Contacts of the strand formed by residues 372 - 384 (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 ALA 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A GLN* 3.6 30.7 - - + +
361A TRP 3.2 7.0 - - - -
362A GLN* 4.1 4.3 - - + -
369A SER 4.4 0.4 - - - +
370A ARG* 4.0 18.2 - - - +
371A PRO* 1.3 76.9 - - - +
373A ILE* 1.3 64.4 + - - +
374A ARG* 4.1 10.7 - - - +
423A MET* 3.2 8.1 - - - +
424A GLU 3.0 26.6 + - - +
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Residues in contact with ILE 373 (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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360A GLN* 3.3 4.0 - - - -
361A TRP* 2.9 41.1 + - + +
372A ALA* 1.3 77.7 - - - +
374A ARG* 1.3 65.7 + - - +
375A ILE* 5.7 2.9 - - + -
421A ALA* 5.9 1.3 - - + -
422A GLN 3.5 3.1 - - - +
423A MET* 4.6 4.3 - - + -
58C PHE* 4.5 10.1 - - + -
86C VAL* 3.9 35.4 - - + +
88C GLY 4.1 4.9 - - - +
100C ILE* 3.7 51.4 - - + +
101C TRP* 4.3 4.9 - - - +
102C ALA* 4.3 16.8 - - + -
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Residues in contact with ARG 374 (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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33A ARG* 5.8 3.2 - - - +
34A LEU* 4.1 27.8 - - + +
35A GLY 6.0 0.2 - - - +
37A GLU* 4.5 4.6 + - - -
113A HIS* 5.1 0.2 + - - -
321A ARG* 4.4 10.1 - - - +
333A LEU* 5.6 1.2 - - + +
358A ALA* 4.6 8.3 - - + -
359A GLN 3.3 6.3 - - - +
360A GLN* 3.1 32.5 + - + +
370A ARG* 3.4 21.2 - - - +
372A ALA* 4.2 5.6 - - - +
373A ILE* 1.3 80.6 - - - +
375A ILE* 1.3 69.4 + - - +
376A PHE* 4.2 7.2 - - + -
421A ALA* 3.1 6.6 - - - +
422A GLN* 2.8 68.0 + - + +
424A GLU* 3.0 41.7 + - - +
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Residues in contact with ILE 375 (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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358A ALA* 3.2 2.3 - - - -
359A GLN* 2.8 54.8 + - + +
361A TRP* 3.9 24.0 - - + -
373A ILE* 5.7 3.1 - - + -
374A ARG* 1.3 79.0 - - - +
376A PHE* 1.3 60.6 + - - +
420A GLY 3.3 7.9 - - - +
421A ALA* 4.4 12.6 - - + -
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Residues in contact with PHE 376 (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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11A ILE 4.9 0.7 - - - -
20A GLN* 3.6 28.0 - - - -
34A LEU* 5.9 0.9 - - + -
35A GLY* 3.6 35.9 - - - +
37A GLU 5.8 0.2 - - - -
356A THR* 4.3 6.5 - - + -
357A LEU 3.2 13.5 - - - +
358A ALA* 3.7 11.7 - - + -
374A ARG* 4.7 7.9 - - + -
375A ILE* 1.3 77.3 - - - +
377A ALA* 1.3 64.6 + - - +
378A THR* 3.9 6.3 - - - -
418A THR* 4.3 2.9 - - - -
419A PHE* 3.1 38.0 - - - +
420A GLY* 2.9 46.3 + - - +
421A ALA* 3.9 12.1 - - - -
422A GLN* 4.3 13.0 - - + -
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Residues in contact with ALA 377 (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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355A ILE 4.0 0.7 - - - +
356A THR* 3.6 2.1 - - - +
357A LEU* 3.1 35.7 + - + +
376A PHE* 1.3 76.5 - - - +
378A THR* 1.3 60.0 + - - +
417A TRP* 5.1 9.0 - - + -
418A THR 3.2 9.9 - - - +
419A PHE* 4.0 5.8 - - + -
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Residues in contact with THR 378 (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* 4.3 13.2 - - + -
35A GLY* 2.7 23.5 + - - +
36A ASN* 5.1 0.2 - - - +
354A LYS* 3.7 22.0 - - + -
355A ILE 3.5 2.7 - - - +
356A THR* 2.8 29.3 + - - +
376A PHE* 3.9 2.0 - - - -
377A ALA* 1.3 73.3 - - - +
379A TYR* 1.3 68.1 + - - +
417A TRP* 2.8 9.8 - - - +
418A THR* 2.7 52.6 + - - +
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Residues in contact with TYR 379 (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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353A TYR* 4.1 17.0 + + - -
354A LYS* 3.1 4.3 - - - +
355A ILE* 2.8 53.6 + - + +
378A THR* 1.3 76.1 - - - +
380A ALA* 1.3 61.2 + - - +
381A LYS* 3.6 24.5 - - + +
415A ASP* 2.8 45.0 + - + +
416A GLU 3.4 13.0 - - - -
417A TRP* 4.2 12.3 - + + -
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Residues in contact with ALA 380 (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* 3.4 44.2 - - + -
352A GLN* 4.6 2.9 - - - -
353A TYR 3.5 5.8 - - - +
354A LYS* 4.0 10.8 - - + -
379A TYR* 1.3 78.0 - - - +
381A LYS* 1.3 60.3 + - - +
382A TRP* 3.5 9.2 - - + -
415A ASP* 3.0 5.5 - - - +
416A GLU 2.8 32.7 + - - -
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Residues in contact with LYS 381 (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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351A ASN* 5.4 0.2 - - - +
352A GLN* 3.4 2.9 - - - +
353A TYR* 3.0 62.6 + - + +
379A TYR* 3.6 18.3 - - + +
380A ALA* 1.3 75.1 - - - +
382A TRP* 1.3 89.8 + - - +
383A ASP* 4.3 3.6 - - - +
413A ASP* 3.1 26.0 + - - -
414A SER 3.1 18.4 + - - +
415A ASP* 3.4 14.8 - - + +
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Residues in contact with TRP 382 (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* 3.8 19.1 - + - -
351A ASN* 3.3 14.1 - - - +
352A GLN* 3.9 9.4 - - + -
380A ALA* 3.5 24.9 - - + -
381A LYS* 1.3 93.7 + - - +
383A ASP* 1.3 61.3 + - - +
384A GLU* 4.1 4.3 - - + -
411A ARG* 3.2 74.5 + - + +
412A GLY 3.3 15.0 - - - -
414A SER* 2.9 49.5 + - - +
415A ASP* 3.8 15.5 - - - -
416A GLU* 3.9 11.4 - - + -
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Residues in contact with ASP 383 (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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349A ARG 4.0 2.8 - - - +
350A ASN* 3.7 2.4 - - - -
351A ASN* 3.0 45.4 + - - +
381A LYS* 4.5 3.4 - - - +
382A TRP* 1.3 75.1 - - - +
384A GLU* 1.3 62.3 + - - +
385A LYS* 3.3 38.7 + - - +
412A GLY 3.5 2.5 - - - -
413A ASP* 3.4 25.8 - - - +
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Residues in contact with GLU 384 (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* 3.6 4.9 - - - +
26A THR* 2.6 44.7 + - - -
350A ASN* 3.0 19.5 - - + +
351A ASN 4.7 1.3 - - - +
382A TRP* 4.1 9.6 - - + +
383A ASP* 1.3 77.7 + - - +
385A LYS* 1.3 62.7 + - - +
386A TRP 3.4 0.7 - - - +
402A THR* 2.8 17.2 + - - -
410A SER* 3.3 13.7 + - - +
411A ARG* 2.7 50.0 + - - +
412A GLY* 2.7 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