Contacts of the helix formed by residues 461 - 473 (chain G) in PDB entry 1MKD
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 SER 461 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459G ASN 4.1 4.4 + - - -
460G ALA* 1.3 74.9 + - - +
462G VAL* 1.3 66.9 + - - +
463G GLU* 3.1 8.1 - - - -
464G LYS* 2.8 50.5 + - - +
465G SER* 2.9 17.2 + - - -
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Residues in contact with VAL 462 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430G THR* 3.8 26.7 - - + -
431G ASP* 5.7 3.1 - - - +
434G MET* 3.9 34.1 - - + -
438G PHE* 4.8 5.6 - - + -
460G ALA* 3.6 8.4 - - + +
461G SER* 1.3 72.7 - - - +
463G GLU* 1.3 77.5 + - - +
465G SER* 3.4 8.0 + - - -
466G GLN* 3.1 23.2 + - - +
503G TYR* 4.7 6.1 - - + +
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Residues in contact with GLU 463 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461G SER* 2.9 7.4 + - - -
462G VAL* 1.3 84.2 + - - +
464G LYS* 1.3 65.5 + - - +
466G GLN* 3.2 4.9 + - - +
467G VAL* 3.1 25.5 + - - +
503G TYR* 3.6 22.1 - - + +
506G THR* 3.5 45.0 - - + +
507G ILE* 3.5 22.4 - - + -
508G PRO* 3.9 15.1 - - + +
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Residues in contact with LYS 464 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461G SER* 2.8 35.3 + - - +
463G GLU* 1.3 73.2 - - + +
465G SER* 1.3 58.1 + - - +
467G VAL* 3.2 4.1 + - - +
468G GLY* 2.8 26.7 + - - -
507G ILE* 3.8 44.6 - - + -
508G PRO* 5.3 6.5 + - + -
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Residues in contact with SER 465 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434G MET* 5.2 1.3 - - - +
454G MET* 3.5 45.3 - - - +
460G ALA* 5.9 0.2 - - - +
461G SER* 2.9 19.5 + - - -
462G VAL* 3.6 12.3 - - - -
464G LYS* 1.3 77.5 - - - +
466G GLN* 1.3 54.4 + - - +
468G GLY* 3.3 1.2 + - - -
469G PHE* 2.7 36.3 + - - +
3007G ZAR 4.1 2.7 - - - +
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Residues in contact with GLN 466 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426G TYR* 2.7 32.3 + - - +
430G THR* 3.4 32.4 - - + +
433G ILE* 4.6 3.2 - - - +
434G MET* 4.8 5.1 - - - -
462G VAL 3.1 15.9 + - - +
463G GLU 3.2 7.4 + - - +
465G SER* 1.3 73.0 - - - +
467G VAL* 1.3 62.0 + - - +
469G PHE* 3.2 7.7 + - - +
470G ILE* 2.9 37.5 + - + +
503G TYR* 3.9 22.9 - - + -
3007G ZAR 3.0 45.5 + - - +
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Residues in contact with VAL 467 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463G GLU 3.1 15.3 + - - +
464G LYS* 3.6 6.7 - - - +
466G GLN* 1.3 75.1 - - - +
468G GLY* 1.3 57.8 + - - +
470G ILE* 3.5 6.0 + - - +
471G ASP* 2.9 39.5 + - - +
500G ARG* 3.3 45.1 - - + +
503G TYR* 4.1 5.4 - - + -
504G GLN* 3.8 32.5 - - - +
507G ILE* 3.8 14.8 - - + -
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Residues in contact with GLY 468 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D SER 5.1 3.8 - - - -
392D SER 5.1 4.5 - - - -
464G LYS 2.8 15.9 + - - -
465G SER* 3.7 1.8 - - - -
467G VAL* 1.3 74.7 - - - +
469G PHE* 1.3 64.8 + - - +
471G ASP* 3.1 3.1 + - - -
472G TYR* 2.8 54.5 + - - +
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Residues in contact with PHE 469 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D SER 5.3 1.9 + - - -
370G MET* 5.5 3.4 - - + -
416G LEU* 3.7 26.7 - - + -
419G PRO* 4.1 15.5 - - + -
465G SER 2.7 21.9 + - - +
466G GLN* 3.5 13.5 - - - +
468G GLY* 1.3 70.8 - - - +
470G ILE* 1.3 58.7 + - - +
472G TYR* 5.2 0.2 - - - -
473G ILE* 3.0 49.3 + - + +
474G VAL* 3.1 34.7 + - + -
3007G ZAR 3.6 65.7 - + - -
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Residues in contact with ILE 470 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419G PRO* 4.0 21.3 - - + -
426G TYR* 3.4 27.8 - - + +
466G GLN* 2.9 21.0 + - + +
467G VAL* 3.7 4.3 - - - +
469G PHE* 1.3 78.0 - - + +
471G ASP* 1.3 60.8 + - - +
474G VAL* 3.9 6.7 - - + -
475G HIS* 2.7 45.4 + - + +
476G PRO* 3.4 1.0 - - - +
496G LEU* 3.9 22.0 - - + +
497G GLU* 6.1 0.2 - - - -
499G ASN 4.8 0.2 - - - +
500G ARG* 3.9 46.2 - - + +
503G TYR* 5.5 1.1 - - + -
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Residues in contact with ASP 471 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486D HIS* 4.0 25.2 + - - +
487D PRO* 4.1 11.1 - - + +
467G VAL* 2.9 27.5 + - - +
468G GLY* 3.1 5.7 + - - +
470G ILE* 1.3 78.9 - - - +
472G TYR* 1.3 74.2 + - + +
475G HIS* 4.7 4.8 - - - +
476G PRO* 3.2 19.7 - - - +
500G ARG* 2.7 45.6 + - - -
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Residues in contact with TYR 472 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D ALA* 5.9 0.3 - - - +
387D LYS* 5.2 8.7 - - - -
389D VAL* 4.1 26.0 - - + -
390D THR 4.7 1.1 - - - +
391D SER 4.0 9.9 - - - -
392D SER 3.7 5.7 + - - -
393D GLY* 3.2 43.3 + - - -
486D HIS* 3.8 25.1 + - + -
487D PRO* 4.9 4.0 - - - +
373G HIS* 4.5 3.3 + - - -
374G MET* 4.6 8.1 - - + +
468G GLY* 2.8 44.4 + - - +
471G ASP* 1.3 87.4 + - + +
473G ILE* 1.3 75.7 + - + +
476G PRO* 3.6 12.1 - - - +
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Residues in contact with ILE 473 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370G MET* 3.8 25.8 - - + -
373G HIS* 3.7 34.7 + - + +
374G MET* 4.6 9.2 - - + -
416G LEU* 3.9 15.0 - - + -
469G PHE* 3.0 34.2 + - + +
471G ASP 3.7 0.2 - - - -
472G TYR* 1.3 98.4 - - + +
474G VAL* 1.3 66.7 + - - +
476G PRO* 3.3 4.9 - - - +
477G LEU* 3.1 24.4 + - - +
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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