Contacts of the strand formed by residues 459 - 465 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287E LEU* 5.0 4.0 - - + -
302E ALA* 3.8 37.2 - - + +
303E ARG 4.5 3.8 - - - +
304E GLY* 3.5 24.2 - - - +
305E GLY 4.5 0.9 - - - +
306E GLU 4.5 3.8 - - - +
308E ILE* 4.5 10.5 - - + -
329E TRP* 5.3 0.4 - - + -
419E ASP* 2.6 21.8 + - + +
420E VAL* 3.2 22.8 - - + +
421E ILE 2.8 29.1 + - - +
457E GLY 3.6 0.6 + - - +
458E VAL* 1.3 71.9 - - - +
460E LEU* 1.3 62.6 + - - +
461E VAL* 4.7 3.6 - - + -
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Residues in contact with LEU 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306E GLU 3.6 8.3 + - - +
307E VAL* 3.3 27.9 - - + +
308E ILE 3.0 24.8 + - - +
409E LEU* 4.3 4.5 - - + -
421E ILE* 3.4 34.3 - - + +
423E LEU* 5.4 2.0 - - + -
449E LEU* 3.9 32.5 - - + +
452E PHE* 4.1 20.9 - - + -
453E ALA* 4.5 6.5 - - + -
458E VAL* 3.7 3.3 + - + +
459E VAL* 1.3 77.0 - - - +
461E VAL* 1.3 59.0 + - - +
462E VAL* 3.6 27.1 + - + -
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Residues in contact with VAL 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289E PHE* 5.6 2.7 - - + -
308E ILE* 3.1 18.4 - - + +
310E VAL* 3.8 26.7 - - + -
322E VAL* 4.9 10.3 - - + -
325E GLN* 6.4 1.1 - - + -
329E TRP* 3.9 19.1 - - + -
420E VAL* 3.7 16.2 - - + -
421E ILE 3.0 4.1 + - - +
422E ILE* 3.7 30.5 - - + -
423E LEU* 2.9 24.9 + - - +
459E VAL* 4.7 5.8 - - + -
460E LEU* 1.3 70.7 - - - +
462E VAL* 1.3 67.3 + - - +
463E ILE 4.3 0.4 - - - -
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Residues in contact with VAL 462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E VAL* 5.3 5.2 - - + -
308E ILE 2.6 11.7 + - - +
309E MET* 3.1 33.7 - - + +
310E VAL 2.9 23.2 + - - +
423E LEU* 3.6 15.3 - - + +
426E ILE* 4.0 20.0 - - + -
446E MET* 5.4 1.3 - - + -
449E LEU* 3.9 14.4 - - + -
460E LEU* 3.6 27.8 - - + +
461E VAL* 1.3 80.7 - - - +
463E ILE* 1.3 71.6 + - - +
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Residues in contact with ILE 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E VAL* 3.4 7.0 - - + -
318E MET* 3.1 42.0 - - + +
319E SER* 4.6 0.7 - - - +
322E VAL* 3.1 40.8 - - + -
422E ILE* 5.3 0.9 - - + -
423E LEU 3.1 7.7 + - - +
424E ASP* 3.5 33.4 - - - +
425E HIS* 3.5 20.4 - - + +
426E ILE 3.1 22.0 + - - -
461E VAL* 5.9 0.4 - - + -
462E VAL* 1.3 74.5 - - - +
464E CYS* 1.3 70.2 + - - +
465E HIS* 4.1 6.7 - - - +
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Residues in contact with CYS 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E MET* 4.2 21.5 - - + -
310E VAL 2.9 8.1 + - - +
311E THR* 2.8 37.2 + - - +
318E MET* 3.6 3.6 - - - +
425E HIS* 4.5 2.2 - - - -
426E ILE* 3.6 23.3 - - + -
427E SER* 5.0 0.4 - - - -
463E ILE* 1.3 83.1 - - - +
465E HIS* 1.3 77.8 + - - +
466E LEU* 5.0 0.9 - - - -
486E LEU* 5.4 3.8 - - - -
487E ARG* 4.5 12.6 - - - -
492E LEU* 4.4 15.5 - - - -
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Residues in contact with HIS 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312E SER 4.2 3.6 - - - +
313E GLY 5.3 1.6 - - - +
314E SER 5.5 3.4 - - - -
315E GLY 4.4 9.2 + - - -
318E MET* 2.9 36.6 - - + +
319E SER* 5.9 3.4 + - - -
343E GLU* 5.2 2.5 - - + -
424E ASP* 4.9 1.9 + - - -
425E HIS* 3.0 47.0 + + + +
427E SER* 3.7 7.0 + - - +
463E ILE* 4.1 7.3 - - + +
464E CYS* 1.3 84.9 - - - +
466E LEU* 1.3 63.4 + - - +
487E ARG* 3.3 27.8 - - - +
494F GLN* 4.3 22.4 + - + +
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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