Contacts of the strand formed by residues 419 - 426 (chain A) in PDB entry 1QHP
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 419 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A MET* 3.7 1.7 - - - +
414A TRP* 3.8 23.8 - - + -
415A ILE* 3.2 7.8 - - - +
416A ASN* 2.7 42.2 + - - +
418A ASP* 1.3 78.4 - - - +
420A TYR* 1.3 63.2 + - - +
421A ILE* 3.9 14.4 - - + -
435A ILE 3.3 7.6 - - - +
436A ASN* 3.9 12.1 - - + +
443A TYR* 3.4 41.1 - - + -
445A ILE* 4.3 2.2 - - + -
482A LEU* 3.8 17.5 - - + -
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Residues in contact with TYR 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A MET* 3.7 23.5 - - + +
304A LEU* 4.0 21.5 - - + -
305A ASN* 2.6 52.8 + - + -
308A VAL* 4.1 14.8 - - + +
349A PHE* 3.9 15.7 - + - -
410A THR* 4.6 4.5 - - - +
412A GLN* 4.0 11.6 - - + +
414A TRP 3.7 2.9 - - - -
415A ILE* 4.0 13.0 - - + -
419A VAL* 1.3 73.8 - - - +
421A ILE* 1.3 67.4 + - - +
422A TYR* 3.6 43.0 + + + +
433A VAL 3.6 2.8 - - - +
435A ILE* 2.9 38.2 + - + +
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Residues in contact with ILE 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A GLN* 3.8 1.7 - - - -
413A ARG 2.8 24.0 + - - -
414A TRP* 2.8 37.6 + - + +
419A VAL* 3.9 17.0 - - + -
420A TYR* 1.3 77.7 - - - +
422A TYR* 1.3 59.8 + - - +
432A LEU* 3.8 26.0 - - + -
433A VAL 3.1 15.0 - - - +
434A ALA* 3.6 24.5 - - + -
445A ILE* 3.8 26.5 - - + -
448A LEU* 3.9 19.7 - - + -
480A PHE* 4.5 2.9 - - + -
482A LEU* 4.9 0.4 - - + -
490A TRP* 4.9 0.4 - - + -
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Residues in contact with TYR 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A PHE* 3.5 27.2 + + - -
352A THR* 2.7 33.2 + - - -
353A SER* 3.5 24.7 + - - -
410A THR* 4.3 19.3 - - + -
411A THR 3.3 11.7 - - - +
413A ARG* 4.3 0.4 - - - +
420A TYR* 3.6 41.5 - + + +
421A ILE* 1.3 75.5 - - - +
423A GLU* 1.3 62.6 + - - +
424A ARG* 4.6 7.2 - - + -
431A VAL 4.0 0.5 - - - +
432A LEU* 3.6 4.2 - - - +
433A VAL* 2.8 60.6 + - + +
435A ILE* 3.9 13.4 - - + +
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Residues in contact with GLU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A THR* 3.5 1.2 + - - +
410A THR* 3.4 5.4 - - - -
411A THR* 2.8 43.2 + - - +
413A ARG* 2.8 37.2 + - + +
422A TYR* 1.3 77.4 - - - +
424A ARG* 1.3 68.4 + - - +
425A LYS* 4.1 5.2 + - + +
430A VAL* 3.5 20.4 - - + +
431A VAL 3.3 10.1 - - - +
432A LEU* 4.0 12.0 - - + +
450A THR* 2.7 29.5 + - - -
451A ALA* 2.8 16.5 + - - +
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Residues in contact with ARG 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A GLU* 5.2 1.2 - - - +
352A THR 2.9 39.1 + - - +
353A SER* 3.2 14.0 - - - +
354A ARG* 3.6 21.0 - - - +
404A ALA* 3.3 29.4 + - + +
405A ILE* 2.9 40.6 + - + +
406A GLN 4.5 1.4 + - - -
407A TYR 4.1 2.6 - - - +
408A GLY 2.9 23.4 + - - +
409A THR 3.2 13.0 + - - -
410A THR* 3.4 23.6 + - - -
422A TYR* 4.6 10.8 - - + -
423A GLU* 1.3 75.7 - - - +
425A LYS* 1.3 61.1 + - - +
430A VAL* 3.4 5.5 - - - +
431A VAL* 2.8 36.1 + - + +
433A VAL* 5.5 1.3 - - + -
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Residues in contact with LYS 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A ALA* 4.0 0.2 - - - -
408A GLY* 3.1 3.8 - - - -
409A THR* 2.9 45.0 + - - +
411A THR* 6.1 0.2 - - - +
423A GLU* 4.1 6.0 + - + +
424A ARG* 1.3 77.2 - - - +
426A PHE* 1.3 62.0 + - - +
427A PHE* 2.6 35.6 + - - +
428A ASN* 5.3 0.7 - - - +
429A ASP 3.3 9.2 - - - +
430A VAL* 4.2 9.0 - - + -
451A ALA* 3.8 30.1 - - + -
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Residues in contact with PHE 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A ALA* 3.7 32.3 - - + +
404A ALA* 3.8 8.6 - - - +
407A TYR* 3.5 38.4 - + + -
408A GLY* 4.1 2.5 - - - -
425A LYS* 1.3 71.9 - - - +
427A PHE* 1.3 91.1 + + - +
428A ASN 3.1 1.2 + - - -
429A ASP* 2.9 26.5 + - - +
500A GLN* 3.5 30.7 - - + -
501A ILE 3.6 26.5 - - - -
502A GLY* 3.8 9.9 - - - -
520A LYS* 4.2 10.3 - - + -
570A ASN* 5.2 0.2 - - - -
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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