Contacts of the strand formed by residues 466 - 473 (chain A) in PDB entry 3HS0
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 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PRO* 4.9 0.2 - - - -
12A ARG* 5.0 8.9 - - - +
15A THR* 2.8 36.9 + - - +
16A GLU* 3.3 23.1 + - - +
17A GLU* 3.4 23.3 - - - +
18A GLN 6.1 0.4 - - - +
103A SER 5.2 2.0 + - - -
129A ASP* 3.9 12.9 + - - -
462A LEU* 3.3 6.8 - - - -
463A ASN 2.9 34.1 + - - +
464A LYS* 4.3 8.3 - - + +
465A GLY* 1.3 82.0 - - - +
467A ILE* 1.3 65.0 + - - +
468A PHE* 3.1 5.4 + - + +
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Residues in contact with ILE 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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6A ILE* 4.0 19.3 - - + +
7A THR* 4.3 11.2 - - - -
8A PRO* 4.3 6.8 - - + +
17A GLU* 4.5 4.0 + - - -
18A GLN* 3.3 52.6 + - + +
19A ILE* 4.3 5.6 - - - +
20A LEU* 4.6 1.6 - - + +
62A THR* 6.1 0.2 - - + -
460A LEU* 4.2 17.7 - - + -
461A ILE 3.9 4.7 - - - +
462A LEU* 3.9 18.6 - - + -
465A GLY 4.4 0.4 + - - -
466A LYS* 1.3 70.3 - - - +
468A PHE* 1.3 61.8 + - - +
469A LYS 4.4 7.2 - - - +
470A VAL* 3.9 25.8 - - + -
604A LEU* 4.1 9.4 - - + -
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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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18A GLN* 3.6 17.0 + - - +
461A ILE* 2.8 24.0 + - + +
463A ASN* 4.3 18.2 - - + +
466A LYS* 3.1 6.7 + - + +
467A ILE* 1.3 75.1 - - - +
469A LYS* 1.3 86.5 + - + +
489A THR* 4.6 7.6 - - - -
491A ASP* 3.9 35.9 - - + -
492A LEU* 3.7 28.0 - - + -
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Residues in contact with LYS 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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18A GLN* 4.7 2.0 - - - -
459A TYR* 5.2 9.2 - - + +
460A LEU* 3.4 2.6 - - - +
461A ILE* 2.7 46.1 + - + +
467A ILE* 4.5 1.2 - - - +
468A PHE* 1.3 106.5 - - + +
470A VAL* 1.3 76.5 + - - +
486A LEU* 4.1 26.4 - - - +
487A HIS* 4.7 8.3 + - - +
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Residues in contact with VAL 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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18A GLN* 4.9 3.2 + - - +
20A LEU* 3.7 42.6 - - + -
60A LEU* 4.0 22.9 - - + -
62A THR* 3.8 20.0 - - + -
458A THR* 4.9 0.7 - - + -
459A TYR* 3.4 9.5 + - - +
460A LEU* 4.1 8.5 - - + -
467A ILE* 3.9 20.4 - - + -
469A LYS* 1.3 90.1 - - - +
471A GLY* 1.3 65.2 + - - +
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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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60A LEU* 5.6 0.7 - - - -
458A THR* 3.6 6.4 - - - +
459A TYR* 2.9 55.2 + - - +
470A VAL* 1.3 83.0 - - - +
472A ARG* 1.3 63.3 + - - +
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Residues in contact with ARG 472 (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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22A GLU* 2.9 37.7 + - - +
23A ALA 4.4 5.1 + - - -
24A HIS* 3.9 4.2 + - - -
58A GLY* 3.0 36.1 + - - -
59A MET 4.5 0.6 + - - -
60A LEU* 3.8 17.5 - - + +
456A TYR* 3.3 57.4 + - + -
457A PHE 3.4 8.7 - - - -
458A THR* 3.3 8.5 + - - +
459A TYR* 3.7 5.4 + - - -
471A GLY* 1.3 76.4 - - - -
473A GLN* 1.3 66.1 + - - +
474A PRO* 4.1 5.7 - - + +
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Residues in contact with GLN 473 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442A PHE* 3.8 38.1 - - + -
456A TYR* 3.2 3.9 - - - -
457A PHE* 2.8 45.5 + - + +
459A TYR* 4.6 5.4 - - + -
472A ARG* 1.3 79.4 + - - +
474A PRO* 1.3 87.9 - - - +
482A VAL* 3.9 14.9 - - + +
483A THR 4.1 5.9 - - - +
484A MET* 3.8 28.4 - - + +
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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