Contacts of the strand formed by residues 469 - 473 (chain A) in PDB entry 2FO1
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 LEU 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A VAL* 3.4 5.0 - - - -
455A VAL* 2.5 47.5 + - + +
457A LEU* 5.2 7.6 - - + +
466A LEU* 4.5 10.8 - - + -
467A PRO* 3.2 16.2 - - + +
468A ARG* 1.3 86.7 - - - +
470A ARG* 1.3 57.8 + - - +
471A ILE 3.7 1.0 + - - -
498A PHE* 3.5 48.0 - - + +
499A GLN 3.8 6.1 - - - +
500A MET* 3.6 25.8 - - - +
501A ILE* 5.2 0.9 - - - +
508A LEU* 3.6 28.9 - - + -
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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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452A GLY* 3.6 34.5 + - - -
453A SER 3.5 4.5 - - - +
454A VAL* 4.4 24.7 - - + +
469A LEU* 1.3 73.1 - - - +
471A ILE* 1.3 66.6 + - - +
472A ARG* 2.9 37.7 + - - +
497A ALA 3.6 0.2 - - - +
498A PHE* 4.1 0.4 - - - -
499A GLN* 2.9 47.7 + - + +
500A MET 4.8 3.1 - - - +
501A ILE* 5.5 12.3 - - - +
504A GLU* 5.7 3.2 + - - -
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Residues in contact with ILE 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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427A ILE* 4.8 3.1 - - + -
449A VAL* 4.2 14.6 - - + -
450A TYR 3.9 20.2 - - - +
451A TYR* 4.1 2.9 - - + -
452A GLY* 2.8 32.5 + - - +
453A SER 3.4 8.5 + - - +
455A VAL* 4.3 6.9 - - + +
469A LEU 3.7 3.6 + - - -
470A ARG* 1.3 73.0 - - - +
472A ARG* 1.3 58.8 + - - +
490A VAL* 4.0 27.4 - - + -
496A CYS* 3.9 24.0 - - + -
497A ALA 3.5 4.5 - - - +
498A PHE* 3.1 34.6 - - + -
538A ILE* 4.0 19.5 - - + -
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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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451A TYR* 4.1 7.0 - - + -
452A GLY* 4.5 11.0 - - - +
470A ARG* 2.9 41.2 - - - +
471A ILE* 1.3 79.9 - - - +
473A LYS* 1.3 65.2 + - - +
479A VAL* 4.2 13.2 - - + -
480A ILE 4.5 0.4 - - - +
481A LEU* 3.5 49.4 + - + +
482A ASP 5.4 2.0 + - - -
496A CYS* 2.9 24.3 - - - +
497A ALA 2.7 25.6 + - - +
499A GLN* 2.7 39.4 + - - +
507A TYR* 4.8 2.9 - - + -
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Residues in contact with LYS 473 (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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371A LYS 4.1 14.5 + - - -
372A LYS* 5.4 4.9 - - - +
451A TYR* 3.7 34.3 - - + +
472A ARG* 1.3 74.5 - - - +
474A VAL* 1.3 86.1 + - - +
475A ASP* 5.5 4.3 - - - -
479A VAL* 3.3 21.8 - - - +
480A ILE* 3.6 29.3 + - + +
485A CYS* 4.2 11.9 - - - -
488A GLU* 3.1 35.1 + - - +
494A HIS* 3.5 28.2 + - + -
495A LYS 4.4 2.0 - - - -
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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