Contacts of the strand formed by residues 467 - 474 (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 SER 467 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410G PHE* 3.7 5.4 - - - -
411G PHE* 2.7 39.2 + - - +
447G PHE* 4.1 1.9 - - - -
453G SER* 5.2 0.7 + - - -
455G SER* 3.4 25.4 - - - -
456G PHE* 4.0 14.9 - - - -
465G ILE 3.7 0.2 + - - -
466G ALA* 1.3 74.8 - - - +
468G GLY* 1.3 58.5 + - - +
250O PRO* 3.0 25.4 + - - +
251O VAL 3.3 14.3 + - - -
252O GLN* 3.8 6.1 + - - +
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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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409G LEU 4.0 4.0 - - - -
410G PHE* 3.4 5.4 - - - -
411G PHE 4.6 0.2 - - - -
447G PHE* 3.9 18.6 - - - -
467G SER* 1.3 78.4 + - - +
469G CYS* 1.3 65.2 + - - -
470G PRO* 3.3 8.8 - - - +
249O ACE 4.9 0.5 - - - +
250O PRO* 3.6 6.5 - - - +
251O VAL* 2.6 33.9 + - - +
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Residues in contact with CYS 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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409G LEU 2.9 35.2 + - - +
410G PHE* 4.1 2.2 - - - -
432G LEU* 4.0 21.1 - - - -
445G ASP* 3.7 33.9 - - - +
447G PHE* 4.4 12.1 - - - -
468G GLY* 1.3 77.3 - - - -
470G PRO* 1.3 66.3 - - - +
471G LEU 3.2 2.0 - - - +
472G PHE* 3.2 27.1 + - + +
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Residues in contact with PRO 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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399G ASP* 3.8 14.1 - - - +
400G GLY* 5.5 0.9 - - - -
401G THR* 3.3 24.9 - - - +
402G GLY* 3.6 11.8 - - - -
406G HIS* 3.7 4.5 - - - +
408G SER* 2.6 28.2 + - - +
410G PHE* 4.1 11.4 - - + -
468G GLY 3.3 11.9 - - - +
469G CYS* 1.3 83.3 - - - +
471G LEU* 1.3 64.1 + - + +
472G PHE 3.4 1.3 + - - -
251O VAL* 3.7 32.3 - - + -
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Residues in contact with LEU 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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401G THR* 3.6 23.1 - - - +
402G GLY* 3.5 20.6 - - - +
406G HIS* 3.4 46.3 + - + +
407G LEU 4.4 0.2 - - - -
445G ASP* 6.1 0.4 - - - -
469G CYS* 3.2 2.1 - - - -
470G PRO* 1.3 80.6 - - + +
472G PHE* 1.3 66.1 + - - +
473G CYS* 3.3 3.1 + - - -
474G PRO* 5.1 1.0 - - - +
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Residues in contact with PHE 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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407G LEU* 3.2 22.2 + - + +
409G LEU* 3.8 30.1 - - + +
432G LEU* 3.3 44.6 - - + -
433G MET* 3.8 9.9 - - - -
434G LEU* 3.9 25.1 - - + -
443G VAL* 3.9 24.7 - - + +
445G ASP* 4.1 19.5 - - + +
469G CYS* 3.2 36.0 + - + +
470G PRO 3.4 1.2 - - - -
471G LEU* 1.3 78.0 - - - +
473G CYS* 1.3 67.9 + - + +
474G PRO* 4.5 1.6 - - - +
492G ILE* 5.0 1.6 - - + -
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Residues in contact with CYS 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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406G HIS* 3.2 5.4 - - - -
407G LEU* 2.6 42.7 + - + +
434G LEU* 3.8 15.7 - - + -
443G VAL* 4.4 8.7 - - + -
471G LEU 3.3 0.4 + - - -
472G PHE* 1.3 94.1 - - + +
474G PRO* 1.3 79.1 - - - +
477G LYS* 4.3 14.4 - - - -
478G MET* 3.6 30.7 - - - -
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Residues in contact with PRO 474 (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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405G THR 3.7 2.2 - - - +
406G HIS* 3.4 26.9 - - + +
443G VAL* 6.2 0.4 - - + -
471G LEU 5.1 0.7 - - - +
472G PHE 4.5 2.0 - - - +
473G CYS* 1.3 95.2 - - - +
475G VAL* 1.3 67.0 + - - +
476G SER* 3.9 15.3 - - - +
477G LYS* 3.1 34.1 + - + +
478G MET* 3.7 2.1 + - - +
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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