Contacts of the strand formed by residues 413 - 426 (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 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381A LYS* 3.1 24.8 + - - -
382A TRP 3.4 3.6 - - - -
383A ASP* 3.4 25.2 - - - +
385A LYS* 5.2 2.6 + - - +
411A ARG 3.7 0.6 + - - -
412A GLY* 1.3 72.1 - - - +
414A SER* 1.3 66.3 + - - +
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Residues in contact with SER 414 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381A LYS* 3.1 10.0 - - - +
382A TRP* 2.9 56.5 + - - +
411A ARG 4.7 3.4 - - - -
413A ASP* 1.3 81.7 + - - +
415A ASP* 1.3 75.3 + - - +
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Residues in contact with ASP 415 (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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379A TYR* 2.8 29.6 + - + +
380A ALA 3.0 17.3 - - - +
381A LYS* 3.4 15.6 - - + +
382A TRP* 3.8 7.1 - - - -
414A SER* 1.3 88.8 + - - +
416A GLU* 1.3 70.7 + - - +
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Residues in contact with GLU 416 (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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14A THR* 3.3 21.1 - - + +
15A GLY* 3.9 1.0 + - - -
16A SER* 2.8 45.1 + - - -
21A GLN* 5.0 6.8 + - - +
23A PHE* 3.7 32.2 - - + -
379A TYR* 3.4 6.4 - - - -
380A ALA* 2.8 31.5 + - - +
382A TRP* 3.9 6.3 - - + -
415A ASP* 1.3 80.5 - - - +
417A TRP* 1.3 82.1 + - - +
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Residues in contact with TRP 417 (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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14A THR* 3.7 0.2 - - - -
15A GLY* 2.6 56.6 + - - -
16A SER 5.1 0.2 - - - -
23A PHE* 5.0 0.7 - - - -
377A ALA* 5.1 8.7 - - + -
378A THR 2.8 17.3 - - - +
379A TYR* 4.2 13.5 - + + -
416A GLU* 1.3 85.3 + - - +
418A THR* 1.3 66.3 + - - +
419A PHE* 3.1 42.8 - + + -
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Residues in contact with THR 418 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A TRP 3.1 15.0 - - - +
14A THR* 3.8 16.4 - - + +
20A GLN* 4.1 9.8 - - - +
21A GLN 3.6 25.4 + - - +
23A PHE* 3.7 16.7 - - + -
35A GLY 4.1 6.2 + - - -
376A PHE* 4.3 2.5 - - - -
377A ALA* 3.2 1.4 - - - -
378A THR* 2.7 49.0 + - - +
417A TRP* 1.3 84.4 - - - +
419A PHE* 1.3 68.0 + - - +
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Residues in contact with PHE 419 (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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12A GLY* 3.3 1.6 - - - -
13A TRP* 2.8 75.3 + + + +
14A THR 4.6 1.1 - - - -
15A GLY* 4.4 7.4 - - - -
376A PHE* 3.1 27.1 - - - +
377A ALA* 4.0 6.5 - - + -
417A TRP* 3.1 42.8 - + + -
418A THR* 1.3 78.0 - - - +
420A GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 420 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ILE 3.3 11.7 - - - -
12A GLY* 4.0 0.9 - - - -
13A TRP* 4.1 11.7 - - - -
375A ILE* 3.3 5.9 - - - +
376A PHE* 2.9 42.9 + - - +
419A PHE* 1.3 77.4 - - - +
421A ALA* 1.3 60.6 + - - -
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Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLY* 3.2 1.5 - - - -
11A ILE* 2.9 34.5 + - + +
13A TRP* 4.9 1.1 - - + -
373A ILE* 5.9 1.1 - - + -
374A ARG 3.1 11.4 - - - +
375A ILE* 4.4 11.2 - - + -
376A PHE* 3.9 2.6 - - - -
420A GLY* 1.3 75.8 - - - +
422A GLN* 1.3 62.9 + - - +
102C ALA* 4.5 6.5 - - + -
127C ALA* 3.6 30.7 - - + -
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Residues in contact with GLN 422 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ARG* 3.9 17.6 - - - +
9A SER 3.4 18.8 - - - +
10A GLY* 3.9 3.6 - - - +
35A GLY* 5.0 7.8 + - - -
37A GLU* 2.9 40.8 + - - +
39A GLU 5.5 1.2 + - - -
372A ALA 3.9 0.3 - - - +
373A ILE* 3.5 2.3 - - - +
374A ARG* 2.8 66.6 + - - +
376A PHE* 4.3 15.7 - - + -
421A ALA* 1.3 77.3 - - - +
423A MET* 1.3 70.1 + - - +
424A GLU* 5.1 0.6 - - - +
102C ALA* 4.0 6.6 - - - +
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Residues in contact with MET 423 (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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7A ALA* 4.0 16.8 - - + +
8A ARG* 3.3 2.6 - - - -
9A SER* 2.8 39.2 + - - +
372A ALA 3.2 11.9 - - - +
373A ILE* 4.6 3.1 - - + -
374A ARG* 5.3 0.4 - - - -
422A GLN* 1.3 81.4 - - - +
424A GLU* 1.3 70.4 + - - +
425A ILE* 4.2 1.3 - - - -
60C PHE* 4.1 16.6 - - + -
84C ALA* 3.6 30.7 - - + +
85C ASN* 3.9 7.4 - - - -
86C VAL* 3.7 24.9 - - + -
102C ALA* 3.4 27.8 - - + +
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Residues in contact with GLU 424 (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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6A TYR* 2.5 42.1 + - + +
7A ALA 3.4 5.6 - - - +
8A ARG* 4.6 3.3 - - + +
33A ARG* 3.4 15.3 + - - -
37A GLU* 4.5 3.0 - - - +
113A HIS* 3.8 10.1 + - - -
370A ARG* 2.8 40.7 + - - +
371A PRO* 3.3 1.6 - - - +
372A ALA* 3.0 30.2 + - + +
374A ARG* 3.0 32.1 + - - +
422A GLN* 5.0 0.7 - - - +
423A MET* 1.3 75.8 - - - +
425A ILE* 1.3 68.3 + - - +
426A TRP* 4.3 1.8 - - + -
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Residues in contact with ILE 425 (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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6A TYR* 3.3 7.1 - - - -
7A ALA* 2.9 41.3 + - + +
370A ARG* 3.9 7.0 - - - -
371A PRO* 3.9 23.1 - - + -
423A MET* 4.2 5.6 - - - -
424A GLU* 1.3 79.2 - - - +
426A TRP* 1.3 74.7 + - - +
427A TRP* 3.9 23.1 - - + -
50C VAL* 4.1 24.9 - - + -
60C PHE* 3.7 46.9 - - + -
86C VAL* 4.5 1.8 - - + -
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Residues in contact with TRP 426 (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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5A GLY 3.3 14.8 - - - +
6A TYR* 3.9 24.2 - + + -
113A HIS* 3.5 27.1 - + - -
368A TRP* 3.5 49.9 + + + -
370A ARG* 3.5 53.0 - - + +
424A GLU* 4.1 3.8 - - - -
425A ILE* 1.3 80.4 - - - +
427A TRP* 1.3 65.2 + - - +
3D GLC 3.8 29.8 - - - +
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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