Contacts of the strand formed by residues 211 - 223 (chain A) in PDB entry 2MPR
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 ASP 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A TYR* 2.7 31.8 + - + +
194A GLY 3.2 15.3 - - - +
195A ARG* 3.6 4.9 - - + -
209A SER 2.9 12.4 + - - +
210A LYS* 1.3 85.7 - - + +
212A GLY* 1.3 61.9 + - - +
213A TRP* 5.7 1.5 - - - -
237A ASP* 3.2 14.9 - - - +
238A ALA* 3.2 22.6 + - - +
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Residues in contact with GLY 212 (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 TYR* 3.3 7.8 - - - -
194A GLY 3.1 27.5 + - - -
211A ASP* 1.3 82.1 + - - +
213A TRP* 1.3 66.3 + - - -
236A THR* 3.5 22.9 - - - -
238A ALA* 4.1 1.5 - - - +
239A MET* 3.5 11.1 - - - +
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Residues in contact with TRP 213 (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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191A VAL* 3.7 32.5 - - + -
192A ASP 3.3 12.6 - - - -
193A TYR* 3.4 39.8 - + + -
211A ASP* 5.7 1.7 + - - -
212A GLY* 1.3 80.2 - - - -
214A MET* 1.3 62.1 + - - +
215A PHE* 3.7 28.9 - + + -
234A TYR 4.0 0.6 - - - +
235A ALA* 3.3 1.9 - - - -
236A THR* 2.8 44.1 + - + -
239A MET* 3.5 5.3 - - - +
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Residues in contact with MET 214 (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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120A TRP* 5.2 0.9 - - - -
190A GLY 4.6 0.2 - - - -
191A VAL* 3.5 3.3 - - - -
192A ASP* 2.9 40.6 + - + +
213A TRP* 1.3 76.2 - - - +
215A PHE* 1.3 74.2 + - - +
216A THR* 4.5 4.3 - - - +
233A GLN* 4.3 16.2 - - + +
234A TYR 3.2 11.4 - - - +
235A ALA* 3.8 9.2 - - + -
239A MET* 4.0 18.6 - - + +
243A GLY* 3.4 32.5 - - - +
244A LYS* 3.9 3.6 - - - +
245A GLY* 3.6 23.6 - - - +
279A MET* 3.5 24.0 - - + -
281A ARG* 4.4 4.3 - - - +
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Residues in contact with PHE 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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190A GLY 3.5 4.0 - - - +
191A VAL* 4.0 32.3 - - + -
213A TRP* 3.7 38.1 - + + -
214A MET* 1.3 77.8 - - - +
216A THR* 1.3 64.2 + - - +
232A VAL 3.9 0.4 - - - +
233A GLN* 3.2 7.3 - - - +
234A TYR* 2.9 62.8 + + + +
236A THR* 5.4 0.9 - - - -
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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
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119A TYR* 5.7 0.9 - - + -
120A TRP* 3.6 47.5 + - + -
189A LEU* 3.4 5.2 - - - +
190A GLY 2.9 32.7 + - - +
192A ASP* 5.1 0.9 + - - -
214A MET* 4.5 6.1 - - - +
215A PHE* 1.3 77.9 - - - +
217A ALA* 1.3 72.0 + - - +
218A GLU* 4.5 4.0 - - + +
231A VAL* 4.4 6.1 - - + -
232A VAL 3.6 4.0 - - - -
233A GLN* 2.9 33.3 + - + +
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Residues in contact with ALA 217 (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 LEU* 4.7 6.7 - - + -
188A GLU 3.4 6.3 - - - -
189A LEU* 3.9 16.4 - - + -
216A THR* 1.3 76.1 - - - +
218A GLU* 1.3 60.7 + - - +
219A HIS 4.3 0.2 - - - -
230A PHE 3.7 1.3 - - - +
231A VAL* 3.4 4.3 - - - +
232A VAL* 3.0 43.3 + - + +
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Residues in contact with GLU 218 (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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110A HIS* 2.9 34.3 + - + +
119A TYR* 2.6 36.3 + - - -
120A TRP* 5.4 0.2 - - - -
186A VAL 3.8 0.7 - - - +
187A LEU* 3.5 4.7 - - - +
188A GLU* 2.9 49.4 + - + +
216A THR* 4.3 7.4 - - + -
217A ALA* 1.3 74.6 - - - +
219A HIS* 1.3 64.8 + - - +
220A THR* 4.1 9.3 + - - +
229A LYS* 3.3 27.7 + - + -
230A PHE 3.3 3.8 - - - +
231A VAL* 3.7 14.5 - - + +
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Residues in contact with HIS 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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181A THR* 3.3 15.6 + - + -
182A ASN* 3.0 22.6 + - - -
185A GLY* 3.6 4.9 - - - -
186A VAL 3.3 19.1 - - - -
187A LEU* 4.2 13.7 - - + -
218A GLU* 1.3 73.5 - - - +
220A THR* 1.3 70.2 + - - +
221A GLN* 3.4 31.3 + - + +
228A ASN* 3.5 3.5 + - - +
229A LYS* 3.2 5.4 - - - -
230A PHE* 2.8 50.8 + - + +
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Residues in contact with THR 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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184A ASP 3.6 1.7 - - - +
185A GLY* 3.3 3.1 - - - -
186A VAL* 2.8 43.8 + - - +
218A GLU* 4.3 5.7 + - - +
219A HIS* 1.3 77.1 - - - +
221A GLN* 1.3 64.8 + - - +
222A SER* 5.1 4.7 + - - +
227A TYR* 4.2 17.9 - - + -
228A ASN 3.5 2.2 - - - -
229A LYS* 3.0 40.0 + - + +
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Residues in contact with GLN 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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182A ASN* 2.9 24.5 + - - +
183A PRO 3.1 22.8 + - - -
184A ASP* 3.1 20.7 + - - +
185A GLY* 3.4 8.0 - - - -
219A HIS* 3.4 14.8 + - + +
220A THR* 1.3 73.6 - - - +
222A SER* 1.3 70.1 + - - +
223A MET* 3.7 15.3 + - + +
227A TYR* 3.1 7.3 - - - -
228A ASN* 2.9 41.6 + - + +
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Residues in contact with SER 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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184A ASP* 2.9 34.3 + - - +
220A THR* 5.3 5.4 + - - +
221A GLN* 1.3 83.0 + - - +
223A MET* 1.3 66.0 + - - +
226A GLY 3.6 9.6 + - - -
227A TYR* 4.4 2.0 - - - +
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Residues in contact with MET 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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221A GLN* 3.9 20.0 - - + +
222A SER* 1.3 77.9 - - - +
224A LEU* 1.3 83.2 + - + +
225A LYS 3.0 3.6 - - - -
226A GLY* 2.6 39.1 + - - +
227A TYR* 4.5 2.7 - - - -
228A ASN* 4.4 14.6 - - + +
288A ILE* 3.9 20.9 - - + +
298A TYR* 4.5 11.9 - - - +
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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