Contacts of the strand formed by residues 349 - 362 (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 ARG 349 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A GLU* 3.1 25.1 + - - -
316A TRP* 4.2 11.5 - - - +
340A ASN* 2.8 44.1 + - - +
341A VAL 3.3 3.1 - - - +
342A LYS* 3.4 45.6 - - + +
347A GLY 4.5 3.1 + - - +
348A ASP* 1.3 75.2 - - - +
350A ASN* 1.3 63.9 + - - +
351A ASN* 5.3 4.2 + - - +
383A ASP 4.0 2.1 - - - +
385A LYS* 3.3 30.2 + - + +
386A TRP* 3.9 0.2 - - - -
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Residues in contact with ASN 350 (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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25A ALA* 5.3 2.5 - - + -
26A THR* 3.1 36.6 + - - +
340A ASN* 3.2 4.9 - - - -
341A VAL* 2.8 38.1 + - + +
349A ARG* 1.3 72.7 - - - +
351A ASN* 1.3 61.8 + - - +
383A ASP 3.7 2.9 - - - -
384A GLU* 3.0 16.7 - - + +
385A LYS 2.7 31.0 + - - -
386A TRP* 3.0 44.2 + - - -
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Residues in contact with ASN 351 (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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25A ALA* 5.1 3.4 - - - -
338A TYR* 3.8 16.5 + - + +
339A ASP 3.1 12.1 - - - +
340A ASN* 3.6 19.6 - - - +
349A ARG* 5.3 4.4 + - - +
350A ASN* 1.3 76.8 - - - +
352A GLN* 1.3 64.5 + - - +
353A TYR* 5.7 3.8 - - - -
381A LYS 5.4 0.2 - - - +
382A TRP* 3.3 4.9 - - - +
383A ASP* 3.0 55.0 + - - +
384A GLU* 4.7 2.5 - - - +
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Residues in contact with GLN 352 (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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23A PHE* 3.2 35.2 + - - +
24A GLN* 4.0 0.6 - - - +
25A ALA* 4.0 21.4 - - + +
31A LYS* 5.6 1.0 - - - +
32A TYR* 6.1 1.8 - - - +
337A GLY 3.9 0.3 - - - +
338A TYR* 3.3 7.3 - - - -
339A ASP* 2.9 42.3 + - + +
351A ASN* 1.3 78.8 - - - +
353A TYR* 1.3 73.0 + - - +
354A LYS* 4.7 10.7 - - - +
380A ALA* 4.6 2.9 - - - -
381A LYS 3.4 16.4 - - - +
382A TRP* 3.9 6.7 - - + -
411A ARG* 2.8 37.9 + - - -
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Residues in contact with TYR 353 (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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336A VAL* 5.9 2.2 - - + -
337A GLY 3.1 10.5 - - - +
338A TYR* 4.1 18.4 - + + -
351A ASN* 5.7 3.4 - - - -
352A GLN* 1.3 80.2 - - - +
354A LYS* 1.3 60.4 + - - +
355A ILE* 3.8 28.0 - - + -
379A TYR* 4.1 23.9 + + - -
380A ALA* 3.5 1.4 - - - -
381A LYS* 3.0 58.3 + - + +
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Residues in contact with LYS 354 (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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23A PHE* 5.3 0.7 - - + +
32A TYR* 2.9 39.9 - - + +
34A LEU 3.3 9.6 + - - -
36A ASN* 3.7 16.2 - - - +
335A GLU* 2.9 30.7 + - - +
336A VAL* 3.4 3.8 - - - -
337A GLY 3.0 33.3 + - - +
352A GLN* 4.7 10.3 - - - +
353A TYR* 1.3 76.9 - - - +
355A ILE* 1.3 64.0 + - - +
356A THR* 2.8 27.7 + - - +
378A THR* 3.7 20.0 - - + -
379A TYR 3.1 9.9 - - - +
380A ALA* 4.0 11.2 - - + -
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Residues in contact with ILE 355 (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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334A LEU* 3.9 15.0 - - + -
335A GLU 3.3 2.2 - - - -
336A VAL* 3.7 34.5 - - + -
353A TYR* 3.8 28.5 - - + -
354A LYS* 1.3 81.3 - - - +
356A THR* 1.3 66.5 + - - +
357A LEU* 6.3 0.4 - - + -
377A ALA 4.0 0.9 - - - +
378A THR* 3.5 1.0 - - - -
379A TYR* 2.8 43.4 + - + +
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Residues in contact with THR 356 (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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34A LEU* 3.1 36.7 + - + +
333A LEU 3.8 0.2 - - - +
334A LEU* 3.1 10.6 - - - +
335A GLU 2.7 38.3 + - - -
354A LYS* 2.8 29.7 + - - -
355A ILE* 1.3 76.2 + - - +
357A LEU* 1.3 69.7 + - - +
376A PHE* 4.3 9.0 - - + -
377A ALA 3.6 5.8 - - - +
378A THR* 2.8 27.8 + - - +
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Residues in contact with LEU 357 (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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332A THR* 4.0 20.9 - - + -
333A LEU 3.4 13.0 - - - +
334A LEU* 4.3 18.8 - - + -
355A ILE* 6.3 0.2 - - + -
356A THR* 1.3 73.6 - - - +
358A ALA* 1.3 67.0 + - - +
359A GLN* 5.4 2.2 - - + +
376A PHE* 3.2 3.1 - - - +
377A ALA* 3.1 39.7 + - + +
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Residues in contact with ALA 358 (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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34A LEU* 4.1 26.9 - - + -
332A THR* 3.4 5.7 - - - +
333A LEU* 2.7 45.3 + - + +
357A LEU* 1.3 78.9 - - - +
359A GLN* 1.3 64.2 + - - +
360A GLN* 4.0 0.4 + - - -
374A ARG* 4.6 8.5 - - + -
375A ILE 3.2 12.6 - - - +
376A PHE* 3.7 12.1 - - + -
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Residues in contact with GLN 359 (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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326A TRP* 3.8 9.5 - - - +
330A MET* 3.5 30.2 - - + +
331A SER 3.4 12.5 + - - -
332A THR* 2.7 29.9 + - - +
357A LEU* 5.4 2.9 - - + +
358A ALA* 1.3 74.3 - - - +
360A GLN* 1.3 60.9 + - - +
361A TRP* 3.9 21.1 - - + -
373A ILE 3.8 0.2 - - - +
374A ARG* 3.3 3.6 - - - -
375A ILE* 2.8 51.3 + - + +
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Residues in contact with GLN 360 (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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323A MET* 4.2 6.1 - - - +
330A MET* 3.2 7.8 - - - +
331A SER* 2.8 40.9 + - - +
333A LEU* 3.5 35.8 - - + +
358A ALA 4.0 0.6 + - - +
359A GLN* 1.3 77.5 - - - +
361A TRP* 1.3 73.0 + - - +
362A GLN* 2.9 31.1 + - - +
366A SER 5.4 1.0 + - - -
367A ILE* 5.8 1.8 + - - +
369A SER 5.1 1.8 + - - -
370A ARG* 5.5 3.1 + - - +
372A ALA* 3.6 14.9 - - + +
373A ILE 3.3 11.9 - - - +
374A ARG* 3.1 33.6 + - + +
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Residues in contact with TRP 361 (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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329A ILE* 3.0 15.9 - - + +
330A MET* 3.3 42.6 - - + +
359A GLN* 3.9 23.6 - - + -
360A GLN* 1.3 73.2 - - - +
362A GLN* 1.3 61.4 + - - +
372A ALA* 3.2 1.6 - - - -
373A ILE* 2.9 46.0 + - + +
375A ILE* 3.9 33.7 - - + -
58C PHE* 4.1 6.5 - - + -
91C LEU* 4.0 42.0 + - + -
92C ILE* 3.5 28.2 - - + +
100C ILE* 3.9 20.9 - - + -
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Residues in contact with GLN 362 (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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323A MET* 3.6 19.9 - - - +
325A LYS* 6.1 0.8 - - - +
327A THR 4.8 0.4 + - - -
328A PRO 3.3 13.1 + - - -
329A ILE* 3.0 36.2 + - - +
330A MET 3.9 3.0 + - - +
331A SER* 3.0 12.4 + - - -
360A GLN* 2.9 34.6 + - - +
361A TRP* 1.3 74.3 - - - +
363A ALA* 1.3 59.0 + - - +
364A GLY 2.7 36.1 + - - +
365A ASP* 4.2 1.2 - - - +
366A SER 4.3 4.5 - - - +
369A SER* 3.8 20.9 - - - +
371A PRO 3.2 12.8 - - - +
372A ALA* 4.1 2.0 - - + -
58C PHE* 3.7 7.2 - - - -
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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