Contacts of the strand formed by residues 372 - 384 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360C GLN* 3.5 30.3 - - - +
361C TRP 3.3 6.3 - - - -
362C GLN* 4.1 4.7 - - + -
369C SER 4.3 0.7 - - - +
370C ARG* 4.0 18.6 - - - +
371C PRO* 1.3 76.1 - - - +
373C ILE* 1.3 63.2 + - - +
374C ARG* 4.1 10.0 - - - +
422C GLN 3.9 0.2 - - - +
423C MET* 3.2 8.3 - - - +
424C GLU 3.0 27.9 + - - +
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Residues in contact with ILE 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PHE* 4.5 7.9 - - + -
86B VAL* 3.9 36.8 - - + +
88B GLY 4.2 4.9 - - - +
100B ILE* 3.8 47.8 - - + +
101B TRP* 4.3 4.9 - - - +
102B ALA* 4.3 14.6 - - + +
360C GLN* 3.3 3.8 - - - -
361C TRP* 2.9 42.3 + - + +
372C ALA* 1.3 76.6 - - - +
374C ARG* 1.3 65.1 + - - +
375C ILE* 5.7 2.9 - - + -
421C ALA* 6.0 0.9 - - + -
422C GLN 3.4 7.2 - - - +
423C MET* 4.6 4.3 - - + -
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Residues in contact with ARG 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ARG* 5.8 3.0 - - - +
34C LEU* 4.0 27.4 - - + +
37C GLU* 4.4 4.9 + - - -
321C ARG* 4.4 10.1 - - - +
333C LEU* 6.2 1.2 - - - +
358C ALA* 4.6 9.2 - - + -
359C GLN 3.4 6.5 - - - +
360C GLN* 3.2 31.2 + - + +
370C ARG* 3.5 19.8 - - - +
372C ALA* 4.2 5.3 - - - +
373C ILE* 1.3 81.5 - - - +
375C ILE* 1.3 69.4 + - - +
376C PHE* 4.2 7.6 - - + -
421C ALA* 3.1 6.4 - - - +
422C GLN* 2.8 67.7 + - - +
424C GLU* 2.9 42.3 + - - +
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Residues in contact with ILE 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358C ALA* 3.2 2.3 - - - -
359C GLN* 2.8 55.9 + - + +
361C TRP* 3.9 23.6 - - + -
373C ILE* 5.7 3.6 - - + -
374C ARG* 1.3 78.7 - - - +
376C PHE* 1.3 60.2 + - - +
420C GLY 3.3 7.2 - - - +
421C ALA* 4.3 13.0 - - + -
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Residues in contact with PHE 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE 5.0 0.4 - - - -
20C GLN* 3.5 29.4 - - - -
34C LEU* 5.8 0.4 - - + -
35C GLY* 3.5 36.3 - - - +
356C THR* 4.2 6.3 - - + -
357C LEU 3.2 12.3 - - - +
358C ALA* 3.7 12.6 - - + -
374C ARG* 4.7 7.6 - - + -
375C ILE* 1.3 77.8 - - - +
377C ALA* 1.3 65.5 + - - +
378C THR* 3.8 7.9 - - - -
418C THR* 4.3 2.2 - - - -
419C PHE* 3.2 17.5 - - - +
420C GLY* 2.9 62.5 + - - +
421C ALA* 4.0 12.6 - - - -
422C GLN* 4.4 13.7 - - + -
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Residues in contact with ALA 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C ILE 4.0 0.9 - - - +
356C THR* 3.4 2.4 - - - +
357C LEU* 3.0 38.6 + - + +
376C PHE* 1.3 76.5 - - - +
378C THR* 1.3 61.4 + - - +
417C TRP* 5.2 9.0 - - + -
418C THR 3.4 7.9 - - - +
419C PHE* 4.1 5.8 - - + -
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Residues in contact with THR 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PHE* 4.3 13.7 - - + -
35C GLY 2.8 21.3 + - - +
36C ASN* 5.2 0.2 - - + -
354C LYS* 3.7 21.3 - - + -
355C ILE 3.5 3.6 - - - +
356C THR* 2.7 32.0 + - - +
376C PHE* 3.8 2.8 - - - -
377C ALA* 1.3 72.9 - - - +
379C TYR* 1.3 68.2 + - - +
417C TRP* 2.8 9.7 - - - +
418C THR* 2.8 53.0 + - - +
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Residues in contact with TYR 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C TYR* 4.1 16.7 + + - -
354C LYS* 3.2 4.3 - - - +
355C ILE* 2.9 53.3 + - + +
378C THR* 1.3 76.3 - - - +
380C ALA* 1.3 61.2 + - - +
381C LYS* 3.7 23.5 - - + +
415C ASP* 2.8 44.5 + - + +
416C GLU 3.4 13.2 - - - -
417C TRP* 4.2 12.8 - + + -
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Residues in contact with ALA 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PHE* 3.4 43.7 - - + -
352C GLN* 4.5 3.1 - - - +
353C TYR 3.5 6.3 - - - +
354C LYS* 4.1 10.8 - - + -
378C THR 4.3 0.2 - - - -
379C TYR* 1.3 78.2 - - - +
381C LYS* 1.3 59.5 + - - +
382C TRP* 3.5 9.8 - - + -
415C ASP* 3.0 5.1 - - - +
416C GLU 2.9 32.7 + - - +
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Residues in contact with LYS 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351C ASN* 5.3 0.3 - - - +
352C GLN* 3.4 3.3 - - - +
353C TYR* 3.1 63.1 + - + +
379C TYR* 3.7 18.1 - - + +
380C ALA* 1.3 74.3 - - - +
382C TRP* 1.3 91.2 + - - +
383C ASP* 4.3 3.4 - - - +
413C ASP* 3.1 26.5 + - - -
414C SER* 3.2 13.2 + - - +
415C ASP* 3.5 14.6 - - + +
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Residues in contact with TRP 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 3.8 19.5 - + - -
351C ASN* 3.3 13.9 - - - +
352C GLN* 3.9 9.6 - - + -
380C ALA* 3.5 25.4 - - + -
381C LYS* 1.3 99.5 + - - +
383C ASP* 1.3 60.9 + - - +
384C GLU* 4.1 5.4 - - + -
411C ARG* 3.2 74.4 + - + +
412C GLY 3.3 17.0 - - - -
413C ASP* 3.3 0.2 - - - -
414C SER* 2.8 48.8 + - - +
415C ASP* 3.8 16.8 - - - -
416C GLU* 3.9 10.1 - - + -
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Residues in contact with ASP 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349C ARG 4.0 2.9 - - - +
350C ASN* 3.6 2.8 - - - -
351C ASN* 3.0 46.5 + - - +
381C LYS* 4.5 3.8 - - - +
382C TRP* 1.3 75.0 - - - +
384C GLU* 1.3 63.6 + - - +
385C LYS* 3.4 36.8 + - - +
412C GLY 3.6 2.2 - - - -
413C ASP* 3.4 25.7 - - - +
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Residues in contact with GLU 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ALA* 3.6 4.3 - - - +
26C THR* 2.6 44.1 + - - -
350C ASN* 3.0 21.7 - - + +
351C ASN 4.7 1.8 - - - +
382C TRP* 4.1 9.7 - - + +
383C ASP* 1.3 76.4 + - - +
385C LYS* 1.3 61.6 + - - +
386C TRP 3.4 0.9 - - - +
402C THR* 2.8 17.2 + - - +
410C SER* 3.3 12.9 + - - +
411C ARG* 2.7 50.3 + - - +
412C GLY* 2.7 26.0 + - - +
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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