Contacts of the helix formed by residues 423 - 440 (chain M) in PDB entry 6NR8
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 423 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422M GLY* 1.3 76.3 - - - +
424M ALA* 1.3 60.8 + - - +
426M GLU* 2.6 18.2 + - - -
427M ILE* 3.4 21.0 + - - +
459M PRO* 3.7 21.8 - - - +
477M VAL* 3.8 11.4 - - - +
490M GLY* 4.3 4.5 - - - -
491M ILE* 4.2 7.0 - - - -
501M MET* 4.1 3.6 - - - -
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Residues in contact with ALA 424 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420M TYR 3.3 16.5 + - - +
423M GLY* 1.3 76.2 - - - +
425M ALA* 1.3 63.6 + - - +
426M GLU* 3.2 1.5 + - - -
427M ILE* 3.3 8.6 - - - +
428M SER* 3.2 22.0 + - - -
477M VAL* 4.6 0.4 - - - -
487M PRO* 3.3 32.3 - - + +
490M GLY* 3.7 12.8 - - - +
501M MET* 3.7 21.3 - - + +
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Residues in contact with ALA 425 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148M LEU* 5.6 2.2 - - + -
151M ILE* 4.5 17.7 - - + -
419M VAL* 3.9 27.4 - - + -
420M TYR 3.5 8.1 + - - +
424M ALA* 1.3 76.9 - - - +
426M GLU* 1.3 66.1 + - - +
428M SER* 3.7 8.3 - - - -
429M CYS* 3.2 29.2 + - - +
487M PRO* 5.0 1.1 - - - +
513M LYS* 4.1 14.4 - - + +
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Residues in contact with GLU 426 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421M GLY 4.0 0.2 - - - -
422M GLY* 3.2 14.9 + - - -
423M GLY* 2.6 31.5 + - - -
424M ALA 3.2 2.1 + - - -
425M ALA* 1.3 76.7 + - - +
427M ILE* 1.3 61.2 + - - +
429M CYS* 5.6 0.2 - - - -
430M ALA* 3.3 22.3 + - - +
455M LEU* 3.7 21.5 - - + +
456M GLU* 4.3 0.4 - - - +
458M ILE* 3.9 35.5 - - + +
459M PRO* 3.9 22.7 - - + -
462M LEU* 5.4 0.2 - - - +
513M LYS* 3.1 28.5 + - + -
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Residues in contact with ILE 427 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423M GLY 3.4 15.6 + - - +
424M ALA 3.3 15.0 - - - +
426M GLU* 1.3 77.4 - - - +
428M SER* 1.3 63.4 + - - +
430M ALA* 3.8 1.0 - - - +
431M LEU* 3.1 7.1 + - - +
456M GLU* 3.3 34.1 - - - +
459M PRO* 5.1 4.7 - - + +
474M MET* 3.6 24.2 - - - +
477M VAL* 3.7 26.9 - - + -
478M ARG* 3.1 54.0 + - + +
481M GLN* 3.9 16.8 - - + +
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Residues in contact with SER 428 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147M HIS* 3.0 33.4 + - - -
151M ILE* 3.9 7.1 - - - +
424M ALA 3.2 18.2 + - - -
425M ALA* 3.7 8.7 - - - -
426M GLU 3.2 0.4 - - - -
427M ILE* 1.3 76.8 - - - +
429M CYS* 1.3 63.8 + - - +
431M LEU* 3.3 9.3 + - - +
432M ALA 3.2 11.8 + - - -
481M GLN* 3.7 13.7 + - - +
486M ASN 4.4 3.1 + - - -
487M PRO* 3.6 24.2 - - - +
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Residues in contact with CYS 429 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M ALA* 3.9 15.5 - - + -
147M HIS* 3.3 34.8 - - + +
148M LEU* 3.7 26.0 - - - -
151M ILE* 3.7 9.0 - - - -
425M ALA 3.2 13.6 + - - +
428M SER* 1.3 77.1 - - - +
430M ALA* 1.3 57.0 + - - +
431M LEU 3.2 0.2 - - - -
432M ALA* 4.0 0.9 - - - -
433M VAL* 2.7 37.3 + - + +
455M LEU* 3.8 16.4 - - + -
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Residues in contact with ALA 430 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D ARG* 4.6 2.9 + - - -
426M GLU 3.3 19.7 + - - +
427M ILE 3.8 2.2 - - - +
428M SER 3.2 0.6 - - - -
429M CYS* 1.3 74.5 - - - +
431M LEU* 1.3 53.7 + - - +
434M SER* 2.7 33.4 + - - -
452M ALA* 3.5 27.5 - - - +
455M LEU* 3.6 12.9 - - + +
456M GLU* 3.3 23.1 - - + +
478M ARG* 4.6 2.6 + - - -
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Residues in contact with LEU 431 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D ARG* 5.4 0.2 - - - -
442D THR* 6.3 2.9 - - + -
147M HIS* 6.0 1.3 - - + -
427M ILE 3.1 7.0 + - - +
428M SER* 3.3 11.4 - - - +
429M CYS 3.2 0.2 - - - -
430M ALA* 1.3 77.4 - - - +
432M ALA* 1.3 61.3 + - + +
434M SER* 2.7 17.3 + - - -
435M GLN* 2.9 28.3 + - + +
478M ARG* 3.3 38.7 - - - +
481M GLN* 3.9 30.1 - - + +
482M VAL* 6.3 1.1 - - + -
485M MET* 5.7 12.3 - - + -
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Residues in contact with ALA 432 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M VAL 5.2 3.4 - - - +
147M HIS* 3.4 41.1 - - + +
428M SER 3.2 1.0 + - - -
429M CYS* 2.9 6.1 + - - +
431M LEU* 1.3 81.4 - - + +
433M VAL* 1.3 57.3 + - + +
435M GLN* 3.0 7.8 + - - +
436M GLU* 2.6 43.1 + - + +
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Residues in contact with VAL 433 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140M ALA* 3.9 7.4 - - + +
143M VAL* 3.8 18.8 - - + -
144M ALA* 4.1 12.1 - - + +
429M CYS* 2.7 25.4 + - + +
432M ALA* 1.3 71.7 - - + +
434M SER* 1.3 56.4 + - - +
436M GLU* 3.1 7.8 + - - +
437M ALA* 2.8 28.1 + - - +
448M MET* 3.4 35.4 - - + +
451M PHE* 3.6 38.1 - - + -
452M ALA* 4.4 5.4 - - + -
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Residues in contact with SER 434 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D ARG* 3.3 43.9 + - - -
430M ALA 2.7 25.5 + - - -
431M LEU* 2.7 16.1 + - - -
433M VAL* 1.3 77.2 - - - +
435M GLN* 1.3 59.7 + - - +
437M ALA* 3.5 15.9 + - - +
438M ASP* 3.3 17.4 - - - +
448M MET 5.0 1.3 - - - -
449M ARG* 5.7 1.6 - - - +
452M ALA* 3.9 12.6 - - - +
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Residues in contact with GLN 435 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438D GLU* 4.4 12.6 + - - +
431M LEU* 2.9 29.3 + - + +
432M ALA* 3.0 8.7 + - - +
434M SER* 1.3 77.0 + - - +
436M GLU* 1.3 52.1 + - - +
438M ASP* 2.8 20.0 + - - +
439M LYS* 2.6 69.6 + - + +
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Residues in contact with GLU 436 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M VAL* 3.8 34.0 - - + +
146M GLU* 5.3 5.7 - - - +
432M ALA* 2.6 25.9 + - + +
433M VAL* 3.1 8.3 + - - +
435M GLN* 1.3 71.6 - - + +
437M ALA* 1.3 60.6 + - - +
438M ASP 3.1 0.2 - - - -
439M LYS* 4.0 17.5 - - - +
440M CYS* 2.9 54.3 + - - +
448M MET* 3.4 13.7 - - + +
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Residues in contact with ALA 437 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433M VAL 2.8 12.0 + - - +
434M SER* 3.6 13.7 - - - +
435M GLN 3.2 0.4 - - - -
436M GLU* 1.3 76.9 - - - +
438M ASP* 1.3 64.5 + - - +
440M CYS 3.1 13.1 - - - +
441M PRO* 3.3 9.9 - - - +
445M GLN* 3.6 41.9 - - + +
448M MET* 3.5 15.0 - - + -
449M ARG* 4.7 6.7 - - + +
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Residues in contact with ASP 438 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434D LEU* 3.3 21.6 - - + +
437D THR* 5.0 1.9 + - - -
438D GLU* 3.0 35.3 - - - +
441D ARG* 5.2 3.1 + - - -
481D ARG* 3.5 13.4 + - - -
485D ALA* 3.6 17.3 - - + +
486D GLN* 4.0 2.9 - - - +
434M SER 3.3 15.5 - - - +
435M GLN* 2.8 19.5 + - - +
437M ALA* 1.3 84.8 - - - +
439M LYS* 1.3 65.3 + - - +
440M CYS 4.4 0.2 - - - -
441M PRO* 3.6 13.7 - - - +
445M GLN* 4.9 0.3 - - - +
449M ARG* 5.2 0.9 + - - -
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Residues in contact with LYS 439 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486D GLN* 4.0 13.0 + - - +
435M GLN* 2.6 53.6 + - + +
436M GLU* 4.0 21.5 - - - +
438M ASP* 1.3 71.7 - - - +
440M CYS* 1.3 61.1 + - - +
441M PRO* 3.3 13.2 - - - +
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Residues in contact with CYS 440 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436M GLU* 2.9 41.9 + - - +
437M ALA* 3.1 9.0 - - - +
439M LYS* 1.3 74.6 - - - +
441M PRO* 1.3 66.6 - - - +
442M THR* 3.3 9.9 + - + +
444M GLU* 4.1 21.1 - - - +
448M MET* 4.6 5.5 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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