Contacts of the helix formed by residues 392 - 407 (chain M) in PDB entry 6FF7
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 GLY 392 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390M ALA 4.2 0.4 - - - -
391M THR* 1.3 70.7 - - - +
393M LYS* 1.3 58.2 + - - +
394M PRO 3.6 1.7 - - - -
395M HIS* 3.9 3.0 - - - +
396M THR* 2.9 33.1 + - - -
431M ASP* 3.6 29.5 - - - +
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Residues in contact with LYS 393 (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 HIS* 4.0 31.0 - - + +
359M GLU* 4.7 4.9 - - - +
390M ALA* 4.6 8.7 - - + -
391M THR 3.2 6.9 + - - +
392M GLY* 1.3 76.8 - - - +
394M PRO* 1.3 58.8 - - - +
396M THR* 4.1 2.9 - - - -
397M LEU* 2.9 34.3 + - - +
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Residues in contact with PRO 394 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358M HIS* 4.8 9.6 - - + -
390M ALA* 5.3 5.2 - - + -
392M GLY 3.6 0.8 - - - -
393M LYS* 1.3 77.2 - - - +
395M HIS* 1.3 57.6 + - - +
397M LEU* 4.6 4.0 - - + -
398M TRP* 2.8 30.3 + - - +
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Residues in contact with HIS 395 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392M GLY* 3.5 3.9 + - - +
393M LYS 3.2 0.6 - - - -
394M PRO* 1.3 77.0 - - - +
396M THR* 1.3 60.8 + - - +
398M TRP* 3.3 5.8 + - - +
399M VAL* 2.9 27.9 + - - +
421M ALA* 6.0 2.2 - - - -
431M ASP* 3.5 44.6 - - + +
434M SER* 6.1 0.4 - - - -
435M VAL* 4.2 16.6 - - + +
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Residues in contact with THR 396 (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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392M GLY 2.9 17.9 + - - -
393M LYS* 4.1 2.9 - - - -
395M HIS* 1.3 76.3 - - - +
397M LEU* 1.3 59.7 + - - +
399M VAL* 3.2 7.6 + - - +
400M ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 397 (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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362M LYS* 5.5 11.4 - - + -
393M LYS 2.9 18.8 + - - +
394M PRO* 4.4 4.3 - - + +
396M THR* 1.3 77.6 - - - +
398M TRP* 1.3 57.5 + - - +
400M ALA* 3.8 8.1 - - - +
401M PHE* 2.9 26.9 + - - +
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Residues in contact with TRP 398 (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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394M PRO 2.8 22.7 + - - +
395M HIS* 3.6 7.6 - - - +
396M THR 3.2 0.2 - - - -
397M LEU* 1.3 76.1 - - - +
399M VAL* 1.3 59.3 + - - +
401M PHE* 3.4 8.4 + - - +
402M ALA* 2.9 24.8 + - - +
417M ILE* 5.4 6.1 - - + +
421M ALA* 4.5 21.3 - - + -
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Residues in contact with VAL 399 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395M HIS 2.9 16.7 + - - +
396M THR* 3.2 6.9 + - - +
398M TRP* 1.3 74.9 - - - +
400M ALA* 1.3 59.6 + - - +
402M ALA* 3.0 10.8 + - - +
403M LYS* 2.9 25.1 + - - +
435M VAL* 5.4 6.9 - - + +
438M GLN* 4.3 24.0 - - + -
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Residues in contact with ALA 400 (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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396M THR 2.9 15.4 + - - +
397M LEU* 3.9 9.4 - - - +
399M VAL* 1.3 78.5 - - - +
401M PHE* 1.3 55.9 + - - +
403M LYS* 3.1 10.3 + - - +
404M PHE* 2.9 26.2 + - - +
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Residues in contact with PHE 401 (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 VAL* 4.0 30.1 - - + +
397M LEU 2.9 19.1 + - - +
398M TRP* 3.6 9.4 - - - +
399M VAL 3.2 0.2 - - - -
400M ALA* 1.3 75.7 - - - +
402M ALA* 1.3 57.1 + - - +
404M PHE* 3.5 10.3 + - - +
405M TYR* 2.9 24.9 + - - +
417M ILE* 6.2 1.8 - - + -
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Residues in contact with ALA 402 (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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398M TRP 2.9 14.1 + - - +
399M VAL* 3.0 15.4 + - - +
401M PHE* 1.3 75.7 - - - +
403M LYS* 1.3 58.7 + - - +
405M TYR* 3.4 11.3 + - + +
406M GLU* 2.9 23.0 + - - +
414M ALA* 5.1 11.3 - - + +
417M ILE* 5.3 11.4 - - + -
418M LEU 6.3 0.2 - - - +
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Residues in contact with LYS 403 (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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399M VAL 2.9 10.9 + - - +
400M ALA* 3.1 12.5 + - - +
402M ALA* 1.3 73.7 - - - +
404M PHE* 1.3 60.5 + - - +
405M TYR 3.1 1.1 - - - -
406M GLU* 2.8 24.1 + - + +
407M ASP* 2.9 14.2 + - - +
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Residues in contact with PHE 404 (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 TYR* 5.3 17.5 - - + +
381M ALA* 6.5 0.7 - - + -
382M VAL* 6.2 2.2 - - + -
400M ALA 2.9 13.5 + - - +
401M PHE* 3.7 12.3 - - - +
403M LYS* 1.3 75.5 - - - +
405M TYR* 1.3 58.1 + - - +
407M ASP* 3.4 9.1 + - - +
408M ASN* 3.0 24.8 + - - +
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Residues in contact with TYR 405 (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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401M PHE 2.9 15.8 + - - +
402M ALA* 3.4 14.6 - - - +
403M LYS 3.1 0.4 - - - -
404M PHE* 1.3 73.5 - - - +
406M GLU* 1.3 59.5 + - - +
408M ASN* 3.1 19.6 + - + +
410M GLN 3.0 25.1 + - - +
412M ASP 4.1 13.0 - - - +
413M ASP* 4.8 6.5 - - + +
414M ALA* 4.5 14.8 - - + +
417M ILE* 6.0 1.8 - - + -
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Residues in contact with GLU 406 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402M ALA 2.9 12.4 + - - +
403M LYS* 2.8 17.1 + - - +
405M TYR* 1.3 77.3 - - - +
407M ASP* 1.3 54.4 + - - +
408M ASN 3.2 0.4 - - - -
409M GLY* 3.8 1.4 + - - -
410M GLN* 3.2 30.2 + - + +
414M ALA* 6.2 0.4 - - - -
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Residues in contact with ASP 407 (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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371M PRO 6.1 1.6 - - - +
403M LYS 2.9 11.1 + - - +
404M PHE* 3.4 11.0 + - - +
406M GLU* 1.3 73.9 - - - +
408M ASN* 1.3 56.5 + - - +
409M GLY 3.3 5.1 + - - -
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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