Contacts of the helix formed by residues 461 - 473 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459B ASN 4.4 4.3 + - - -
460B ALA* 1.3 75.7 + - - +
462B VAL* 1.3 66.5 + - - +
463B GLU* 3.1 8.3 - - - -
464B LYS* 2.8 50.8 + - - +
465B SER* 2.9 17.4 + - - -
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Residues in contact with VAL 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B THR* 3.8 27.6 - - + -
431B ASP* 5.7 3.1 - - - +
434B MET* 3.9 35.2 - - + -
438B PHE* 4.8 5.2 - - + -
460B ALA* 3.6 7.9 + - + +
461B SER* 1.3 72.9 - - - +
463B GLU* 1.3 78.3 + - - +
465B SER* 3.4 7.2 + - - -
466B GLN* 3.1 22.7 + - - +
503B TYR* 4.7 5.4 - - + -
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Residues in contact with GLU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B SER* 2.9 6.6 + - - -
462B VAL* 1.3 89.8 + - - +
464B LYS* 1.3 62.5 + - + +
466B GLN* 3.1 5.0 + - - +
467B VAL* 3.1 24.8 + - - +
503B TYR* 3.6 22.7 - - + +
506B THR* 3.5 44.1 - - + +
507B ILE* 3.5 22.0 - - + -
508B PRO* 3.9 15.7 - - + +
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Residues in contact with LYS 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B SER* 2.8 34.7 + - - +
463B GLU* 1.3 73.2 - - + +
465B SER* 1.3 57.6 + - - +
467B VAL* 3.1 3.6 + - - +
468B GLY* 2.8 27.4 + - - -
507B ILE* 3.7 43.3 - - + -
508B PRO* 5.3 6.5 - - + -
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Residues in contact with SER 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B MET* 5.2 1.0 - - - +
454B MET* 3.5 45.1 - - - +
460B ALA* 5.9 0.3 - - - +
461B SER* 2.9 20.1 + - - -
462B VAL* 3.6 12.1 - - - -
464B LYS* 1.3 77.1 - - - +
466B GLN* 1.3 55.0 + - - +
468B GLY* 3.3 2.0 + - - -
469B PHE* 2.7 36.0 + - - +
3002B ZAR 4.2 2.3 - - - +
391E SER 6.1 0.9 - - - -
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Residues in contact with GLN 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B TYR* 2.7 31.4 + - - +
430B THR* 3.4 33.6 - - + +
433B ILE* 4.6 3.4 - - - +
434B MET* 4.8 5.3 - - - -
462B VAL 3.1 19.2 + - - +
463B GLU 3.1 6.7 + - - +
465B SER* 1.3 72.3 - - - +
467B VAL* 1.3 61.5 + - - +
469B PHE* 3.2 7.9 + - - +
470B ILE* 2.9 37.1 + - + +
503B TYR* 3.9 23.1 - - + -
3002B ZAR 3.1 45.1 + - - +
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Residues in contact with VAL 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B GLU 3.1 14.7 + - - +
464B LYS* 3.1 7.6 + - - +
466B GLN* 1.3 75.1 - - - +
468B GLY* 1.3 58.0 + - - +
470B ILE* 3.4 6.0 + - - +
471B ASP* 2.9 38.1 + - - +
500B ARG* 3.3 45.3 - - + +
503B TYR* 4.0 5.4 - - + -
504B GLN* 3.8 37.9 - - - +
507B ILE* 3.9 9.6 - - + -
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Residues in contact with GLY 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B LYS 2.8 14.3 + - - -
465B SER* 3.7 2.9 - - - -
467B VAL* 1.3 74.9 - - - +
469B PHE* 1.3 58.9 + - - +
471B ASP* 4.3 2.9 - - - -
472B TYR* 2.8 59.4 + - - +
391E SER 5.7 3.6 - - - -
392E SER 6.1 0.4 - - - -
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Residues in contact with PHE 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B MET* 5.4 3.1 - - + -
416B LEU* 3.6 30.5 - - + -
419B PRO* 4.1 14.1 - - + -
465B SER 2.7 21.9 + - - +
466B GLN* 3.5 11.7 - - - +
468B GLY* 1.3 72.4 - - - +
470B ILE* 1.3 58.7 + - - +
472B TYR* 5.4 0.2 - - - -
473B ILE* 3.0 50.0 + - + +
474B VAL* 3.1 31.0 + - + -
3002B ZAR 3.5 71.8 - + - -
391E SER 5.9 0.2 + - - -
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Residues in contact with ILE 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B PRO* 4.0 21.5 - - + -
426B TYR* 3.4 26.9 - - + +
466B GLN* 2.9 21.6 + - + +
467B VAL* 3.7 4.5 - - - +
469B PHE* 1.3 78.0 - - + +
471B ASP* 1.3 63.7 + - - +
474B VAL* 3.9 5.4 - - - -
475B HIS* 2.7 42.6 + - + +
476B PRO* 3.4 0.9 - - - +
496B LEU* 3.9 23.1 - - + -
497B GLU* 6.1 0.2 - - - -
500B ARG* 3.9 44.9 - - + +
503B TYR* 5.6 1.3 - - + -
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Residues in contact with ASP 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467B VAL* 2.9 27.1 + - - +
468B GLY* 3.7 6.1 - - - +
470B ILE* 1.3 77.7 - - - +
472B TYR* 1.3 73.9 + - + +
475B HIS* 4.8 4.3 - - - +
476B PRO* 3.2 19.6 - - - +
500B ARG* 2.7 46.1 + - - -
486E HIS* 3.7 23.1 + - + +
487E PRO* 5.2 3.1 - - - +
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Residues in contact with TYR 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B HIS* 4.6 2.6 + - - -
374B MET* 4.7 8.5 - - + +
468B GLY* 2.8 42.7 + - - +
471B ASP* 1.3 88.1 + - + +
473B ILE* 1.3 76.0 + - + +
476B PRO* 3.6 12.7 - - - +
387E LYS* 4.5 20.2 - - + -
389E VAL* 4.7 26.9 - - + -
390E THR 5.4 0.4 - - - -
391E SER 5.0 6.5 - - - -
392E SER 5.0 2.5 - - - -
393E GLY* 4.2 28.9 + - - -
486E HIS* 3.0 31.4 + - + -
487E PRO* 4.3 6.2 - - - +
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Residues in contact with ILE 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B MET* 3.8 25.8 - - + -
373B HIS* 3.7 36.1 + - + +
374B MET* 4.5 9.6 - - + -
416B LEU* 3.8 15.3 - - + -
469B PHE* 3.0 33.2 + - + +
472B TYR* 1.3 97.9 - - + +
474B VAL* 1.3 67.9 + - - +
475B HIS 3.5 0.9 - - - -
476B PRO* 3.3 3.9 - - - +
477B LEU* 3.2 24.7 + - - +
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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