Contacts of the helix formed by residues 378 - 392 (chain M) in PDB entry 6G0L
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 378 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377M ARG* 1.3 80.1 - - - +
379M PHE* 1.3 74.7 + - - +
380M GLN 3.2 1.6 - - - -
381M LEU* 3.4 6.7 + - - +
382M THR* 2.7 37.2 + - - +
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Residues in contact with PHE 379 (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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377M ARG* 4.0 18.4 - - + -
378M ASP* 1.3 92.2 + - - +
380M GLN* 1.3 94.4 + - + +
382M THR* 3.7 6.7 - - - -
383M GLY 2.9 11.1 + - - -
405M LEU* 3.7 37.7 - - + -
410M GLN* 4.6 0.2 - - - -
597M ARG* 2.4 54.0 + - - +
601M ASP* 5.8 1.3 - - + -
602M VAL* 3.7 29.2 - - + -
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Residues in contact with GLN 380 (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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376M LEU* 3.7 30.1 - - + -
377M ARG* 3.0 60.1 - - - +
378M ASP 3.2 0.2 - - - -
379M PHE* 1.3 99.1 - - - +
381M LEU* 1.3 60.8 + - - +
383M GLY* 3.1 2.8 + - - -
384M ILE* 2.9 33.9 + - - +
405M LEU 4.0 10.4 + - - +
406M GLY* 5.1 2.2 - - - +
409M VAL* 6.3 1.6 - - + -
410M GLN* 3.3 27.0 - - + +
1501M ADP 4.5 6.6 + - - +
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Residues in contact with LEU 381 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365M SER 3.5 25.1 - - - +
366M VAL* 3.5 23.6 - - - +
367M GLN* 3.9 22.7 - - + +
368M PRO* 4.7 6.5 - - + -
371M ILE* 6.0 0.2 - - + -
376M LEU* 4.2 22.9 - - + +
377M ARG 4.0 18.2 - - - +
378M ASP* 3.4 7.8 + - - +
380M GLN* 1.3 75.9 - - - +
382M THR* 1.3 57.8 + - - +
384M ILE* 3.4 15.3 + - + +
385M ASN* 2.9 40.7 + - - +
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Residues in contact with THR 382 (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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378M ASP* 2.7 24.5 + - - +
379M PHE* 3.6 10.8 - - - -
381M LEU* 1.3 78.3 - - - +
383M GLY* 1.3 56.5 + - - +
385M ASN* 3.3 10.1 + - + +
386M TRP* 2.9 27.9 + - + +
597M ARG* 4.3 9.4 - - - +
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Residues in contact with GLY 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 PHE 2.9 16.1 + - - -
380M GLN 3.6 2.9 - - - -
382M THR* 1.3 73.0 - - - +
384M ILE* 1.3 60.8 + - - +
386M TRP* 3.1 7.6 + - - +
387M MET* 2.9 38.6 + - - +
399M LEU* 6.2 0.2 - - - -
410M GLN* 4.6 7.4 - - - -
595M LEU* 4.8 7.0 - - - -
597M ARG* 3.6 15.0 - - - +
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Residues in contact with ILE 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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368M PRO* 6.0 3.8 - - + -
376M LEU* 4.5 9.4 - - + -
380M GLN 2.9 19.9 + - - +
381M LEU* 3.8 25.4 - - + +
383M GLY* 1.3 76.1 - - - +
385M ASN* 1.3 61.2 + - - +
387M MET* 3.4 6.6 + - - +
388M ALA* 2.9 32.4 + - + +
410M GLN* 4.3 22.4 - - + +
413M ALA* 3.7 30.3 - - + +
414M PHE* 4.2 19.0 - - + -
417M TRP* 5.3 12.8 - - + -
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Residues in contact with ASN 385 (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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361M PHE* 4.1 7.0 - - - -
363M LYS* 4.8 11.4 - - + +
364M LEU* 2.6 51.6 + - - +
365M SER* 4.5 3.6 - - - +
366M VAL 5.8 0.4 + - - -
381M LEU* 2.9 28.2 + - - +
382M THR* 3.3 9.4 + - + +
384M ILE* 1.3 81.1 - - - +
386M TRP* 1.3 49.9 + - - +
388M ALA* 3.9 3.9 - - - +
389M PHE* 2.6 37.8 + - - +
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Residues in contact with TRP 386 (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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382M THR* 2.9 15.0 + - + +
383M GLY* 3.1 9.8 + - - +
385M ASN* 1.3 77.0 - - - +
387M MET* 1.3 80.5 + - + +
389M PHE* 3.5 11.2 - + - +
390M LEU* 2.9 45.0 + - + +
397M GLY* 3.6 30.3 - - - -
398M ILE 4.0 12.1 - - - -
399M LEU* 5.3 0.9 - - - -
538M MET* 4.5 8.7 - - + -
592M PRO 4.4 9.9 + - - -
593M PHE 4.3 1.6 - - - -
594M ILE 4.1 20.0 + - - -
595M LEU* 3.5 50.3 - - + +
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Residues in contact with MET 387 (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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383M GLY 2.9 22.3 + - - +
384M ILE* 4.0 1.3 - - - +
386M TRP* 1.3 95.3 - - + +
388M ALA* 1.3 57.9 + - - +
390M LEU* 3.9 1.9 - - - +
391M TRP* 2.9 29.8 + - - +
399M LEU* 3.9 25.6 - - + -
410M GLN* 4.7 10.8 - - - +
411M THR* 5.2 9.0 - - + +
414M PHE* 3.5 49.0 - - + -
509M PHE* 4.8 2.0 - - + -
538M MET* 3.7 44.1 - - + +
595M LEU* 5.5 0.2 - - + -
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Residues in contact with ALA 388 (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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361M PHE* 3.3 24.3 - - + -
384M ILE* 2.9 19.4 + - + +
385M ASN* 4.7 1.3 - - - +
387M MET* 1.3 75.0 - - - +
389M PHE* 1.3 62.9 + - - +
391M TRP* 3.8 8.6 - - + +
392M SER* 3.2 26.0 + - - -
414M PHE* 3.3 11.8 - - + -
417M TRP* 3.7 25.1 - - + -
418M LEU* 6.4 0.2 - - + -
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Residues in contact with PHE 389 (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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361M PHE* 3.6 25.0 - + + -
363M LYS* 3.8 26.9 - - + -
385M ASN 2.6 25.1 + - - +
386M TRP* 3.2 15.9 + + - +
388M ALA* 1.3 80.1 - - - +
390M LEU* 1.3 64.5 + - + +
392M SER* 3.9 8.1 + - - -
393M LYS* 3.2 51.8 + - + +
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Residues in contact with LEU 390 (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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386M TRP* 2.9 36.1 + - + +
387M MET* 4.3 2.7 - - - +
389M PHE* 1.3 81.2 - - + +
391M TRP* 1.3 64.1 + - - +
392M SER 3.2 0.7 - - - -
393M LYS* 3.3 21.4 + - + +
395M ASP* 3.4 42.1 + - + +
396M ASN* 3.6 32.3 - - - +
397M GLY* 3.6 11.0 - - - +
538M MET* 6.0 0.9 - - + -
592M PRO 5.0 5.8 - - - +
593M PHE* 4.5 16.4 - - + -
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Residues in contact with TRP 391 (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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354M TYR* 5.3 7.2 - + + -
358M ARG* 2.4 47.5 + - - -
359M PRO* 5.2 7.6 - - + -
361M PHE* 6.0 0.2 - + - -
387M MET 2.9 19.6 + - - +
388M ALA* 4.0 11.2 - - + +
389M PHE 3.4 0.4 - - - -
390M LEU* 1.3 80.0 - - - +
392M SER* 1.3 66.3 + - - +
393M LYS 3.3 0.5 + - - -
394M GLY* 3.4 3.6 + - - -
395M ASP 4.3 6.3 - - - -
414M PHE* 4.2 12.1 - + + -
417M TRP* 6.1 1.1 - + - -
418M LEU* 3.6 39.4 - - + +
422M ARG* 3.8 33.4 - - + -
424M GLN* 4.3 20.6 - - + -
509M PHE* 5.4 4.4 - + - -
536M ASN* 3.0 37.8 + - + +
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Residues in contact with SER 392 (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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358M ARG* 3.3 31.9 - - - +
359M PRO* 5.0 8.4 - - - +
361M PHE* 3.3 33.6 - - - +
388M ALA 3.2 15.7 + - - -
389M PHE 4.2 5.8 - - - -
390M LEU 3.2 0.8 - - - -
391M TRP* 1.3 92.0 - - - +
393M LYS* 1.3 60.0 + - - +
394M GLY 3.4 0.4 - - - -
422M ARG* 5.1 1.4 + - - -
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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