Contacts of the strand formed by residues 459 - 465 (chain G) in PDB entry 1Q57
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 459 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287G LEU* 5.1 3.6 - - + -
302G ALA* 3.8 36.8 - - + +
303G ARG 4.5 3.8 - - - +
304G GLY* 3.5 24.7 - - - +
305G GLY 4.5 1.6 - - - +
306G GLU 4.5 2.9 - - - +
308G ILE* 4.5 11.4 - - + -
329G TRP* 5.2 0.9 - - + -
419G ASP* 2.7 20.9 + - + +
420G VAL* 3.2 19.8 - - + +
421G ILE 2.8 32.7 + - - +
457G GLY 4.8 0.2 - - - +
458G VAL* 1.3 72.6 - - - +
460G LEU* 1.3 58.9 + - - +
461G VAL* 4.6 6.5 - - + -
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Residues in contact with LEU 460 (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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306G GLU 3.7 5.5 + - - +
307G VAL* 3.2 25.7 - - + +
308G ILE 2.9 26.1 + - - +
409G LEU* 4.4 3.8 - - + -
421G ILE* 3.5 34.5 - - + +
423G LEU* 5.5 1.8 - - + -
449G LEU* 3.8 36.6 - - + +
452G PHE* 3.9 24.0 - - + -
453G ALA* 4.5 5.2 - - + -
458G VAL* 3.6 5.9 + - + +
459G VAL* 1.3 73.9 - - - +
461G VAL* 1.3 63.2 + - - +
462G VAL* 3.6 26.0 + - + -
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Residues in contact with VAL 461 (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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289G PHE* 5.5 2.5 - - + -
308G ILE* 3.2 20.4 - - + +
310G VAL* 3.8 26.5 - - + -
322G VAL* 5.0 10.3 - - + -
325G GLN* 6.4 0.7 - - + -
329G TRP* 3.8 20.2 - - + -
420G VAL* 3.8 16.8 - - + -
421G ILE 3.1 4.7 + - - +
422G ILE* 3.7 28.5 - - + -
423G LEU* 3.0 24.6 + - - +
459G VAL* 4.6 5.4 - - + -
460G LEU* 1.3 72.5 - - - +
462G VAL* 1.3 67.4 + - - +
463G ILE* 6.1 0.2 - - - -
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Residues in contact with VAL 462 (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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307G VAL* 5.2 4.0 - - + -
308G ILE 2.8 11.0 + - - +
309G MET* 3.2 33.9 - - + +
310G VAL 3.0 22.1 + - - +
423G LEU* 3.7 14.6 - - + +
426G ILE* 4.0 20.0 - - + -
446G MET* 5.5 1.8 - - + -
449G LEU* 3.9 14.4 - - + -
460G LEU* 3.6 28.5 - - + +
461G VAL* 1.3 82.1 - - - +
463G ILE* 1.3 72.9 + - - +
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Residues in contact with ILE 463 (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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310G VAL* 3.4 6.3 - - + -
318G MET* 3.2 43.3 - - + +
319G SER* 4.6 1.3 - - - +
322G VAL* 3.1 39.3 - - + -
422G ILE* 5.4 1.3 - - + -
423G LEU 3.2 6.0 + - - -
424G ASP* 3.6 33.0 - - - +
425G HIS* 3.6 18.8 - - + +
426G ILE 3.1 22.0 + - - -
461G VAL* 4.2 0.8 - - + -
462G VAL* 1.3 75.1 - - - +
464G CYS* 1.3 69.9 + - - +
465G HIS* 4.1 6.1 - - - +
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Residues in contact with CYS 464 (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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309G MET* 4.2 19.5 - - + -
310G VAL 2.9 8.5 + - - +
311G THR* 2.7 39.8 + - - +
318G MET* 3.6 2.6 - - - +
425G HIS* 4.5 1.6 - - - -
426G ILE* 3.7 22.0 - - + -
463G ILE* 1.3 82.6 - - - +
465G HIS* 1.3 73.7 + - - +
466G LEU* 5.2 0.9 - - - -
486G LEU* 5.4 4.3 - - - -
487G ARG* 4.5 13.5 - - - -
492G LEU* 4.2 16.6 - - - -
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Residues in contact with HIS 465 (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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312G SER 4.2 2.7 - - - +
313G GLY 4.8 4.3 - - - +
314G SER 5.6 3.4 - - - -
315G GLY 4.4 10.6 + - - -
318G MET* 3.3 32.6 - - + +
319G SER* 6.0 3.2 - - - -
343G GLU* 5.2 2.9 - - + -
424G ASP* 4.9 2.0 + - - -
425G HIS* 2.7 47.9 + + + -
427G SER* 3.7 7.4 + - - +
463G ILE* 4.1 4.3 - - + +
464G CYS* 1.3 84.3 - - - +
466G LEU* 1.3 63.3 + - - +
487G ARG* 3.2 33.8 - - - +
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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