Contacts of the strand formed by residues 460 - 466 (chain A) in PDB entry 3F7F
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 ALA 460 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A VAL* 3.9 10.6 - - + +
354A LEU* 3.9 23.6 - - + -
356A LYS* 3.2 31.0 + - + +
359A THR 5.4 1.6 + - - -
361A SER* 4.1 25.1 - - - +
458A ASN 3.1 5.8 + - - +
459A GLU* 1.3 73.7 - - - +
461A SER* 1.3 58.4 + - - +
473A VAL* 4.1 14.1 - - + -
474A ASN 4.3 0.4 - - - -
475A CYS* 4.9 0.7 - - - +
476A PHE* 3.4 3.8 - - - -
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Residues in contact with SER 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 3.5 20.1 - - - -
57A SER* 2.9 38.0 + - - -
105A ARG* 5.4 1.4 + - - -
332A VAL* 3.3 22.8 - - - +
460A ALA* 1.3 75.0 - - - +
462A SER* 1.3 60.3 + - - +
473A VAL* 4.5 0.6 - - - +
474A ASN 3.0 19.0 + - - -
476A PHE* 3.8 19.5 - - - -
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Residues in contact with SER 462 (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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56A TYR* 4.4 5.2 - - - -
57A SER 2.7 22.1 + - - -
58A ASN* 3.3 24.3 - - - -
332A VAL* 4.1 1.9 - - - +
333A ASP* 3.7 15.7 - - - -
354A LEU* 4.3 2.4 - - - +
461A SER* 1.3 81.1 - - - +
463A ILE* 1.3 62.8 + - - +
473A VAL* 3.4 8.7 - - - +
474A ASN* 2.9 40.5 + - - -
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Residues in contact with ILE 463 (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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58A ASN* 3.9 10.0 + - - +
333A ASP* 3.1 46.5 + - + +
334A LEU 4.2 0.2 - - - +
335A VAL* 3.6 34.8 - - + -
352A ILE* 3.8 16.4 - - + +
354A LEU* 3.9 18.6 - - + +
363A LEU* 5.1 1.1 - - + -
462A SER* 1.3 79.0 - - - +
464A THR* 1.3 74.8 + - - +
465A LEU* 4.3 5.8 - - + +
471A ILE* 4.6 10.8 - - + -
472A LEU 3.3 15.9 - - - +
473A VAL* 4.9 4.0 - - + -
474A ASN* 4.1 0.2 - - - -
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Residues in contact with THR 464 (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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58A ASN* 3.5 4.5 + - - -
59A CYS* 3.1 36.1 + - + +
67A TYR* 4.1 16.4 - - + -
463A ILE* 1.3 74.8 - - - +
465A LEU* 1.3 61.3 + - - +
466A TYR 3.2 9.8 + - - +
472A LEU* 2.9 51.4 + - + +
474A ASN* 2.7 26.9 + - - +
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Residues in contact with LEU 465 (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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67A TYR* 3.4 7.3 + - - -
335A VAL* 3.5 34.3 - - + -
337A THR* 4.3 21.1 - - + +
352A ILE* 3.8 24.7 - - + -
463A ILE* 5.1 2.2 - - + -
464A THR* 1.3 76.4 - - - +
466A TYR* 1.3 65.3 + - - +
467A GLY 3.4 11.5 + - - +
468A ASP 4.8 6.5 - - - +
469A GLU* 4.2 20.0 - - - +
470A ILE 3.4 11.4 - - - +
471A ILE* 4.6 2.2 - - + -
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Residues in contact with TYR 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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67A TYR* 3.4 32.5 - + - -
84A LEU* 3.4 32.1 - - + -
85A SER* 6.0 0.3 - - - -
464A THR* 3.2 4.9 + - - -
465A LEU* 1.3 71.7 - - - +
467A GLY* 1.3 63.3 + - - +
470A ILE* 2.9 60.9 + - + +
472A LEU* 4.3 16.8 - - + -
608A ASP* 4.0 8.5 + - - -
610A PHE* 3.6 20.7 - + + +
611A THR* 3.6 19.5 - - + +
691A LYS* 5.3 4.2 - - - +
692A PHE* 3.8 34.3 + + - -
693A PHE* 5.6 5.5 - + - -
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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