Contacts of the strand formed by residues 78 - 83 (chain C) 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 LEU 78 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C GLY 5.3 4.5 - - - +
71C HIS 3.6 0.5 - - - +
72C PHE* 3.0 9.4 - - - -
73C SER* 2.8 44.0 + - - +
76C SER 3.6 0.4 - - - -
77C THR* 1.3 85.4 + - - +
79C LEU* 1.3 64.2 + - - +
80C THR* 3.9 15.9 - - - +
94C ASN* 3.9 13.9 - - + +
95C ILE 3.5 28.0 - - - +
96C HIS* 3.4 37.0 - - + +
97C LEU* 5.1 0.4 - - - -
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Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C TYR* 5.0 5.2 - - + -
71C HIS 3.4 9.2 - - - +
72C PHE* 3.5 32.8 - - + -
78C LEU* 1.3 73.7 - - - +
80C THR* 1.3 62.7 + - - +
81C PHE* 3.6 33.4 - - + -
93C ILE 3.6 0.7 - - - +
94C ASN* 3.5 2.1 - - - -
95C ILE* 2.6 51.3 + - + +
97C LEU* 5.4 5.2 - - + -
108C LEU* 3.8 15.9 - - + -
110C ILE* 4.4 8.3 - - + -
119C VAL* 3.8 26.7 - - + -
121C VAL* 5.5 0.7 - - + -
131C LEU* 4.4 9.0 - - + -
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Residues in contact with THR 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLY* 4.6 8.3 + - - -
70C TYR* 2.9 30.5 - - - +
71C HIS* 2.9 25.6 + - + -
78C LEU* 3.9 11.8 - - - +
79C LEU* 1.3 77.0 - - - +
81C PHE* 1.3 73.0 + - - +
82C TYR* 4.8 10.1 - - + -
92C THR* 4.7 10.1 - - - +
93C ILE 3.2 4.9 - - - +
94C ASN* 2.8 28.3 + - - +
478C PRO* 5.6 6.7 - - + -
479C TYR* 5.5 2.2 - - + +
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Residues in contact with PHE 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ILE* 4.2 14.1 - - + -
69C CYS 3.2 6.7 - - - -
70C TYR* 3.7 23.8 - + + -
79C LEU* 3.6 34.3 - - + -
80C THR* 1.3 76.5 - - - +
82C TYR* 1.3 61.4 + - - +
91C LYS 3.8 1.2 - - - +
92C THR* 2.8 6.8 - - - -
93C ILE* 2.6 58.8 + - + +
95C ILE* 3.6 31.0 - - + -
110C ILE* 4.3 10.1 - - + -
117C LEU* 3.6 27.4 - - + -
119C VAL* 4.2 9.9 - - + -
133C LEU* 3.8 12.3 - - + -
138C LEU* 4.5 7.4 - - + -
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Residues in contact with TYR 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.9 14.6 - - + -
68C ILE* 3.4 7.0 - - - +
69C CYS* 2.7 62.2 + - + +
71C HIS* 3.9 13.5 + + - -
80C THR* 4.8 9.2 - - + -
81C PHE* 1.3 78.7 - - - +
83C PRO* 1.3 74.5 - - + +
87C ALA* 4.4 3.1 - - + -
91C LYS 3.9 1.6 - - - -
92C THR* 3.4 22.7 - - + -
478C PRO* 4.0 12.8 - - + -
479C TYR* 2.9 52.4 + + - -
481C HIS* 2.7 25.8 + - - -
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Residues in contact with PRO 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLU* 5.0 5.6 - - - +
67C TYR 3.5 7.6 - - - +
68C ILE* 3.7 5.6 - - + -
82C TYR* 1.3 89.3 - - + +
84C LEU* 1.3 67.0 + - - +
85C SER 4.6 1.1 - - - +
86C ASP* 3.1 37.3 + - + +
87C ALA* 3.3 12.6 + - - -
90C GLY* 4.0 9.0 - - - -
91C LYS 3.4 20.2 - - - +
92C THR* 5.2 0.2 - - + -
138C LEU 5.2 3.6 - - - +
139C PHE* 4.1 28.0 - - + -
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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