Contacts of the strand formed by residues 489 - 496 (chain G) in PDB entry 1D00
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 ALA 489 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357G LYS* 4.3 15.3 - - + -
358G ILE 3.3 15.5 - - - +
359G SER* 4.0 15.3 - - - +
361G PHE* 4.3 2.0 - - - -
437G GLN* 3.3 7.4 + - - +
485G VAL* 3.4 5.6 - - - +
486G ARG 3.0 30.6 + - - +
487G ASP* 3.9 5.4 - - + +
488G ASP* 1.3 79.7 - - - +
490G ILE* 1.3 66.4 + - - +
491G PHE* 5.5 2.2 - - + -
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Residues in contact with ILE 490 (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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356G TRP 3.6 0.3 - - - +
357G LYS* 3.4 5.2 - - - +
358G ILE* 2.9 59.0 + - + +
361G PHE* 4.0 27.1 - - + -
394G ILE* 4.8 2.0 - - + -
407G LEU* 4.7 7.9 - - + -
434G LEU* 4.1 20.4 - - + -
437G GLN* 4.3 2.0 - - - +
478G MET* 3.7 8.7 - - + -
484G TYR 3.4 21.8 - - - +
485G VAL* 3.6 21.5 - - + -
489G ALA* 1.3 79.5 - - - +
491G PHE* 1.3 66.7 + - - +
492G ILE* 4.1 10.1 - - + -
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Residues in contact with PHE 491 (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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417F PRO 4.0 8.1 - - - -
418F ASN* 3.7 22.2 - - - -
420F ALA* 4.7 7.9 - - + -
421F LEU* 3.9 30.3 - - + -
355G ILE* 3.9 12.3 - - + -
356G TRP 3.4 1.6 - - - -
357G LYS* 3.7 45.1 - - + -
434G LEU* 3.9 2.5 - - - +
435G LEU* 3.2 47.6 + - + +
437G GLN* 3.7 33.4 - - + -
484G TYR 4.6 2.4 + - - -
489G ALA* 5.7 1.8 - - + -
490G ILE* 1.3 78.8 - - - +
492G ILE* 1.3 65.5 + - - +
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Residues in contact with ILE 492 (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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354G PHE* 3.9 0.5 - - - +
355G ILE* 3.3 3.8 - - - +
356G TRP* 2.5 54.6 + - + +
358G ILE* 4.2 24.0 - - + -
392G LEU* 3.9 23.3 - - + -
394G ILE* 4.5 10.5 - - + -
407G LEU* 5.5 1.6 - - + -
409G LEU* 3.7 27.6 - - + -
433G MET 3.4 11.2 - - - +
434G LEU* 3.6 31.6 - - + -
472G PHE* 5.0 2.0 - - + -
490G ILE* 4.1 8.3 - - + -
491G PHE* 1.3 73.9 - - - +
493G LYS* 1.3 64.9 + - - +
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Residues in contact with LYS 493 (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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353G VAL* 3.9 20.2 - - - +
354G PHE 3.2 10.5 - - - +
355G ILE* 3.9 23.6 - - + +
392G LEU* 5.2 0.2 - - - -
431G THR 3.8 0.3 - - - +
432G LEU* 3.5 2.4 - - - -
433G MET* 2.8 51.5 + - + +
435G LEU* 4.1 29.6 - - + +
491G PHE 4.2 0.2 - - - -
492G ILE* 1.3 78.9 - - - +
494G ALA* 1.3 67.0 + - - +
495G ILE* 3.8 23.3 - - + +
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Residues in contact with ALA 494 (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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352G GLY 3.7 1.3 - - - +
353G VAL* 3.5 2.1 - - - +
354G PHE* 2.8 34.6 + - + +
381G PHE* 4.2 15.7 - - + -
392G LEU* 3.9 23.7 - - + +
411G PHE* 5.9 0.2 - - + -
430G VAL* 5.6 1.8 - - + -
431G THR 3.2 8.3 - - - +
432G LEU* 3.9 15.7 - - + -
493G LYS* 1.3 74.7 - - - +
495G ILE* 1.3 68.4 + - - +
496G VAL* 4.2 2.2 - - + -
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Residues in contact with ILE 495 (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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352G GLY 3.6 2.7 - - - -
353G VAL* 4.5 18.4 - - + +
429G LYS 3.9 0.2 - - - +
430G VAL* 3.7 1.4 - - - -
431G THR* 2.9 55.0 + - + +
433G MET* 4.7 13.0 - - - -
493G LYS* 3.8 33.0 - - + +
494G ALA* 1.3 78.8 - - - +
496G VAL* 1.3 68.9 + - - +
497G ASP* 3.8 3.7 + - - +
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Residues in contact with VAL 496 (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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351G ASP 4.9 0.5 - - - +
352G GLY* 2.9 22.1 + - - +
353G VAL* 5.9 0.2 - - - +
381G PHE* 3.8 19.1 - - + -
383G THR* 4.0 15.5 - - + -
390G MET* 3.8 20.4 - - - -
411G PHE* 3.8 14.8 - - + -
426G PHE* 3.9 25.6 - - + -
428G GLN* 3.9 4.9 - - + -
429G LYS 3.6 6.1 - - - +
430G VAL* 4.7 6.3 - - + -
494G ALA* 5.4 0.9 - - + -
495G ILE* 1.3 79.9 - - - +
497G ASP* 1.3 75.4 + - - +
498G LEU* 3.5 14.0 + - - +
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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