRP* 1.3 95.2 - - + +
241A LYS* 1.3 55.4 + - - +
243A PHE* 3.5 3.6 - - - +
244A MET* 2.8 39.5 + - - +
273A PHE* 3.4 21.4 - - + -
277A SER* 4.7 1.1 - - - -
279A MET* 4.3 10.5 - - + +
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Residues in contact with LYS 241 (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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237A PHE* 2.9 41.3 + - + +
238A GLY 3.8 0.2 - - - +
240A GLN* 1.3 75.4 - - - +
242A ASN* 1.3 57.5 + - - +
244A MET 3.4 0.7 + - - -
245A ASP* 3.0 26.0 + - - +
276A GLU* 3.9 14.1 + - - +
277A SER* 3.6 15.5 + - - +
508A MET* 3.5 22.8 - - + +
577A ASN* 4.4 8.8 - - - +
579A LEU* 3.9 26.0 - - - +
583A GLN* 4.1 11.7 - - + +
609A GLU* 4.2 26.1 + - - +
638A SER* 3.7 20.8 + - - +
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Residues in contact with ASN 242 (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 ASP* 3.1 24.5 + - - -
213A LYS* 2.8 23.9 + - - +
238A GLY 3.1 14.6 + - - +
239A TRP* 3.2 29.0 + - - +
241A LYS* 1.3 76.9 - - - +
243A PHE* 1.3 60.3 + - - +
245A ASP* 3.3 5.0 + - - +
246A SER* 3.2 20.1 + - - -
583A GLN* 3.4 20.4 - - + +
584A ILE 4.1 1.1 - - - -
585A CYS* 3.6 23.9 + - + +
638A SER* 3.4 15.3 + - - +
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Residues in contact with PHE 243 (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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137A PHE* 4.0 15.5 - + - -
139A PRO* 4.7 1.8 - - + -
212A LEU* 3.6 26.0 - - + -
213A LYS* 4.1 13.7 - - + +
216A ILE* 3.8 29.6 - - + -
229A LEU* 4.0 33.7 - - + -
239A TRP* 2.8 59.6 + + + +
240A GLN* 3.3 6.7 + - - +
242A ASN* 1.3 72.9 - - - +
244A MET* 1.3 69.1 + - + +
246A SER* 3.1 17.5 + - - -
247A ILE* 3.2 29.1 + - + +
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Residues in contact with MET 244 (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 LEU* 5.4 0.7 - - - -
240A GLN 2.8 23.0 + - - +
241A LYS 3.7 2.2 - - - +
243A PHE* 1.3 77.1 - - + +
245A ASP* 1.3 57.2 + - - +
247A ILE* 3.2 18.8 + - + +
248A LEU* 2.9 49.4 + - + +
253A VAL 5.1 0.2 - - - +
255A THR* 3.6 43.7 - - - +
277A SER 3.6 22.0 - - - +
278A GLY 3.6 18.8 - - - +
279A MET* 3.6 25.1 - - + -
508A MET* 4.0 6.1 - - + -
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Residues in contact with ASP 245 (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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241A LYS 3.0 10.5 + - - +
242A ASN 3.6 6.5 - - - +
243A PHE 3.3 0.2 - - - -
244A MET* 1.3 76.3 - - - +
246A SER* 1.3 57.3 + - - +
248A LEU* 4.5 4.8 - - - +
249A SER* 2.7 39.3 + - - -
508A MET* 3.7 11.6 - - + +
509A THR 5.7 0.3 - - - -
510A LYS* 2.7 26.1 + - - -
513A GLN* 5.2 1.0 + - - -
579A LEU* 3.5 10.1 - - - +
582A ASN* 3.3 12.3 - - - +
583A GLN* 2.8 49.6 + - + +
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Residues in contact with SER 246 (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 LYS* 3.6 35.7 + - - +
216A ILE* 5.6 1.2 - - - +
217A LYS* 3.6 26.4 + - - -
242A ASN 3.2 10.4 + - - -
243A PHE* 3.1 11.7 + - - -
245A ASP* 1.3 75.8 + - - +
247A ILE* 1.3 62.7 + - - +
249A SER* 3.9 4.6 - - - -
250A TYR* 3.3 23.2 + - - +
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Residues in contact with ILE 247 (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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216A ILE* 3.8 24.9 - - + -
217A LYS* 6.0 0.2 - - - +
220A LEU* 4.1 18.9 - - + +
227A ILE* 3.9 28.0 - - + -
243A PHE* 3.2 41.9 + - + +
244A MET* 3.2 22.1 + - + +
246A SER* 1.3 76.3 - - - +
248A LEU* 1.3 69.1 + - + +
250A TYR* 3.0 3.2 + - - +
251A ARG 3.0 39.4 + - - +
253A VAL* 4.3 8.7 - - + -
255A THR* 4.7 4.9 - - + +
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Residues in contact with LEU 248 (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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244A MET* 2.9 36.3 + - + +
245A ASP* 4.1 4.9 - - - +
247A ILE* 1.3 74.3 - - + +
249A SER* 1.3 60.0 + - - +
250A TYR 3.6 0.2 + - - -
252A PRO* 3.6 47.5 - - + +
253A VAL 4.1 15.5 - - - +
278A GLY 4.1 19.3 - - - +
506A PRO* 4.0 18.3 - - + +
508A MET* 3.4 43.3 - - + +
513A GLN* 4.3 14.1 + - - +
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Residues in contact with SER 249 (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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245A ASP* 2.7 25.0 + - - -
246A SER* 3.9 4.9 - - - -
248A LEU* 1.3 77.2 - - - +
250A TYR* 1.3 61.7 + - - +
510A LYS* 2.8 27.9 + - - -
513A GLN* 3.9 12.5 - - - +
582A ASN* 3.4 13.3 + - - -
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Residues in contact with TYR 250 (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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217A LYS* 3.7 50.8 - - + +
220A LEU* 4.0 16.6 - - + -
221A ASP* 2.8 40.9 + - - -
246A SER 3.3 15.8 + - - +
247A ILE 3.0 3.9 + - - +
249A SER* 1.3 81.4 - - - +
251A ARG* 1.3 67.0 + - + +
252A PRO* 4.6 0.7 - - - -
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Residues in contact with ARG 251 (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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9A VAL* 4.4 12.1 - - - +
220A LEU* 2.8 57.0 + - + +
221A ASP* 5.8 0.6 + - - -
223A GLY* 3.6 11.5 - - - -
224A ILE 2.8 29.3 + - - +
225A ASP* 5.3 2.4 + - - -
247A ILE* 3.0 13.1 + - - +
250A TYR* 1.3 90.4 - - + +
252A PRO* 1.3 77.3 - - + +
253A VAL* 3.4 15.1 + - - +
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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