Contacts of the helix formed by residues 375 - 389 (chain A) in PDB entry 5M7R
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 SER 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A LEU 4.3 1.2 + - - -
374A TYR* 1.3 75.6 - - - +
376A PRO* 1.4 68.5 - - - +
377A GLN* 2.9 17.8 + - - +
378A MET* 3.2 34.0 + - - +
379A ALA* 3.0 22.0 + - - +
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Residues in contact with PRO 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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295A PRO* 3.4 29.6 - - + +
296A TYR 4.2 6.5 - - - +
297A LYS* 4.3 26.0 - - + +
298A GLY 5.7 0.4 - - - +
371A ASP* 5.6 1.6 - - + +
374A TYR* 3.7 35.2 - - + +
375A SER* 1.4 81.3 - - - +
377A GLN* 1.3 71.4 + - + +
379A ALA* 3.4 0.7 + - - +
380A LEU* 3.0 24.9 + - - +
566A TYR* 5.6 1.1 - - - +
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Residues in contact with GLN 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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295A PRO* 5.4 0.7 - - - -
297A LYS* 5.8 3.6 - - - +
375A SER* 2.9 18.0 + - - +
376A PRO* 1.3 90.4 - - + +
378A MET* 1.3 62.9 + - + +
380A LEU* 3.2 18.6 + - - +
381A LYS* 3.2 28.4 + - - +
566A TYR* 5.5 6.7 - - - +
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Residues in contact with MET 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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375A SER* 3.2 26.4 + - - +
377A GLN* 1.3 79.0 - - + +
379A ALA* 1.3 57.6 + - - +
381A LYS* 3.4 9.7 + - - +
382A LEU* 3.1 42.8 + - + +
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Residues in contact with ALA 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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326A HIS* 4.4 1.7 - - - -
327A THR* 3.5 21.0 - - + +
330A THR* 4.4 13.5 - - + -
374A TYR* 3.7 29.8 - - + +
375A SER 3.0 16.6 + - - +
376A PRO 3.7 4.0 - - - +
378A MET* 1.3 74.2 - - - +
380A LEU* 1.3 66.0 + - - +
382A LEU* 3.4 11.1 + - - +
383A ALA* 3.1 18.0 + - - +
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Residues in contact with LEU 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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293A LEU 3.8 22.9 - - - +
294A GLY* 4.5 0.4 - - - -
295A PRO* 4.1 11.7 - - + -
323A VAL* 3.9 11.0 - - + -
327A THR* 4.1 6.4 - - - +
376A PRO 3.0 14.4 + - - +
377A GLN* 3.4 12.1 - - - +
379A ALA* 1.3 75.4 - - - +
381A LYS* 1.3 68.0 + - - +
383A ALA* 3.3 1.8 + - - +
384A LEU* 2.9 60.9 + - + +
559A GLN* 5.8 1.3 - - + +
562A ALA* 4.6 3.8 - - + -
563A ASP* 4.5 9.9 - - - +
566A TYR* 4.0 26.9 - - + +
573A PRO* 6.3 0.2 - - + -
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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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377A GLN* 3.2 28.5 + - - +
378A MET* 3.4 11.2 + - - +
379A ALA 3.3 0.2 - - - -
380A LEU* 1.3 88.5 - - - +
382A LEU* 1.3 62.6 + - + +
384A LEU* 4.1 4.6 - - - +
385A THR* 2.8 46.3 + - + +
555A LEU* 5.6 4.7 - - + -
559A GLN* 3.9 30.6 - - + +
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Residues in contact with LEU 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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326A HIS* 3.9 14.2 + - + +
330A THR* 4.4 22.9 - - + +
378A MET* 3.1 30.4 + - + +
379A ALA* 3.7 9.9 - - - +
380A LEU 3.3 0.2 - - - -
381A LYS* 1.3 77.1 - - + +
383A ALA* 1.3 60.8 + - - +
385A THR* 3.1 18.4 + - - +
386A GLU* 3.2 15.1 + - - +
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Residues in contact with ALA 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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322A TYR* 4.0 3.9 - - + -
323A VAL* 4.3 15.9 - - + -
326A HIS* 3.3 39.9 - - + -
327A THR* 4.1 10.5 - - + -
379A ALA 3.1 12.0 + - - +
380A LEU 3.8 2.7 - - - +
382A LEU* 1.3 77.7 - - - +
384A LEU* 1.3 56.7 + - - +
386A GLU* 3.4 1.6 + - - +
387A TRP* 2.7 36.4 + - - +
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Residues in contact with LEU 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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323A VAL* 3.7 23.1 - - + -
380A LEU* 2.9 47.6 + - + +
381A LYS* 4.1 3.6 - - - +
383A ALA* 1.3 71.7 - - - +
385A THR* 1.3 66.2 + - - +
387A TRP* 3.7 20.4 - - + +
388A LEU* 2.9 26.5 + - - +
555A LEU* 4.1 13.9 - - + -
558A LEU* 4.1 22.3 - - + +
559A GLN* 3.9 35.2 - - + -
562A ALA* 4.5 7.2 - - + -
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Residues in contact with THR 385 (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* 2.8 31.4 + - + +
382A LEU* 3.1 16.3 + - - +
384A LEU* 1.3 77.2 - - - +
386A GLU* 1.3 56.1 + - - +
388A LEU* 3.7 5.8 - - + +
389A GLN* 2.8 32.7 + - - -
555A LEU* 3.4 37.0 - - + -
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Residues in contact with GLU 386 (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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87A LYS* 3.6 17.3 - - - +
88A TRP* 3.0 24.1 + - - -
322A TYR* 2.8 28.3 + - + +
326A HIS* 3.5 19.1 + - + -
382A LEU 3.2 16.8 + - - +
383A ALA 3.9 2.9 - - - +
384A LEU 3.2 0.6 - - - -
385A THR* 1.3 74.8 + - - +
387A TRP* 1.3 66.1 + - - +
388A LEU 3.2 0.6 + - - -
389A GLN* 3.4 21.9 + - + +
390A GLU* 4.3 4.2 + - - +
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Residues in contact with TRP 387 (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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293A LEU* 4.2 23.1 - - + -
319A GLU* 3.5 23.5 + - - -
320A ALA* 4.6 1.1 - - - -
322A TYR* 3.3 47.3 - + + +
323A VAL* 4.3 9.6 - - + -
383A ALA 2.7 22.5 + - - +
384A LEU* 3.7 28.9 - - + +
386A GLU* 1.3 73.0 - - - +
388A LEU* 1.3 64.1 + - - +
390A GLU* 2.9 20.8 + - + +
391A PHE* 3.4 35.4 - + - -
558A LEU* 4.4 11.0 - - + -
561A LEU* 5.0 2.7 - - + -
562A ALA* 6.3 0.2 - - + -
636A ILE* 4.0 13.6 - - + +
640A MET* 3.9 32.3 - - + -
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Residues in contact with LEU 388 (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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384A LEU 2.9 15.9 + - - +
385A THR* 3.7 10.1 - - + +
387A TRP* 1.3 75.4 - - - +
389A GLN* 1.3 68.8 + - - +
391A PHE* 2.9 29.5 + - + +
392A GLY 4.2 2.1 + - - -
553A VAL* 3.5 36.6 - - + +
554A THR* 3.8 14.6 - - - +
555A LEU* 3.6 29.6 - - + +
558A LEU* 3.8 14.1 - - + +
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Residues in contact with GLN 389 (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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385A THR* 2.8 25.7 + - - +
386A GLU* 3.7 17.5 - - + +
387A TRP 3.0 0.8 + - - -
388A LEU* 1.3 90.5 - - - +
390A GLU* 1.3 68.3 + - - +
391A PHE 3.3 0.4 + - - -
392A GLY* 4.1 3.5 + - - -
393A VAL* 3.6 19.8 - - - +
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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