Contacts of the strand formed by residues 294 - 307 (chain B) 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 TRP 294 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289B SER* 3.5 1.7 - - - -
290B LEU* 2.7 59.4 + - + +
291B GLY 4.1 1.4 - - - +
292B ASP 3.6 2.0 - - - -
293B LYS* 1.3 88.4 - - + +
295B ASP* 1.3 68.7 + - - +
322B PRO* 4.1 26.9 - - + -
323B MET 3.2 18.6 - - - -
324B TYR* 3.5 42.1 - + + -
325B LYS* 4.3 0.7 - - - -
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Residues in contact with ASP 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE 3.5 5.6 - - - +
289B SER* 2.8 26.7 + - - -
290B LEU* 4.7 0.9 - - - -
294B TRP* 1.3 79.4 - - - +
296B LEU* 1.3 61.9 + - - +
322B PRO* 3.4 3.6 - - - +
323B MET* 2.7 38.4 + - + +
325B LYS* 3.0 30.7 + - - -
366B SER* 3.6 6.4 + - - -
367B ILE* 3.0 46.7 + - + +
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B GLY 3.9 0.2 - - - +
287B ALA* 3.1 5.1 + - - +
288B ILE* 2.8 45.4 + - + +
290B LEU* 3.6 25.8 - - + -
295B ASP* 1.3 77.7 - - - +
297B MET* 1.3 68.3 + - - +
298B TYR* 4.3 16.3 - - + -
320B VAL* 3.8 26.7 - - + -
321B ARG 3.5 2.0 - - - -
322B PRO* 3.7 31.2 - - + -
367B ILE* 4.3 2.8 - - - +
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Residues in contact with MET 297 (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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113B HIS* 3.9 19.7 - - + -
114B MET* 4.0 19.7 - - + -
286B GLY 3.3 11.2 - - - +
287B ALA* 4.1 10.3 - - + -
296B LEU* 1.3 75.5 - - - +
298B TYR* 1.3 62.4 + - - +
320B VAL* 3.6 0.5 - - - -
321B ARG* 2.8 61.5 + - + +
367B ILE* 4.0 26.9 - - + +
368B TRP* 3.4 49.8 - - + -
370B ARG* 5.4 0.2 - - - +
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Residues in contact with TYR 298 (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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112B VAL* 5.2 0.3 - - - +
114B MET* 3.9 3.3 - - - +
223B MET* 4.5 8.1 - - - +
227B TYR 3.8 2.9 + - - -
228B ASN* 2.8 41.3 + - - +
284B ASP* 3.6 12.3 - - - -
285B HIS* 3.2 8.1 - - - +
286B GLY* 3.1 57.0 + - - +
287B ALA 4.1 2.0 - - - -
288B ILE* 4.4 20.6 - - + -
296B LEU* 4.3 16.4 - - + -
297B MET* 1.3 77.6 - - - +
299B VAL* 1.3 67.2 + - - +
319B GLY 3.4 11.7 - - - +
320B VAL* 4.0 13.2 - - + -
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 4.1 20.6 - - + +
112B VAL* 3.5 25.8 - - + -
114B MET* 3.4 35.9 - - + -
115B ILE* 4.1 14.1 - - + -
283B LEU* 3.8 19.7 - - + -
284B ASP 3.5 5.2 - - - -
285B HIS* 3.9 1.8 - - + -
298B TYR* 1.3 75.8 - - - +
300B GLY* 1.3 63.4 + - - +
301B MET* 5.1 2.2 - - + +
317B THR* 5.3 1.3 - - + +
318B VAL* 3.4 7.2 - - - +
319B GLY 3.0 28.7 + - - +
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Residues in contact with GLY 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ILE 4.1 0.3 - - - +
283B LEU* 3.5 1.9 - - - +
284B ASP* 2.9 37.1 + - - +
299B VAL* 1.3 77.1 - - - +
301B MET* 1.3 61.7 + - - +
317B THR 3.5 6.3 - - - -
318B VAL* 4.5 8.7 - - - -
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Residues in contact with MET 301 (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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115B ILE* 4.6 6.5 - - + -
117B PHE* 3.9 21.3 - - + -
281B ARG* 3.8 24.5 - - + -
282B ILE 3.4 11.4 - - - +
283B LEU* 3.7 26.7 - - + -
299B VAL* 5.2 1.1 - - + -
300B GLY* 1.3 76.8 - - - +
302B TYR* 1.3 71.5 + - - +
303B GLN* 4.5 2.2 - - + +
315B TRP* 3.7 35.5 - - + +
316B TRP* 3.4 8.3 - - - -
317B THR* 2.9 58.5 + - + +
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Residues in contact with TYR 302 (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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280B TRP* 4.7 9.9 - - + -
281B ARG* 3.4 2.4 - - - -
282B ILE* 2.9 55.7 + - + +
301B MET* 1.3 75.3 - - - +
303B GLN* 1.3 62.7 + - - +
304B ASN* 3.5 32.5 + - + +
314B GLU* 3.1 35.4 + - + -
315B TRP 3.3 3.8 - - - -
316B TRP* 3.4 52.9 - + + -
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Residues in contact with GLN 303 (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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29B GLN* 3.3 33.5 + - - +
117B PHE* 3.9 4.5 - - - -
279B MET* 4.1 15.3 - - + -
280B TRP 3.3 8.3 - - - +
281B ARG* 2.8 45.8 + - + +
301B MET* 4.2 5.0 - - + +
302B TYR* 1.3 77.4 - - - +
304B ASN* 1.3 60.9 + - - +
305B ILE* 4.0 14.2 - - + +
313B THR* 3.8 3.9 + - - +
314B GLU* 3.5 1.6 - - - +
315B TRP* 2.7 67.5 + - + +
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Residues in contact with ASN 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ASN* 3.6 4.1 + - - +
279B MET* 3.2 5.1 - - - -
280B TRP* 2.9 42.3 + - + +
302B TYR* 3.5 29.8 + - + +
303B GLN* 1.3 74.1 - - - +
305B ILE* 1.3 64.7 + - - +
306B ASP* 3.6 23.2 + - - +
313B THR 3.6 3.7 - - - +
314B GLU* 3.7 20.5 - - + +
342B LYS* 5.9 0.2 + - - -
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Residues in contact with ILE 305 (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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29B GLN* 4.0 14.6 - - - +
240B THR* 4.0 23.8 - - - +
241B THR 5.5 0.7 - - - +
278B ASN 3.7 3.8 - - - +
279B MET* 4.0 18.8 - - + +
303B GLN* 4.0 23.1 - - - +
304B ASN* 1.3 74.2 - - - +
306B ASP* 1.3 59.0 + - - +
307B TRP* 3.6 46.7 - - + +
312B GLY* 3.3 8.1 - - - -
313B THR* 2.9 44.0 + - - +
344B GLN* 3.7 3.1 - - - +
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Residues in contact with ASP 306 (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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277B GLY* 3.1 4.3 - - - -
278B ASN* 2.8 53.4 + - - +
304B ASN* 3.6 20.2 + - - +
305B ILE* 1.3 70.4 - - - +
307B TRP* 1.3 65.2 + - - +
308B ASP* 4.8 1.8 - - - +
344B GLN* 2.8 24.9 + - - +
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Residues in contact with TRP 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B THR* 2.8 36.6 + - - -
241B THR* 3.9 21.8 - - + -
274B ASN 5.1 0.7 - - - -
275B ASN* 3.0 21.1 + - + -
276B ASN 3.2 18.2 - - - +
277B GLY* 4.0 4.3 - - - -
278B ASN 4.8 0.2 - - - -
305B ILE* 3.6 23.5 + - + +
306B ASP* 1.3 80.3 - - - +
308B ASP* 1.3 66.7 + - - +
309B ASN* 3.4 20.9 - - - +
310B ASN* 2.9 13.9 + - - +
311B LEU* 3.6 15.3 - - + -
312B GLY* 3.6 23.1 - - - +
344B GLN* 3.2 21.7 + - - +
397B ARG* 4.2 24.9 - - - -
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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