Contacts of the helix formed by residues 208 - 227 (chain B) in PDB entry 3MDR
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 GLN 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B GLU 5.4 2.4 + - - -
201B THR* 3.1 33.0 - - - +
203B MET* 4.2 9.9 - - + +
207B ALA* 1.3 78.6 - - + +
209B LYS* 1.3 64.5 + - - +
210B PRO* 3.4 6.3 - - - -
211B LEU* 3.2 30.9 + - + +
212B SER* 3.1 20.6 + - - -
249B PHE* 5.8 1.9 - - - -
253B VAL* 5.9 1.6 - - - +
257B TRP* 5.7 3.3 - - - -
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Residues in contact with LYS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TYR* 5.1 14.1 - - + +
206B GLY* 2.9 42.5 + - - +
207B ALA 3.3 3.3 + - - +
208B GLN* 1.3 75.9 - - - +
210B PRO* 1.3 66.2 - - + +
212B SER* 3.3 11.9 + - - +
213B GLN* 3.0 27.9 + - - +
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Residues in contact with PRO 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLN* 3.6 3.8 - - - -
209B LYS* 1.3 93.4 - - + +
211B LEU* 1.3 53.8 + - - +
213B GLN* 3.1 9.2 + - + +
214B ALA* 2.7 34.5 + - - +
249B PHE* 4.0 22.0 - - + -
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B THR* 4.1 15.0 - - + -
203B MET* 3.9 16.2 - - + -
208B GLN* 3.2 33.3 + - + +
210B PRO* 1.3 77.4 - - - +
212B SER* 1.3 62.9 + - - +
214B ALA* 3.1 4.4 + - - +
215B VAL* 3.1 23.4 + - - +
249B PHE* 3.6 25.1 - - + -
250B LEU* 4.1 19.1 - - + -
253B VAL* 4.1 16.6 - - + -
257B TRP* 4.8 7.4 - - + -
300B PHE* 3.6 35.0 - - + -
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Residues in contact with SER 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TYR* 4.1 19.5 + - - -
203B MET* 4.0 23.0 - - - +
207B ALA 5.6 0.2 - - - -
208B GLN 3.1 12.6 + - - -
209B LYS* 3.4 18.3 - - - +
211B LEU* 1.3 76.6 - - - +
213B GLN* 1.3 62.0 + - - +
215B VAL* 3.3 7.9 + - - +
216B LYS* 3.1 20.8 + - - +
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Residues in contact with GLN 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LYS 3.0 13.8 + - - +
210B PRO* 3.5 10.3 - - + +
212B SER* 1.3 76.9 + - - +
214B ALA* 1.3 61.7 + - - +
216B LYS* 3.3 36.0 + - - +
217B LEU* 3.0 53.0 + - + +
242B GLU* 5.6 0.2 + - - -
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B PRO 2.7 16.7 + - - +
211B LEU 3.1 10.3 + - - +
213B GLN* 1.3 73.4 - - - +
215B VAL* 1.3 57.1 + - - +
217B LEU* 3.4 0.6 + - - -
218B MET* 2.9 30.7 + - - +
246B SER* 3.4 26.6 - - - +
249B PHE* 3.8 24.9 - - + -
250B LEU* 4.0 13.8 - - + +
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Residues in contact with VAL 215 (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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189B MET* 5.2 2.0 - - - -
203B MET* 5.8 1.3 - - + -
211B LEU* 3.1 16.3 + - + +
212B SER* 3.3 8.0 + - - +
214B ALA* 1.3 71.7 - - - +
216B LYS* 1.3 68.0 + - - +
218B MET* 3.3 17.5 + - + +
219B LEU* 3.0 47.9 + - + +
250B LEU* 4.0 10.1 - - + -
300B PHE* 3.8 29.2 - - + -
301B ILE* 4.3 2.7 - - + -
304B HIS* 4.1 26.7 - - + +
305B GLU* 5.0 0.2 - - - +
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Residues in contact with LYS 216 (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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212B SER 3.1 13.8 + - - +
213B GLN* 3.3 35.5 + - - +
215B VAL* 1.3 79.4 - - - +
217B LEU* 1.3 64.6 + - - +
219B LEU* 3.4 9.0 + - - +
220B GLU* 2.8 52.7 + - + +
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Residues in contact with LEU 217 (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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213B GLN* 3.0 43.7 + - + +
214B ALA 3.9 0.2 - - - +
216B LYS* 1.3 75.7 - - - +
218B MET* 1.3 60.8 + - - +
220B GLU* 3.3 22.8 + - - +
221B GLY 2.8 24.6 + - - -
239B GLN* 4.7 9.6 - - + +
242B GLU* 3.7 41.3 - - + +
243B VAL* 3.4 15.3 - - + +
246B SER* 3.3 26.9 - - - +
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Residues in contact with MET 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 5.2 0.7 - - - +
120B LEU* 3.7 32.0 - - + +
121B PHE* 4.8 0.9 - - - -
214B ALA 2.9 18.3 + - - +
215B VAL* 3.7 10.1 - - + +
217B LEU* 1.3 76.1 - - - +
219B LEU* 1.3 79.8 + - + +
221B GLY* 3.1 3.5 + - - -
222B ILE* 3.0 47.8 + - - +
243B VAL* 4.6 9.3 - - - +
246B SER* 4.3 5.1 - - - -
247B ILE* 3.9 14.4 - - + +
250B LEU* 5.3 6.5 - - + -
301B ILE* 3.5 39.7 - - + -
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Residues in contact with LEU 219 (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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215B VAL* 3.0 30.5 + - + +
216B LYS* 3.7 7.0 - - - +
218B MET* 1.3 94.0 - - + +
220B GLU* 1.3 64.8 + - + +
222B ILE* 3.1 9.3 + - + +
223B THR* 2.8 26.5 + - - -
301B ILE* 4.2 14.6 - - + -
305B GLU* 3.5 34.5 - - + +
473B GLN* 5.0 9.6 - - + -
474B ALA* 4.0 25.5 + - + -
477B LYS* 4.4 8.5 - - - +
506B GJZ 5.2 0.4 - - + -
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Residues in contact with GLU 220 (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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216B LYS* 2.8 42.2 + - + +
217B LEU* 3.5 25.2 - - - +
219B LEU* 1.3 78.4 - - + +
221B GLY* 1.3 63.1 + - - +
223B THR* 3.2 10.1 + - - -
224B ALA* 3.0 25.2 + - - +
239B GLN* 2.9 29.4 + - - +
243B VAL* 5.1 0.4 - - - -
473B GLN* 4.3 16.6 - - - +
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Residues in contact with GLY 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 3.9 6.7 - - - +
116B PHE* 3.8 12.4 - - - -
217B LEU 2.8 14.1 + - - -
218B MET 3.1 5.8 + - - -
220B GLU* 1.3 77.2 - - - +
222B ILE* 1.3 60.2 + - - +
224B ALA* 5.0 0.4 - - - -
225B SER* 3.1 26.0 + - - -
239B GLN* 6.2 0.2 - - - -
243B VAL* 3.7 25.2 - - - +
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Residues in contact with ILE 222 (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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111B ALA 4.4 5.1 - - - +
112B LEU* 3.8 21.3 - - + -
115B VAL* 4.0 10.8 - - + -
120B LEU* 3.8 12.8 - - + -
121B PHE* 3.7 25.8 - - + -
218B MET* 3.0 36.4 + - - +
219B LEU* 3.1 8.7 + - + +
221B GLY* 1.3 75.1 - - - +
223B THR* 1.3 66.5 + - - +
225B SER* 3.5 6.8 - - - -
226B ARG* 3.2 37.5 + - - +
474B ALA* 3.9 26.7 - - + -
506B GJZ 4.9 0.4 - - + -
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Residues in contact with THR 223 (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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219B LEU 2.8 16.6 + - - -
220B GLU* 3.3 10.5 + - - -
222B ILE* 1.3 76.9 - - - +
224B ALA* 1.3 59.6 + - - +
226B ARG* 2.9 20.8 + - - +
227B ASN* 2.9 30.9 + - + +
472B GLU 3.7 22.4 - - - +
473B GLN* 3.2 37.9 + - - +
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Residues in contact with ALA 224 (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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116B PHE* 4.1 18.6 - - + -
220B GLU 3.0 11.8 + - - +
221B GLY* 5.0 0.2 - - - -
223B THR* 1.3 79.8 - - - +
225B SER* 1.3 62.5 + - - +
227B ASN* 3.1 16.5 + - - +
228B THR 3.1 25.7 - - - +
239B GLN* 5.4 9.6 - - - +
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Residues in contact with SER 225 (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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81B HIS* 3.3 20.8 + - - -
111B ALA* 4.5 19.8 + - - +
114B THR 5.0 2.4 + - - -
115B VAL* 4.6 10.4 - - - +
116B PHE* 4.1 21.3 + - - -
221B GLY 3.1 19.8 + - - -
222B ILE* 3.5 8.3 - - - -
223B THR 3.2 0.2 - - - -
224B ALA* 1.3 77.9 - - - +
226B ARG* 1.3 55.9 + - - +
227B ASN 3.6 0.2 + - - -
228B THR 4.4 3.5 + - - +
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Residues in contact with ARG 226 (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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80B PHE* 3.1 85.4 - - + -
81B HIS* 3.8 6.3 + - - -
108B MET 4.0 11.7 + - - -
109B TYR* 5.1 6.1 - - - -
111B ALA* 3.5 28.7 - - + +
112B LEU* 3.6 35.4 - - - +
222B ILE* 3.2 24.1 + - - +
223B THR* 2.9 11.2 + - - +
225B SER* 1.3 79.2 - - - +
227B ASN* 1.3 65.9 + - - +
228B THR 3.9 1.1 - - - -
371B PHE* 5.8 1.0 - - - -
472B GLU* 5.6 1.4 + - - -
473B GLN 5.3 2.8 + - - -
474B ALA* 4.2 18.2 + - - +
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Residues in contact with ASN 227 (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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60B LEU* 5.0 14.6 - - - +
80B PHE* 5.1 8.3 - - - +
81B HIS* 4.8 0.2 - - - -
223B THR* 2.9 37.2 + - + +
224B ALA* 3.1 7.6 + - - +
226B ARG* 1.3 88.0 + - - +
228B THR* 1.3 69.4 + - - +
472B GLU* 5.4 0.9 - - - +
473B GLN 5.6 0.5 - - - +
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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
------------------------------------------------------------
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