Contacts of the strand formed by residues 56 - 61 (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 TYR 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A GLY 4.2 1.4 - - - +
54A SER 3.8 0.2 - - - -
55A GLU* 1.3 86.2 - - + +
57A SER* 1.3 64.2 + - - +
58A ASN* 2.6 35.1 + - + -
70A TYR* 3.7 32.0 + + - -
71A HIS* 3.1 6.1 - - - +
72A PHE* 2.9 38.2 + - + +
105A ARG* 3.5 72.3 + - + -
108A LEU* 6.1 1.8 - - + -
461A SER* 3.5 28.0 - - - -
462A SER* 4.4 2.3 - - - -
476A PHE* 5.0 1.7 - - - -
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Residues in contact with SER 57 (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* 1.3 79.7 - - - +
58A ASN* 1.3 54.6 + - - +
70A TYR 3.1 6.3 - - - -
71A HIS* 3.1 38.1 - - - -
461A SER* 2.9 17.1 + - - -
462A SER* 2.7 25.3 + - - -
474A ASN* 3.6 12.1 + - - +
475A CYS 2.5 26.8 + - - -
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Residues in contact with ASN 58 (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* 2.6 26.8 + - - +
57A SER* 1.3 74.1 - - - +
59A CYS* 1.3 80.9 + - - +
69A CYS* 3.5 4.7 - - - +
70A TYR* 3.1 59.6 + - + +
333A ASP* 4.9 3.2 + - - -
462A SER* 3.3 22.2 + - - -
463A ILE 3.9 7.3 + - - +
464A THR* 3.5 10.6 + - - -
474A ASN* 3.6 5.8 - - - +
481A HIS* 6.1 0.2 - - - -
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Residues in contact with CYS 59 (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* 1.3 89.1 + - - +
60A LEU* 1.3 61.5 + - - +
61A LEU 4.3 0.5 + - - -
67A TYR* 4.4 7.7 - - + -
68A ILE 3.4 5.6 - - - +
69A CYS* 3.1 35.4 - - - -
70A TYR* 4.9 0.4 - - - -
84A LEU* 4.1 16.4 - - - -
464A THR* 3.1 35.0 + - + +
472A LEU* 4.9 0.9 - - - -
474A ASN* 3.7 15.9 - - - -
481A HIS* 4.1 3.1 - - - -
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Residues in contact with LEU 60 (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 4.3 0.2 - - - -
59A CYS* 1.3 76.3 - - - +
61A LEU* 1.3 78.7 + - + +
62A LEU* 3.9 10.7 + - + -
67A TYR* 3.7 3.2 - - - -
68A ILE* 3.0 43.9 + - + +
70A TYR* 4.5 12.5 - - + -
110A ILE* 3.8 35.2 - - + +
111A GLN* 4.6 5.8 - - - -
112A GLU* 4.7 4.7 - - + +
117A LEU* 4.6 7.6 - - + -
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Residues in contact with LEU 61 (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* 1.3 88.7 - - + +
62A LEU* 1.3 81.2 + - - +
65A SER* 3.7 27.4 - - - +
66A GLU 3.2 15.9 - - - +
67A TYR* 3.9 36.3 - - + +
112A GLU* 4.1 3.3 - - - +
467A GLY* 5.9 1.8 - - - +
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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