Contacts of the strand formed by residues 349 - 362 (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 ARG 349 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B GLU* 3.2 24.5 + - - -
316B TRP* 4.2 12.1 - - - +
340B ASN* 2.8 45.2 + - - +
341B VAL 3.3 3.1 - - - +
342B LYS* 3.5 38.4 - - + +
347B GLY 4.5 2.4 + - - +
348B ASP* 1.3 79.1 - - - +
350B ASN* 1.3 62.2 + - - +
351B ASN* 5.2 4.1 + - - +
383B ASP 4.0 2.3 - - - +
385B LYS* 3.3 29.3 + - + +
386B TRP* 3.8 0.2 - - - -
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Residues in contact with ASN 350 (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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25B ALA* 5.3 2.2 - - + -
26B THR* 3.2 35.6 + - - +
339B ASP 3.9 0.2 - - - +
340B ASN* 3.3 2.4 - - - -
341B VAL* 2.8 37.4 + - + +
349B ARG* 1.3 72.0 - - - +
351B ASN* 1.3 64.4 + - - +
383B ASP 3.7 3.4 - - - -
384B GLU* 3.0 17.3 - - + +
385B LYS 2.8 26.0 + - - -
386B TRP* 3.0 43.8 + - - +
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Residues in contact with ASN 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 5.1 3.8 - - - -
338B TYR* 3.7 16.1 + - + +
339B ASP 3.1 11.7 - - - +
340B ASN* 3.6 20.1 - - - +
349B ARG* 5.2 4.9 + - - +
350B ASN* 1.3 78.0 - - - +
352B GLN* 1.3 63.9 + - - +
353B TYR* 5.7 3.6 - - - -
381B LYS 5.3 0.5 - - - +
382B TRP* 3.3 5.5 - - - +
383B ASP* 3.0 55.5 + - - +
384B GLU* 4.6 1.7 - - - +
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Residues in contact with GLN 352 (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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23B PHE* 3.2 34.6 + - - +
24B GLN* 4.1 1.0 - - - +
25B ALA* 4.1 21.7 - - + +
31B LYS* 5.6 1.2 - - - +
32B TYR* 6.1 1.2 - - - +
36B ASN* 5.3 0.2 - - - +
337B GLY 3.9 0.3 - - - +
338B TYR* 3.3 7.0 - - - -
339B ASP* 2.9 43.8 + - + +
351B ASN* 1.3 77.9 + - - +
353B TYR* 1.3 72.3 + - - +
354B LYS* 4.6 10.7 - - - +
380B ALA* 4.5 3.4 - - + -
381B LYS 3.4 15.0 - - - +
382B TRP* 3.9 6.8 - - + -
411B ARG* 2.8 38.2 + - - -
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Residues in contact with TYR 353 (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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336B VAL* 5.9 2.0 - - + -
337B GLY 3.1 11.0 - - - +
338B TYR* 4.0 18.8 - + + -
351B ASN* 5.7 3.8 - - - -
352B GLN* 1.3 78.5 - - - +
354B LYS* 1.3 60.3 + - - +
355B ILE* 3.8 28.3 - - + -
379B TYR* 4.0 24.0 + + - -
380B ALA* 3.4 1.2 - - - -
381B LYS* 3.0 60.6 + - + +
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Residues in contact with LYS 354 (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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23B PHE* 5.4 0.9 - - + -
32B TYR* 2.9 41.3 - - + +
34B LEU 3.2 9.2 + - - -
36B ASN* 3.7 15.0 - - - +
335B GLU* 2.8 31.5 + - - +
336B VAL* 3.3 4.3 - - - -
337B GLY 2.9 33.0 + - - +
352B GLN* 4.6 10.7 - - - +
353B TYR* 1.3 74.6 - - - +
355B ILE* 1.3 64.5 + - - +
356B THR* 2.7 32.9 + - - +
378B THR* 3.7 14.6 - - + -
379B TYR 3.2 9.2 - - - +
380B ALA* 4.0 11.0 - - + -
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Residues in contact with ILE 355 (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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334B LEU* 4.0 14.8 - - + -
335B GLU 3.3 2.7 - - - -
336B VAL* 3.7 34.3 - - + -
353B TYR* 3.8 28.0 - - + -
354B LYS* 1.3 82.6 - - - +
356B THR* 1.3 66.8 + - - +
357B LEU* 6.2 0.4 - - + -
377B ALA 4.1 0.7 - - - +
378B THR* 3.5 1.4 - - - +
379B TYR* 2.8 43.7 + - + +
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Residues in contact with THR 356 (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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34B LEU* 3.1 35.9 + - + +
333B LEU 4.5 0.2 - - - -
334B LEU* 3.1 10.7 - - - +
335B GLU* 2.7 38.2 + - - -
354B LYS* 2.7 30.2 + - - -
355B ILE* 1.3 75.0 + - - +
357B LEU* 1.3 68.9 + - - +
376B PHE* 4.3 9.2 - - + -
377B ALA 3.6 5.6 - - - +
378B THR* 2.8 26.4 + - - +
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Residues in contact with LEU 357 (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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332B THR* 4.0 20.2 - - + -
333B LEU 3.4 13.0 - - - +
334B LEU* 4.1 19.7 - - + -
355B ILE* 6.2 0.2 - - + -
356B THR* 1.3 73.2 - - - +
358B ALA* 1.3 65.6 + - - +
359B GLN* 5.5 2.7 - - + +
376B PHE* 3.3 2.9 - - - +
377B ALA* 3.1 38.0 + - + +
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Residues in contact with ALA 358 (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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34B LEU* 4.0 25.8 - - + -
332B THR* 3.3 5.8 - - - +
333B LEU* 2.7 46.1 + - + +
357B LEU* 1.3 79.0 - - - +
359B GLN* 1.3 63.8 + - - +
360B GLN 3.9 0.2 + - - -
374B ARG* 4.7 9.4 - - + -
375B ILE 3.2 11.7 - - - +
376B PHE* 3.8 12.6 - - + -
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Residues in contact with GLN 359 (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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326B TRP* 3.8 9.7 - - - +
330B MET* 3.5 28.9 - - + +
331B SER 3.4 12.6 + - - -
332B THR* 2.6 30.1 + - - +
357B LEU* 5.5 2.6 - - + +
358B ALA* 1.3 74.0 - - - +
360B GLN* 1.3 60.5 + - - +
361B TRP* 3.8 21.2 - - + -
374B ARG* 3.4 2.9 - - - -
375B ILE* 2.9 52.1 + - + +
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Residues in contact with GLN 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B MET* 4.1 5.7 - - - +
330B MET* 3.3 8.5 - - - +
331B SER* 2.8 38.6 + - - +
333B LEU* 3.4 36.7 - - + +
359B GLN* 1.3 76.5 - - - +
361B TRP* 1.3 73.6 + - - +
362B GLN* 2.9 31.3 + - - +
366B SER 5.3 1.0 + - - -
367B ILE* 5.8 2.0 + - - +
369B SER 5.1 1.8 + - - -
370B ARG* 5.6 3.1 - - - +
372B ALA* 3.5 15.0 - - + +
373B ILE 3.3 11.0 - - - +
374B ARG* 3.1 34.4 + - + +
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Residues in contact with TRP 361 (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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58A PHE* 4.1 6.6 - - + -
91A LEU* 4.0 42.7 + - + -
92A ILE* 3.5 27.7 - - + +
100A ILE* 3.9 20.2 - - + -
329B ILE* 3.0 16.4 - - + +
330B MET* 3.3 41.1 - - + +
359B GLN* 3.8 25.1 - - + -
360B GLN* 1.3 73.9 - - - +
362B GLN* 1.3 60.2 + - - +
372B ALA* 3.3 1.7 - - - -
373B ILE* 2.8 45.5 + - + +
375B ILE* 3.9 31.2 - - + -
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Residues in contact with GLN 362 (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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58A PHE* 3.6 9.0 - - - -
323B MET* 3.6 19.3 - - - +
325B LYS* 6.0 0.2 - - - +
327B THR 4.8 1.0 + - - -
328B PRO 3.3 13.3 + - - -
329B ILE* 3.0 38.0 + - - +
330B MET 3.9 3.0 - - - +
331B SER* 2.9 12.1 + - - -
360B GLN* 2.9 37.3 + - - +
361B TRP* 1.3 74.4 - - - +
363B ALA* 1.3 58.4 + - - +
364B GLY 2.8 38.5 + - - +
365B ASP* 4.2 1.8 - - - +
366B SER 4.3 4.0 - - - +
369B SER* 3.8 20.6 - - - +
371B PRO 3.3 12.8 - - - +
372B ALA* 4.0 2.2 - - + -
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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