Contacts of the helix formed by residues 373 - 384 (chain M) in PDB entry 6D6Q
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 ASN 373 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321M PHE* 3.1 38.5 - - - -
323M ALA* 3.9 19.8 - - - +
324M GLY* 4.0 4.4 - - - +
372M SER* 1.3 77.9 - - - +
374M VAL* 1.3 64.9 + - - +
375M PHE 3.0 1.5 - - - +
376M LYS* 2.8 26.2 + - - +
377M ILE* 2.9 11.1 + - - +
538M MET* 4.2 15.8 - - + +
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Residues in contact with VAL 374 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372M SER 5.9 0.2 - - - +
373M ASN* 1.3 79.5 - - - +
375M PHE* 1.3 60.6 + - - +
377M ILE* 3.2 11.3 + - + +
378M VAL* 2.9 41.0 + - + +
391M ILE* 5.6 0.4 - - + -
402M TYR* 4.2 46.0 - - + -
405M GLN* 4.4 10.3 - - - +
406M MET* 4.8 7.9 - - + -
480M PHE* 5.5 5.2 - - + -
497M LEU* 4.6 15.5 - - + -
499M THR* 5.2 1.1 - - + +
538M MET* 4.5 23.9 - - + +
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Residues in contact with PHE 375 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372M SER* 4.3 21.3 - - - -
373M ASN 4.0 0.6 - - - +
374M VAL* 1.3 82.8 - - + +
376M LYS* 1.3 67.2 + - + +
378M VAL* 3.2 3.5 + - - +
379M LYS* 2.9 41.0 + - + +
405M GLN* 4.9 6.5 - - + +
406M MET* 3.8 29.6 - - + -
408M LYS* 3.7 42.4 - - + -
409M LEU* 3.6 34.8 - - + +
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Residues in contact with LYS 376 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321M PHE* 5.1 2.2 - - + -
324M GLY* 5.4 6.5 - - - -
326M ASP* 2.9 34.9 + - - +
372M SER 4.1 13.2 + - - +
373M ASN* 2.8 24.4 + - - +
375M PHE* 1.3 81.4 - - + +
377M ILE* 1.3 59.4 + - + +
379M LYS* 3.3 11.3 + - + +
380M MET* 2.9 49.4 + - + +
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Residues in contact with ILE 377 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321M PHE* 3.4 52.5 - - + -
328M LEU* 5.3 2.9 - - + -
373M ASN* 2.9 23.5 + - - +
374M VAL* 3.2 15.0 + - + +
376M LYS* 1.3 77.4 - - + +
378M VAL* 1.3 57.5 + - - +
380M MET* 3.2 20.0 - - + +
381M ILE* 2.9 39.7 + - + +
497M LEU* 4.8 5.6 - - + -
536M ILE* 3.7 29.4 - - + -
538M MET* 4.9 10.1 - - + -
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Residues in contact with VAL 378 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374M VAL* 2.9 27.7 + - + +
375M PHE 3.8 1.6 - - - +
377M ILE* 1.3 72.0 - - - +
379M LYS* 1.3 61.7 + - - +
381M ILE* 3.2 11.0 + - + +
382M MET* 2.9 32.6 + - + +
389M VAL* 5.3 5.2 - - + -
391M ILE* 5.4 0.2 - - + -
406M MET* 3.4 37.7 - - + -
409M LEU* 5.4 0.9 - - + -
411M PHE* 4.7 18.4 - - + -
478M ALA* 4.8 16.2 - - + -
480M PHE* 5.4 3.6 - - + -
497M LEU* 4.5 15.7 - - + -
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Residues in contact with LYS 379 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375M PHE* 2.9 32.6 + - + +
376M LYS* 3.4 13.2 - - + +
378M VAL* 1.3 76.8 - - - +
380M MET* 1.3 62.8 + - - +
382M MET* 3.3 4.1 + - - +
383M GLU* 3.0 45.0 + - + +
409M LEU* 5.3 13.6 - - + +
411M PHE* 5.9 0.9 - - - -
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Residues in contact with MET 380 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321M PHE* 4.2 10.1 - - + -
326M ASP* 3.8 38.8 - - + +
327M GLY* 5.9 0.7 - - - -
328M LEU* 5.2 15.5 - - + -
376M LYS* 2.9 36.8 + - + +
377M ILE* 3.2 26.0 - - + +
379M LYS* 1.3 76.9 - - - +
381M ILE* 1.3 64.2 + - + +
383M GLU* 3.2 5.8 + - - +
384M ARG* 2.9 44.3 + - + +
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Residues in contact with ILE 381 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328M LEU* 6.5 0.9 - - + -
377M ILE* 2.9 33.8 + - + +
378M VAL* 3.2 15.5 + - + +
380M MET* 1.3 73.1 - - + +
382M MET* 1.3 64.2 + - + +
384M ARG* 3.2 3.9 + - - +
385M ASN 3.1 3.5 + - - -
386M PHE* 3.0 62.7 + - + -
387M GLN* 4.5 2.9 - - + +
389M VAL* 4.2 19.1 - - + -
495M THR* 4.2 14.4 - - + +
497M LEU* 3.7 30.3 - - + -
536M ILE* 4.2 10.3 - - + -
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Residues in contact with MET 382 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378M VAL* 2.9 20.1 + - + +
379M LYS* 4.0 3.4 - - - +
381M ILE* 1.3 79.1 - - + +
383M GLU* 1.3 63.7 + - + +
385M ASN* 2.8 21.4 + - - +
387M GLN* 3.1 52.5 - - + +
389M VAL* 6.3 2.5 - - + -
411M PHE* 3.5 48.9 - - + -
477M LYS* 4.4 8.7 - - + -
478M ALA* 6.4 1.3 - - + -
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Residues in contact with GLU 383 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379M LYS* 3.0 37.6 + - + +
380M MET* 3.7 5.6 - - - +
382M MET* 1.3 77.1 - - + +
384M ARG* 1.3 73.1 + - - +
385M ASN* 3.5 1.7 + - - +
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Residues in contact with ARG 384 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328M LEU* 6.4 0.6 - - - +
380M MET* 2.9 36.8 + - + +
381M ILE 3.4 9.4 - - - +
382M MET 3.1 0.2 - - - -
383M GLU* 1.3 87.9 + - - +
385M ASN* 1.3 66.4 + - - +
386M PHE* 3.4 44.6 + - + -
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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