Contacts of the strand formed by residues 465 - 471 (chain A) in PDB entry 1QF6
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 LYS 465 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419A LYS 3.6 0.3 - - - +
420A LEU* 3.3 7.3 - - - +
421A SER* 2.8 42.4 + - - -
441A LEU* 4.3 2.2 - - - -
458A GLU* 4.7 0.6 - - - +
459A GLY* 3.7 10.3 - - - +
460A ALA* 3.3 28.3 - - + +
463A GLY 4.1 0.4 - - - +
464A PRO* 1.3 74.2 - - - +
466A ILE* 1.3 63.7 + - - +
467A GLU* 2.5 40.3 + - + -
479A GLN* 4.8 8.7 + - - +
482A THR* 5.3 3.6 - - - -
483A VAL 3.3 5.2 - - - +
484A GLN* 3.1 47.8 - - + +
1002A AMP 5.2 1.3 - - - -
76B A 4.5 20.9 + - - -
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Residues in contact with ILE 466 (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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397A VAL* 4.5 4.5 - - + -
401A ILE* 3.7 23.3 - - + -
418A VAL* 3.7 25.6 - - + -
419A LYS 3.3 5.2 - - - +
420A LEU* 4.4 1.3 - - + -
441A LEU* 3.9 40.8 - - + +
445A LEU* 3.9 23.8 - - + +
465A LYS* 1.3 76.3 - - - +
467A GLU* 1.3 61.4 + - - +
468A PHE* 3.7 19.6 + - + -
482A THR* 3.1 8.0 - - - -
483A VAL* 2.9 40.7 + - + +
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Residues in contact with GLU 467 (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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417A VAL 3.4 5.2 - - - +
418A VAL* 3.5 1.7 - - - -
419A LYS* 3.0 40.9 + - + +
421A SER* 2.6 22.5 + - - +
455A GLN* 3.4 17.1 - - - +
458A GLU* 4.1 6.1 - - - +
465A LYS* 2.5 35.0 + - + +
466A ILE* 1.3 75.6 - - - +
468A PHE* 1.3 62.8 + - - +
469A THR* 3.8 6.4 - - + +
479A GLN* 2.9 34.3 - - + +
481A GLY 3.9 3.1 - - - -
482A THR* 4.2 2.9 - - + -
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Residues in contact with PHE 468 (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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401A ILE* 3.9 18.6 - - + -
404A VAL* 3.8 34.3 - - + -
405A TYR* 3.5 33.9 - + - -
408A TYR* 4.2 19.5 - - + +
416A ILE* 4.0 9.6 - - + -
417A VAL 3.6 2.7 - - - -
418A VAL* 3.8 20.2 - - + -
445A LEU* 5.1 0.9 - - + -
450A ILE* 5.0 1.3 - - + -
466A ILE* 3.7 26.7 - - + -
467A GLU* 1.3 74.6 - - - +
469A THR* 1.3 58.7 + - - +
479A GLN* 3.8 1.6 - - - +
480A CYS* 2.8 25.4 + - - +
481A GLY 2.8 27.8 + - - +
483A VAL* 4.4 13.9 - - + -
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Residues in contact with THR 469 (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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416A ILE* 3.6 2.1 - - - +
417A VAL* 3.0 56.5 + - + +
419A LYS* 4.4 9.6 - - + -
467A GLU* 3.8 11.2 - - + +
468A PHE* 1.3 76.3 - - - +
470A LEU* 1.3 76.7 + - - +
471A TYR* 3.6 19.3 + - - +
477A ALA* 3.9 9.8 - - + +
478A TRP 3.5 10.9 + - - -
479A GLN* 4.2 7.9 - - - -
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Residues in contact with LEU 470 (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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408A TYR* 4.0 23.8 - - + -
413A PHE* 3.5 37.9 - - + -
415A LYS 3.7 13.2 - - - +
416A ILE* 4.0 11.9 - - + -
469A THR* 1.3 83.0 + - - +
471A TYR* 1.3 71.0 + - - +
478A TRP* 3.0 31.7 + - - +
480A CYS* 4.0 24.5 - - + -
521A PHE* 3.9 16.2 - - + -
524A ILE* 4.2 19.5 - - + -
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Residues in contact with TYR 471 (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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415A LYS* 3.4 36.4 + - + +
417A VAL* 3.1 45.8 - - + +
469A THR* 3.6 19.0 + - - +
470A LEU* 1.3 76.8 - - - +
472A ASP* 1.3 63.4 + - - +
475A ASP* 3.6 33.0 - - - +
476A ARG 3.2 22.4 - - - +
477A ALA* 3.5 20.6 - - + +
524A ILE* 3.8 18.8 - - - +
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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