Contacts of the strand formed by residues 470 - 475 (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 ILE 470 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A LEU* 3.4 4.9 - - - +
466A TYR* 2.9 66.3 + - + +
469A GLU* 1.3 72.1 - - - +
471A ILE* 1.3 65.2 + - - +
472A LEU 3.4 0.9 + - - -
483A LEU* 3.4 36.6 - - + -
692A PHE* 4.7 10.3 - - + -
693A PHE 3.5 12.8 - - - +
694A ASN 3.4 35.7 - - - +
695A TYR* 3.7 23.1 - - + +
698A LEU* 5.2 2.5 - - + -
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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
----------------------------------------------------------
4A LEU* 3.8 14.4 - - + -
340A LEU* 4.7 5.4 - - + -
352A ILE* 3.3 41.7 - - + -
363A LEU* 3.7 28.9 - - + -
365A ILE* 3.5 29.6 - - + -
463A ILE* 4.6 7.0 - - + -
464A THR 4.3 1.1 - - - -
465A LEU* 4.6 3.1 - - + -
469A GLU 3.2 6.3 + - - +
470A ILE* 1.3 71.4 - - - +
472A LEU* 1.3 63.5 + - - +
483A LEU* 3.9 6.4 - - - +
484A TYR* 3.2 34.8 + - + +
695A TYR* 2.8 18.8 + - - +
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Residues in contact with LEU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A CYS* 4.9 0.9 - - - -
84A LEU* 4.7 13.9 - - + -
463A ILE* 3.3 8.9 - - - +
464A THR* 2.9 60.2 + - + +
466A TYR* 4.3 20.6 - - + -
470A ILE* 4.2 4.0 - - + +
471A ILE* 1.3 77.2 - - - +
473A VAL* 1.3 69.2 + - - +
474A ASN* 4.0 14.4 - - - +
481A HIS* 4.2 12.8 - - + +
482A SER 3.8 19.3 - - - +
483A LEU* 4.1 6.5 - - + +
610A PHE* 3.8 28.9 - - + -
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Residues in contact with VAL 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU* 4.0 33.0 - - + -
363A LEU* 4.4 8.1 - - + -
460A ALA* 4.1 15.5 - - + -
462A SER 3.4 9.2 - - - +
463A ILE* 4.9 2.5 - - + -
471A ILE* 5.0 0.4 - - + -
472A LEU* 1.3 79.6 - - - +
474A ASN* 1.3 74.0 + - - +
475A CYS* 4.0 3.0 + - - +
481A HIS* 3.4 6.1 - - - +
482A SER* 2.8 47.2 + - - +
484A TYR* 3.8 26.2 - - + -
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Residues in contact with ASN 474 (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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57A SER* 3.7 21.8 - - - +
58A ASN* 4.1 5.8 - - - +
59A CYS* 3.6 15.1 - - - +
71A HIS* 5.8 0.2 - - - +
461A SER* 3.0 29.3 + - - -
462A SER* 2.9 29.9 + - - +
464A THR* 2.7 32.0 + - - -
472A LEU* 4.0 7.3 - - - +
473A VAL* 1.3 76.4 - - - +
475A CYS* 1.3 61.5 + - - +
481A HIS* 3.1 28.9 + - + +
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Residues in contact with CYS 475 (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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57A SER* 2.5 24.9 + - - -
71A HIS* 3.1 10.2 - - - -
457A PHE 3.2 16.8 - - - +
458A ASN* 3.9 20.9 - - - -
459A GLU 3.3 10.3 - - - +
473A VAL* 4.3 4.3 - - - -
474A ASN* 1.3 72.5 - - - +
476A PHE* 1.3 66.0 + - - +
477A GLN 3.3 0.8 - - - +
480A ASN* 3.1 36.5 + - + +
481A HIS* 3.7 14.5 - - - -
482A SER* 4.2 11.4 - - - -
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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