Contacts of the helix formed by residues 436 - 448 (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 THR 436 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432M VAL* 3.2 11.3 - - - +
433M PRO* 3.2 25.8 + - + +
435M SER* 1.3 76.0 - - - +
437M MET* 1.3 59.2 + - - +
438M PRO 3.5 1.3 - - - -
439M ALA* 3.2 3.4 + - + +
440M TRP* 2.9 46.8 + - + +
513M ASP* 4.9 8.1 + - - +
751M ARG* 3.6 4.3 - - - +
776M LEU 4.8 2.2 - - - +
777M GLY* 3.6 13.5 - - - -
778M ILE* 3.3 34.8 - - + +
1501M ADP 5.7 2.5 - - - +
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Residues in contact with MET 437 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432M VAL 3.6 21.1 - - - +
433M PRO 3.0 11.2 + - - +
434M LEU* 3.7 8.5 - - - +
435M SER 3.4 0.2 - - - -
436M THR* 1.3 76.3 - - - +
438M PRO* 1.3 63.9 - - + +
440M TRP* 3.3 3.3 + - - +
441M LEU* 2.9 34.4 + - + +
455M CYS* 3.6 26.0 - - + -
456M TYR 4.3 2.7 - - - +
457M MET* 3.5 32.8 - - + +
489M LEU* 3.4 45.3 - - + +
491M THR* 3.7 18.8 - - - +
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Residues in contact with PRO 438 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313M ARG* 4.1 18.8 - - - +
434M LEU 3.5 11.4 - - - +
437M MET* 1.3 95.0 - - + +
439M ALA* 1.3 55.3 + - - +
441M LEU* 3.5 12.8 - - + +
442M ASP* 2.9 40.6 + - - +
457M MET* 5.8 6.3 - - + -
747M SER* 5.6 5.2 - - - -
751M ARG* 3.4 41.3 - - + +
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Residues in contact with ALA 439 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436M THR* 3.2 7.1 + - + +
438M PRO* 1.3 76.2 - - - +
440M TRP* 1.3 61.6 + - + +
442M ASP* 3.4 6.9 + - - +
443M THR* 2.9 35.9 + - - +
751M ARG* 3.1 29.8 - - - +
778M ILE* 4.2 14.8 - - + -
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Residues in contact with TRP 440 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407M LYS 5.3 0.2 - - - -
408M THR* 3.2 50.5 + - + -
411M THR* 4.6 21.3 - - + -
412M VAL* 5.0 8.5 - - + -
430M ILE* 4.3 20.0 - - + -
432M VAL* 3.9 21.4 - - + +
436M THR* 2.9 46.3 + - + +
437M MET 3.8 0.2 - - - +
439M ALA* 1.3 79.4 - - + +
441M LEU* 1.3 59.1 + - - +
443M THR* 4.3 5.3 - - - -
444M PHE* 2.8 36.3 + + + +
489M LEU* 3.7 19.1 - - + -
511M ALA* 6.2 0.9 - - + -
512M VAL 5.9 0.9 - - - -
513M ASP* 3.7 34.8 + - + -
540M ILE* 6.2 4.9 - - + -
1501M ADP 4.9 4.2 + - - -
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Residues in contact with LEU 441 (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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288M GLU* 5.5 7.0 - - - +
437M MET* 2.9 22.5 + - + +
438M PRO* 3.5 15.5 - - + +
439M ALA 3.2 0.2 - - - -
440M TRP* 1.3 75.5 - - - +
442M ASP* 1.3 63.0 + - - +
444M PHE* 3.7 2.4 - - + +
445M GLU* 2.9 33.6 + - - +
453M CYS* 3.4 46.3 - - + +
455M CYS* 3.9 23.1 - - + -
457M MET* 5.6 3.8 - - + -
489M LEU* 3.8 20.2 - - + -
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Residues in contact with ASP 442 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313M ARG* 5.8 2.4 + - - -
438M PRO* 2.9 26.8 + - - +
439M ALA* 3.9 5.5 - - - +
441M LEU* 1.3 78.3 - - - +
443M THR* 1.3 58.5 + - - +
445M GLU* 3.3 15.9 - - - +
446M LYS* 2.9 32.7 + - - +
751M ARG* 5.6 1.6 + - - -
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Residues in contact with THR 443 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408M THR* 4.7 15.9 - - + -
409M VAL* 4.5 15.7 - - + -
412M VAL* 5.5 4.0 - - + -
439M ALA* 2.9 20.1 + - - +
440M TRP* 4.3 4.7 - - - -
442M ASP* 1.3 76.3 - - - +
444M PHE* 1.3 57.9 + - - +
446M LYS* 4.3 7.1 - - - +
447M TRP* 2.9 61.3 + - + +
1501M ADP 5.5 9.7 + - - +
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Residues in contact with PHE 444 (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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412M VAL* 3.6 43.7 - - + +
415M ILE* 5.6 9.0 - - + -
440M TRP* 2.8 27.1 + + - +
441M LEU* 3.7 6.1 - - + +
443M THR* 1.3 77.8 - - - +
445M GLU* 1.3 57.4 + - - +
448M ALA* 2.9 40.1 + - + +
451M LEU* 3.8 30.5 - - + -
452M ASN 3.7 18.8 - - - -
453M CYS* 3.9 19.3 - - + -
487M VAL* 4.0 32.3 - - + -
489M LEU* 6.3 3.6 - - + -
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Residues in contact with GLU 445 (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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441M LEU 2.9 21.6 + - - +
442M ASP* 3.3 22.6 - - - +
444M PHE* 1.3 76.8 - - - +
446M LYS* 1.3 69.6 + - - +
447M TRP 3.4 0.2 - - - -
448M ALA 4.1 5.8 - - - -
449M PRO* 3.4 28.3 - - + +
451M LEU 5.7 1.1 - - - +
453M CYS* 4.8 11.4 - - - -
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Residues in contact with LYS 446 (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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372M LYS* 4.3 4.9 - - - +
373M GLY* 3.7 25.4 + - - -
442M ASP 2.9 20.2 + - - +
443M THR* 3.3 8.0 + - - +
445M GLU* 1.3 88.1 - - - +
447M TRP* 1.3 93.6 + - - +
449M PRO* 4.7 1.8 - - - +
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Residues in contact with TRP 447 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370M PHE 3.3 21.5 - - - +
371M ILE* 4.0 18.8 - - + +
372M LYS 3.7 8.7 + - - -
373M GLY* 4.2 4.7 - - - +
374M GLY* 3.3 45.5 - - - -
376M LEU* 3.6 15.0 - - + -
409M VAL* 3.9 24.8 - - + +
412M VAL* 4.9 11.4 - - + -
443M THR* 2.9 45.4 + - + +
444M PHE 4.6 0.2 - - - +
446M LYS* 1.3 107.4 - - - +
448M ALA* 1.3 60.9 + - + +
449M PRO* 3.7 5.2 - - - +
1501M ADP 3.7 43.6 - + - -
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Residues in contact with ALA 448 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370M PHE 5.0 2.2 - - - +
412M VAL* 4.1 19.7 - - + -
416M SER* 5.0 9.0 - - - +
444M PHE* 2.9 27.4 + - + +
445M GLU* 4.1 0.5 - - - -
447M TRP* 1.3 79.5 - - - +
449M PRO* 1.3 66.4 - - - +
450M ASP* 3.3 3.4 + - - +
451M LEU* 3.6 34.0 + - + +
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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