Contacts of the strand formed by residues 466 - 471 (chain A) in PDB entry 3Q0F
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 466 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A ALA* 4.1 13.0 - - + +
408A THR 3.9 2.5 - - - -
409A SER* 3.8 20.9 - - - +
410A ILE* 4.0 12.8 - - + +
456A LEU* 5.0 0.7 - - + -
459A SER* 4.4 4.9 - - - +
464A ASN* 3.8 17.7 - - - +
465A PRO* 1.3 79.7 - - - +
467A ARG* 1.3 76.9 + - - +
468A VAL* 3.7 0.7 + - + -
491A LEU* 3.4 5.2 - - - -
492A TYR* 2.7 40.5 + - - +
494A VAL* 4.2 20.2 - - + -
513A LEU* 4.5 15.0 - - + -
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Residues in contact with ARG 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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362A GLN* 4.2 5.3 + - - -
363A ILE 3.0 30.3 + - - -
365A GLY* 2.6 48.4 + - - +
367A VAL* 3.6 24.2 - - - +
386A GLY 3.8 8.7 + - - -
387A ILE* 3.0 41.7 + - - +
396A ASP* 5.2 0.8 + - - -
408A THR* 3.1 33.2 + - - +
409A SER* 3.2 7.8 + - - -
410A ILE 2.9 26.5 + - - -
466A VAL* 1.3 77.5 - - - +
468A VAL* 1.3 60.2 + - - +
469A ILE* 4.3 5.2 - - + -
488A TYR* 3.8 17.7 - - + +
490A GLY 3.7 4.9 - - - -
491A LEU* 3.7 12.6 - - + -
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Residues in contact with VAL 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ILE* 3.6 26.9 - - + -
412A SER* 5.5 1.8 - - - -
426A LEU* 4.1 20.4 - - + -
466A VAL 4.1 2.9 - - - +
467A ARG* 1.3 80.2 - - - +
469A ILE* 1.3 72.6 + - - +
470A ARG* 4.3 5.8 - - + -
488A TYR* 3.8 3.7 - - - -
489A ASP* 2.8 43.4 + - + +
490A GLY 3.2 7.6 + - - +
492A TYR* 3.5 40.8 - - + -
513A LEU* 4.6 1.6 - - + -
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Residues in contact with ILE 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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376A PHE* 5.7 0.2 - - + -
382A LEU* 4.1 18.6 - - + -
387A ILE* 3.7 30.3 - - + -
388A HIS* 4.7 8.1 - - + -
409A SER* 4.8 1.8 - - - -
410A ILE 3.0 19.1 + - - +
411A VAL* 3.4 13.6 - - + +
412A SER* 2.7 34.3 + - - +
467A ARG* 4.4 5.8 - - + -
468A VAL* 1.3 85.9 - - - +
470A ARG* 1.3 59.9 + - - +
486A TYR* 3.7 37.5 - - + -
487A VAL 3.2 12.8 - - - +
488A TYR* 4.5 8.7 - - + -
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Residues in contact with ARG 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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412A SER* 3.2 11.7 - - - +
420A LEU* 3.8 31.9 + - + +
421A ASP 3.9 15.4 + - - -
423A SER 4.6 10.9 + - - -
425A VAL 5.1 2.2 + - - -
426A LEU* 4.3 19.9 - - - +
468A VAL* 4.3 7.6 - - + +
469A ILE* 1.3 80.4 - - - +
471A GLY* 1.3 69.5 + - - +
472A ILE* 4.9 1.1 - - + -
486A TYR* 3.2 3.3 - - - -
487A VAL* 2.9 39.8 + - + +
489A ASP* 2.8 30.3 + - + -
492A TYR* 3.1 25.3 + - - -
522A LEU* 5.0 9.9 - - + -
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Residues in contact with GLY 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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411A VAL* 5.3 0.2 - - - +
412A SER 2.8 17.0 + - - +
413A SER* 4.2 13.6 - - - -
470A ARG* 1.3 78.4 - - - +
472A ILE* 1.3 67.0 + - - +
485A ASN 3.0 11.9 - - - -
486A TYR* 3.9 11.5 - - - -
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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