Contacts of the strand formed by residues 80 - 87 (chain B) in PDB entry 2P80
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 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ALA* 4.0 9.7 - - - +
9B ILE* 4.7 10.8 - - + -
12B LEU* 4.2 24.5 - - + -
36B PRO* 4.9 5.2 - - + -
37B LYS 3.6 4.7 + - - -
38B VAL* 3.4 14.2 - - + +
39B VAL* 2.8 31.2 + - - +
75B VAL* 5.7 0.2 - - - -
78B ASP 3.2 14.8 - - - -
79B ASP* 1.3 75.5 - - - +
81B LEU* 1.3 60.6 + - - +
82B GLU 3.7 0.3 + - - -
123B ARG* 3.8 29.6 - - + -
124B PHE 3.3 8.1 - - - +
125B LYS* 2.8 64.5 + - + -
329C ASP* 2.9 29.0 + - - -
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Residues in contact with LEU 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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39B VAL* 3.8 4.5 - - - -
41B PHE* 4.2 10.8 - - + -
73B MET* 4.0 33.0 - - + -
75B VAL* 4.2 22.0 - - + -
79B ASP 3.9 1.6 + - - -
80B TYR* 1.3 72.4 - - - +
82B GLU* 1.3 64.9 + - - +
83B LEU* 3.7 26.5 - - + -
99B PHE* 5.6 2.7 - - + -
122B LEU 3.5 1.8 - - - +
123B ARG* 3.2 2.2 - - - -
124B PHE* 3.0 66.0 + - + -
154B ILE* 4.1 17.3 - - + -
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Residues in contact with GLU 82 (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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14B ARG* 5.5 3.6 + - - +
38B VAL* 4.0 16.2 - - + +
39B VAL 2.8 17.0 + - - +
40B GLU* 3.4 23.4 - - + +
41B PHE 3.0 24.3 + - - +
80B TYR 3.7 0.4 + - - -
81B LEU* 1.3 75.6 - - - +
83B LEU* 1.3 61.1 + - - +
84B THR* 4.1 1.4 + - - +
121B ILE* 3.5 30.0 - - + +
122B LEU 3.4 2.5 - - - +
123B ARG* 3.5 23.8 + - + +
334C VAL* 3.4 22.8 - - - +
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Residues in contact with LEU 83 (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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41B PHE* 3.1 32.8 - - + +
43B MET* 3.8 37.2 - - + +
73B MET* 4.6 2.9 - - - -
81B LEU* 3.7 17.9 - - + +
82B GLU* 1.3 75.3 - - - +
84B THR* 1.3 64.6 + - - +
85B LEU* 3.4 14.3 + - + +
97B ILE* 3.8 36.8 - - + -
99B PHE* 3.8 13.9 - - + -
120B THR* 4.6 0.5 - - - +
121B ILE* 3.6 1.6 - - - -
122B LEU* 3.0 36.7 + - + +
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Residues in contact with THR 84 (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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41B PHE 2.9 7.9 + - - -
42B THR* 3.2 22.9 + - + +
43B MET 3.1 22.7 + - - -
82B GLU* 4.1 1.5 + - - +
83B LEU* 1.3 71.5 - - - +
85B LEU* 1.3 59.5 + - - +
86B ILE* 4.1 21.3 - - + -
119B LYS* 4.4 13.2 - - + +
120B THR 3.3 13.5 - - - +
121B ILE* 3.0 31.5 - - + +
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Residues in contact with LEU 85 (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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43B MET* 3.0 31.6 - - + +
45B ILE* 3.2 23.3 - - + -
64B PHE* 3.4 35.2 - - + -
83B LEU* 3.4 20.6 + - + +
84B THR* 1.3 71.6 - - - +
86B ILE* 1.3 63.9 + - - +
96B ASN* 4.8 4.0 - - - -
97B ILE* 4.5 22.2 - - + +
112B THR* 5.0 4.0 - - + +
114B ILE* 3.8 17.7 - - + +
119B LYS* 3.0 20.1 - - - +
120B THR* 3.1 23.8 + - + +
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Residues in contact with ILE 86 (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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42B THR* 4.0 26.0 - - + -
43B MET 3.2 4.6 + - - -
44B VAL* 3.4 21.9 - - + -
45B ILE* 3.0 27.7 + - - +
84B THR* 4.1 7.4 - - + -
85B LEU* 1.3 86.4 - - - +
87B ASN* 1.3 67.5 + - - +
88B PRO* 3.1 9.9 - - + +
114B ILE* 4.2 2.2 - - - -
118B GLU 4.8 1.6 - - - +
119B LYS* 3.2 36.1 - - + +
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Residues in contact with ASN 87 (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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45B ILE* 4.3 5.1 - - + +
86B ILE* 1.3 73.5 - - - +
88B PRO* 1.3 55.8 - - - +
91B ASN* 2.6 35.1 + - - +
93B LEU 3.1 25.7 + - - -
95B HIS* 3.5 14.5 - - - -
114B ILE* 3.3 36.3 + - + +
115B ASN 4.4 1.6 - - - +
116B PRO* 3.5 16.3 - - - +
117B GLY* 2.8 31.4 + - - -
118B GLU 3.2 15.7 + - - +
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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