Contacts of the helix formed by residues 460 - 472 (chain B) in PDB entry 3DYQ
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 VAL 460 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365B MET* 3.8 21.3 - - + -
368B HIS* 3.4 35.7 + - + +
372B MET* 5.9 0.2 - - - +
403B ILE* 4.0 13.0 - - + -
455B GLY 4.9 0.2 - - - +
456B PHE* 3.0 35.1 + - + +
459B PHE* 1.3 85.0 - - + +
461B LEU* 1.3 64.8 + - - +
462B ILE 3.7 0.4 - - - -
463B PRO* 3.7 2.0 - - - +
464B MET* 3.3 24.1 + - - +
900B IBM 5.4 4.7 - - + -
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Residues in contact with LEU 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ILE* 3.3 52.0 - - + +
406B GLU* 4.1 15.3 - - + +
456B PHE* 3.0 37.2 + - + +
457B ILE* 3.6 15.0 - - + +
460B VAL* 1.3 73.6 - - - +
462B ILE* 1.3 70.4 + - - +
464B MET* 3.1 3.6 + - + +
465B PHE* 3.0 42.8 + - + -
483B LEU* 3.9 28.7 - - + -
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Residues in contact with ILE 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ILE* 2.8 40.7 + - + +
458B LYS* 4.0 12.3 - - + +
461B LEU* 1.3 73.5 - - - +
463B PRO* 1.3 61.8 - - + +
465B PHE* 3.0 2.1 + - - +
466B GLU* 2.7 63.4 + - + +
480B LEU* 3.9 12.0 - - + +
483B LEU* 4.2 16.8 - - + +
484B TRP* 3.8 28.0 - - + +
487B ARG* 4.0 18.2 - - - +
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Residues in contact with PRO 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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372B MET* 4.4 7.2 - - + -
376B LYS* 6.4 1.3 - - - -
458B LYS 3.2 25.1 - - - +
459B PHE* 3.5 18.8 - - + +
460B VAL 3.7 9.2 - - - +
461B LEU 3.5 3.1 - - - -
462B ILE* 1.3 93.1 - - + +
464B MET* 1.3 61.3 + - - +
466B GLU* 3.2 17.3 + - - +
467B THR* 3.1 30.5 + - + +
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Residues in contact with MET 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B HIS* 4.0 17.3 - - + -
372B MET* 3.8 25.8 - - + +
396B ILE* 4.5 7.4 - - + +
399B LYS* 4.0 15.9 - - - +
400B CYS* 3.8 37.9 - - - +
403B ILE* 3.2 40.6 - - + -
460B VAL 3.3 15.0 + - - +
461B LEU* 3.1 10.6 + - + +
463B PRO* 1.3 79.8 - - - +
465B PHE* 1.3 67.1 + - + +
467B THR* 3.2 20.1 + - - -
468B VAL* 3.2 10.3 + - - +
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Residues in contact with PHE 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B MET* 4.4 2.7 - - + -
400B CYS* 3.6 42.6 - - + -
404B SER* 4.7 6.3 - - - -
407B VAL* 4.1 14.8 - - + -
461B LEU* 3.0 45.0 + - + +
462B ILE 3.0 4.0 + - - +
464B MET* 1.3 83.1 - - + +
466B GLU* 1.3 59.9 + - - +
468B VAL* 3.3 9.0 + - + +
469B THR* 2.9 33.6 + - - -
475B VAL* 4.1 19.7 - - + +
479B MET* 3.7 28.0 - - + -
480B LEU* 3.9 18.8 - - + -
483B LEU* 3.6 17.7 - - + -
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Residues in contact with GLU 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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462B ILE* 2.7 42.6 + - + +
463B PRO* 3.4 18.0 - - - +
464B MET 3.2 0.2 - - - -
465B PHE* 1.3 73.9 - - - +
467B THR* 1.3 62.8 + - + +
469B THR* 3.4 14.4 + - - +
470B LYS* 3.5 13.7 - - - +
480B LEU* 4.1 21.0 - - + +
484B TRP* 5.3 4.2 + - - -
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Residues in contact with THR 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B MET* 4.0 18.6 - - + +
375B PHE* 3.5 30.4 - - - -
376B LYS* 4.5 20.4 - - + -
379B MET* 4.7 10.2 - - - +
396B ILE* 5.2 0.2 - - - +
463B PRO* 3.1 16.2 - - + +
464B MET 3.2 8.2 + - - -
465B PHE 3.2 0.2 - - - -
466B GLU* 1.3 76.7 - - + +
468B VAL* 1.3 69.1 + - - +
469B THR 3.1 0.2 - - - -
470B LYS* 3.1 27.0 + - - +
471B LEU* 4.0 1.6 + - - +
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Residues in contact with VAL 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B MET* 5.7 2.0 - - + -
271B CYS* 5.6 0.4 - - - -
375B PHE* 4.8 7.2 - - + -
393B LEU* 5.3 3.1 - - + -
396B ILE* 3.5 30.5 - - + -
397B LEU* 4.7 14.6 - - + -
400B CYS* 4.0 15.0 - - - -
464B MET 3.2 14.7 + - - +
465B PHE* 3.3 11.4 + - + +
467B THR* 1.3 80.4 + - - +
469B THR* 1.3 56.8 + - - +
471B LEU* 3.1 6.6 + - - +
472B PHE* 3.0 45.7 + - + +
475B VAL* 4.5 14.4 - - + -
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Residues in contact with THR 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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465B PHE 2.9 16.4 + - - -
466B GLU* 3.5 12.8 - - - +
467B THR 3.1 0.4 - - - -
468B VAL* 1.3 73.9 - - - +
470B LYS* 1.3 66.9 + - + +
471B LEU 3.2 0.5 + - - -
472B PHE 3.5 8.1 - - - -
473B PRO* 3.2 35.8 - - + +
475B VAL* 3.5 16.8 - - - +
476B GLU* 3.6 28.8 + - + +
480B LEU* 3.7 11.0 - - + +
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Residues in contact with LYS 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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379B MET* 4.2 26.0 + - + +
466B GLU 3.5 11.7 - - - +
467B THR* 3.1 21.0 + - - +
469B THR* 1.3 81.3 - - + +
471B LEU* 1.3 60.3 + - - +
473B PRO* 5.0 2.8 - - - +
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Residues in contact with LEU 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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375B PHE* 4.0 7.0 - - + -
379B MET* 3.7 26.5 - - + -
382B PHE* 3.9 29.4 - - + -
384B TYR* 3.5 31.1 + - + +
393B LEU* 3.7 36.3 - - + -
467B THR 5.0 0.9 - - - +
468B VAL* 3.1 9.6 + - - +
470B LYS* 1.3 78.7 - - - +
472B PHE* 1.3 73.4 + - + +
473B PRO* 3.7 7.4 - - - +
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Residues in contact with PHE 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B CYS* 3.5 51.6 - - + -
273B LEU* 3.6 22.2 - - + -
276B LYS* 4.8 9.2 - - + -
277B PHE* 5.2 0.2 - + - -
384B TYR* 3.6 23.6 - + - -
393B LEU* 4.3 20.6 - - + -
397B LEU* 5.2 4.9 - - + -
468B VAL* 3.0 27.8 + - + +
469B THR* 3.3 7.3 - - - -
471B LEU* 1.3 95.3 - - + +
473B PRO* 1.3 62.8 - - - +
474B MET* 3.2 10.5 - - - -
475B VAL* 2.9 28.1 + - + +
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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