Contacts of the strand formed by residues 76 - 81 (chain B) in PDB entry 3I8E
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 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B PHE* 4.2 0.2 - - - -
66B LEU* 3.4 8.7 - - - +
67B PHE* 2.9 50.9 + - + +
69B PRO* 4.7 5.6 - - + -
72B GLU* 3.3 38.8 - - + +
74B LYS* 4.2 2.0 - - + +
75B ASP* 1.3 75.7 - - - +
77B LEU* 1.3 62.3 + - - +
88B ILE* 4.3 21.5 - - + -
89B LEU 3.3 5.6 - - - +
90B GLU* 3.6 39.7 - - + +
103B ARG* 4.4 18.4 - - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 5.1 0.2 - - + -
23B PHE* 3.3 21.0 - - + -
32B LEU* 3.8 28.0 - - + -
39B LEU* 3.9 28.9 - - + -
64B MET* 3.8 22.2 - - + -
65B GLU 3.2 20.6 - - - +
66B LEU* 4.2 3.1 - - + -
67B PHE* 4.2 2.0 - - - -
76B LEU* 1.3 75.3 - - - +
78B PHE* 1.3 61.3 + - - +
79B ILE* 3.9 10.3 - - + -
88B ILE* 3.1 8.3 - - - +
89B LEU* 2.6 62.5 + - + +
100B ILE* 5.9 0.2 - - + -
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Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B VAL* 4.3 19.5 - - + -
64B MET* 3.4 5.4 - - - -
65B GLU* 2.9 38.4 + - + +
67B PHE* 3.7 17.5 - - + -
76B LEU 4.0 0.2 + - - -
77B LEU* 1.3 75.5 - - - +
79B ILE* 1.3 68.4 + - - +
80B LEU* 3.9 27.4 - - + -
86B ALA* 4.3 15.7 - - + -
87B CYS 3.7 15.9 - - - -
88B ILE* 4.3 4.7 - - + -
122B GLY* 5.5 1.1 - - - -
124B ILE* 4.4 7.6 - - + -
131B ILE* 3.3 36.8 - - + -
133B LEU* 4.2 21.3 - - + -
143B ILE* 4.9 5.4 - - + -
152B LEU* 5.0 4.7 - - + -
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 4.1 21.8 - - + -
57B MET* 3.7 32.8 - - + -
61B ILE* 3.9 32.5 - - + -
63B VAL 3.5 4.3 - - - +
64B MET* 4.2 9.9 - - + -
77B LEU* 3.9 6.6 + - + -
78B PHE* 1.3 82.0 - - - +
80B LEU* 1.3 70.4 + - - +
81B THR* 4.7 1.8 - - - +
85B ASN 4.8 1.3 - - - +
86B ALA* 3.3 4.9 - - - +
87B CYS* 3.0 45.1 + - - +
89B LEU* 3.7 21.1 - - + -
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 3.9 1.4 - - - -
62B ALA* 3.0 24.9 + - - -
63B VAL* 3.1 39.3 + - + +
78B PHE* 3.9 10.3 - - + -
79B ILE* 1.3 78.1 - - - +
81B THR* 1.3 63.3 + - - +
84B TYR* 3.6 25.8 - - + -
85B ASN 3.3 17.3 - - - +
86B ALA* 3.8 3.6 - - + +
108B VAL* 3.7 17.9 - - + -
120B ILE* 3.8 22.2 - - + -
133B LEU* 4.0 13.0 - - + -
135B LEU* 3.9 15.9 - - + -
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B MET* 5.5 8.3 - - - -
58B TYR 5.1 0.2 - - - +
59B GLY* 2.9 34.3 - - - -
60B LYS 2.9 14.7 + - - -
61B ILE* 4.8 0.9 - - - +
62B ALA* 4.5 1.8 - - - -
79B ILE* 4.7 1.3 - - - +
80B LEU* 1.3 78.7 - - - +
82B ALA* 1.3 51.7 + - - +
83B LYS* 3.4 12.2 + - + +
84B TYR* 2.5 32.1 + - - -
85B ASN* 2.8 61.6 + - + +
120B ILE* 4.6 0.7 - - - +
1068B ILE* 5.6 0.7 - - + -
1073B TRP* 4.9 0.2 - - - -
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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