Contacts of the strand formed by residues 499 - 503 (chain A) in PDB entry 3FZT
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 TRP 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A ARG* 3.4 42.6 - - + +
425A VAL* 4.1 25.8 - - + -
427A LEU* 3.7 31.4 - - + -
456A VAL* 3.6 25.6 - - + -
457A LYS 3.5 1.8 - - - -
458A THR* 3.8 25.6 - - + +
492A ILE* 3.4 6.5 - - - +
493A ILE* 2.8 54.1 + - + +
497A PRO* 3.4 28.4 + - + +
498A THR* 1.3 86.9 - - - +
500A ILE* 1.3 62.7 + - - +
501A ILE* 4.0 6.2 + - + +
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Residues in contact with ILE 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ALA 3.4 4.2 - - - +
456A VAL* 3.5 0.7 - - - -
457A LYS* 2.8 48.6 + - + +
471A PHE* 3.1 56.1 - - + +
472A MET* 4.2 3.8 - - - -
474A GLU* 4.3 11.2 - - + +
475A ALA* 4.1 26.2 - - + +
489A LEU* 3.7 23.1 - - + -
491A GLY 3.9 2.2 - - - -
492A ILE* 4.6 4.9 - - + +
498A THR* 5.4 0.9 - - + -
499A TRP* 1.3 75.7 - - - +
501A ILE* 1.3 62.6 + - - +
502A MET* 4.2 13.5 - - - -
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Residues in contact with ILE 501 (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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420A ILE* 3.9 32.1 - - + -
425A VAL* 4.1 9.2 - - + -
444A TYR* 5.0 4.0 - - + -
454A VAL* 3.5 38.8 - - + -
455A ALA 3.7 2.5 - - - -
456A VAL* 4.5 10.8 - - + -
489A LEU* 3.7 2.4 - - - +
490A ILE* 2.7 41.0 + - + -
491A GLY 2.8 25.8 + - - +
493A ILE* 3.9 22.9 - - + -
499A TRP* 4.2 11.9 - - + +
500A ILE* 1.3 75.8 - - - +
502A MET* 1.3 54.6 + - - +
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Residues in contact with MET 502 (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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454A VAL* 3.2 8.7 - - - +
455A ALA* 2.8 40.6 + - + +
457A LYS* 4.0 24.9 - - + -
474A GLU* 4.9 4.3 - - - +
478A MET* 4.4 8.7 - - + -
487A VAL* 3.9 21.3 - - + -
488A LYS 3.7 20.0 - - - +
489A LEU* 3.8 29.4 - - + +
490A ILE* 3.9 2.7 - - - -
500A ILE* 4.2 8.7 - - + -
501A ILE* 1.3 75.0 - - - +
503A GLU* 1.3 66.7 + - - +
999A 4JZ 3.6 37.5 - - + +
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Residues in contact with GLU 503 (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 ILE* 5.0 6.9 - - + +
453A ASN 4.0 6.5 - - - +
455A ALA 4.4 0.2 - - - -
487A VAL* 5.8 0.5 - - - +
488A LYS* 2.9 46.7 + - - +
490A ILE* 3.6 18.3 - - + +
502A MET* 1.3 77.0 - - - +
504A LEU* 1.3 67.6 + - - +
505A TYR* 3.5 44.5 + - + +
564A LYS* 5.9 0.2 - - - -
999A 4JZ 3.3 16.6 - - - +
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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