Contacts of the helix formed by residues 469 - 480 (chain X) in PDB entry 2DE0
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 469 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363X HIS* 3.4 14.1 - - - -
365X ARG* 3.2 35.5 + - - +
466X THR* 2.8 24.6 + - - -
467X PHE 2.8 4.1 - - - +
468X SER* 1.3 78.5 - - - +
470X GLN* 1.3 61.3 + - - +
472X CYS* 2.9 23.3 + - - +
473X ARG* 3.2 11.7 + - - +
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Residues in contact with GLN 470 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221X GLY* 3.5 3.5 - - - +
222X CYS* 3.4 47.9 + - + +
225X HIS* 2.6 31.8 + - - +
365X ARG* 3.6 19.6 - - - +
468X SER 3.9 1.5 + - - +
469X SER* 1.3 69.3 - - - +
471X VAL* 1.3 63.6 + - - +
473X ARG* 3.4 33.6 + - - +
474X VAL* 3.1 27.5 + - - +
500X GLY* 5.8 4.8 - - - -
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Residues in contact with VAL 471 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220X TYR* 6.2 0.2 - - + -
221X GLY* 5.1 8.7 - - - +
363X HIS* 4.1 23.8 - - + +
365X ARG* 3.1 23.0 - - - +
450X VAL* 5.0 11.9 - - + -
453X ASP* 5.4 4.3 - - + -
454X ILE* 3.5 32.4 - - + +
457X LEU* 4.6 8.1 - - + -
469X SER* 3.0 2.7 + - - +
470X GLN* 1.3 76.3 - - + +
472X CYS* 1.3 65.5 + - - +
474X VAL* 3.0 18.2 + - - +
475X ALA* 3.0 12.3 + - - +
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Residues in contact with CYS 472 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363X HIS* 4.1 6.7 - - + +
457X LEU* 5.1 2.0 - - - -
463X LEU* 3.6 21.1 - - - -
465X CYS* 2.0 54.1 - - + -
466X THR 4.0 4.9 - - - +
467X PHE* 3.8 7.0 - - + -
469X SER* 2.9 16.4 + - - +
471X VAL* 1.3 79.7 - - - +
473X ARG* 1.3 58.0 + - - +
474X VAL 3.2 0.3 + - - -
475X ALA* 3.2 6.4 + - - +
476X TYR* 2.9 27.8 + - - +
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Residues in contact with ARG 473 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225X HIS* 4.0 16.2 + - + -
467X PHE* 2.8 33.5 + - + +
468X SER 3.5 6.5 + - - -
469X SER 3.2 3.4 + - - -
470X GLN* 3.4 65.0 + - - +
472X CYS* 1.3 77.9 - - - +
474X VAL* 1.3 56.7 + - - +
476X TYR* 3.7 5.7 - - - +
477X GLU* 2.9 39.5 + - - +
497X TYR* 4.1 15.7 - - + -
498X TYR* 2.7 71.1 + - - +
499X PHE* 5.2 0.8 - - - +
500X GLY* 4.5 8.1 - - - +
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Residues in contact with VAL 474 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221X GLY* 4.1 19.5 - - - +
224X LEU* 3.9 24.2 - - + -
225X HIS* 3.3 24.5 - - + +
332X VAL* 4.7 5.6 - - + -
336X ILE* 5.1 0.2 - - + -
454X ILE* 3.9 16.6 - - + -
470X GLN 3.1 19.1 + - - +
471X VAL* 3.0 9.3 + - - +
473X ARG* 1.3 73.6 - - - +
475X ALA* 1.3 58.0 + - - +
477X GLU* 3.1 7.9 + - - +
478X ILE* 2.8 58.4 + - + +
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Residues in contact with ALA 475 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454X ILE* 4.1 9.5 - - - +
457X LEU* 3.6 36.3 - - + -
458X SER* 3.2 25.5 - - - +
463X LEU* 4.3 8.1 - - + -
471X VAL 3.0 11.0 + - - +
472X CYS 3.4 9.2 - - - +
474X VAL* 1.3 77.5 - - - +
476X TYR* 1.3 57.0 + - - +
479X MET* 3.0 23.7 + - - +
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Residues in contact with TYR 476 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322X ASP* 4.5 4.0 + - - +
325X VAL* 3.5 33.6 - - + +
463X LEU* 4.0 8.9 - - + +
467X PHE* 3.7 21.3 - + + -
472X CYS 2.9 18.6 + - - +
473X ARG 3.7 3.4 - - - +
475X ALA* 1.3 70.4 - - - +
477X GLU* 1.3 66.8 + - - +
479X MET* 3.3 20.3 - - + +
480X GLN* 3.2 45.7 + - - +
486X ALA 3.8 3.4 - - - -
487X SER* 2.7 29.0 + - - -
490X PHE* 3.4 35.2 - + + -
497X TYR* 3.6 30.9 - + + +
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Residues in contact with GLU 477 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225X HIS* 2.8 37.0 + - - -
325X VAL* 3.8 7.4 - - + -
328X VAL* 3.7 20.4 - - + +
329X SER* 2.9 30.5 - - - -
332X VAL* 3.9 14.0 - - + +
473X ARG* 2.9 26.6 + - - +
474X VAL* 3.5 8.4 - - - +
476X TYR* 1.3 77.4 - - - +
478X ILE* 1.3 61.0 + - - +
480X GLN* 3.3 13.2 - - - +
497X TYR* 2.7 40.7 + - + +
498X TYR 4.9 0.7 - - - +
499X PHE* 4.0 5.0 - - - -
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Residues in contact with ILE 478 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329X SER* 5.2 0.2 - - - -
332X VAL* 3.7 20.2 - - + -
336X ILE* 4.4 25.4 - - + -
454X ILE* 3.6 31.6 - - + -
455X HIS* 5.8 0.9 - - - -
458X SER* 3.5 24.9 - - - +
459X GLN* 5.8 0.9 - - - +
474X VAL* 2.8 26.1 + - + +
477X GLU* 1.3 71.7 - - - +
479X MET* 1.3 56.6 + - - +
481X THR* 2.7 47.7 + - - +
482X LEU* 3.6 11.5 + - + +
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Residues in contact with MET 479 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457X LEU 5.3 2.0 - - - +
458X SER* 3.5 23.3 - - - +
460X ALA 4.3 13.7 - - - +
461X ASP 5.2 0.2 - - - +
462X PHE* 5.3 0.4 - - - -
463X LEU* 4.7 13.5 - - + -
475X ALA 3.0 15.4 + - - +
476X TYR* 3.3 23.3 - - + +
478X ILE* 1.3 76.1 - - - +
480X GLN* 1.3 74.5 + - - +
481X THR 2.7 12.1 + - - -
482X LEU* 2.7 21.1 + - - +
483X HIS* 3.7 17.8 + - + +
486X ALA* 3.3 21.9 - - + +
489X ASN* 3.5 31.6 - - + +
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Residues in contact with GLN 480 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320X HIS* 2.9 33.4 + - - +
325X VAL* 4.3 19.3 - - + +
326X TRP* 4.0 18.7 + - - -
329X SER* 3.7 12.8 - - - +
476X TYR* 3.2 33.3 + - - +
477X GLU* 3.3 15.7 - - - +
478X ILE 3.1 0.2 + - - -
479X MET* 1.3 88.7 - - - +
481X THR* 1.3 58.5 + - - +
482X LEU 3.3 1.1 - - - -
483X HIS 3.6 14.1 - - - +
486X ALA* 2.9 38.6 + - - +
487X SER* 3.3 3.5 + - - -
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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
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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