Contacts of the strand formed by residues 80 - 87 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A ASP* 3.0 29.0 + - - -
4C ALA* 4.0 10.2 - - - +
9C ILE* 4.6 11.0 - - + -
12C LEU* 4.1 21.7 - - + +
36C PRO* 4.8 4.9 - - + -
37C LYS 3.5 5.4 + - - -
38C VAL* 3.3 21.9 - - + +
39C VAL* 2.9 29.7 + - - +
78C ASP 3.1 14.4 - - - -
79C ASP* 1.3 75.3 - - - +
81C LEU* 1.3 61.3 + - - +
82C GLU 3.7 0.2 + - - -
123C ARG* 3.9 25.4 - - + -
124C PHE 3.2 8.5 - - - +
125C LYS* 2.9 65.0 + - + -
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Residues in contact with LEU 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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39C VAL* 3.8 7.2 - - - +
41C PHE* 4.8 7.0 - - + -
73C MET* 3.9 33.4 - - + -
75C VAL* 4.1 28.7 - - + -
79C ASP 3.9 2.2 + - - -
80C TYR* 1.3 70.7 - - - +
82C GLU* 1.3 65.8 + - - +
83C LEU* 3.7 26.7 - - + -
99C PHE* 5.6 4.0 - - + -
122C LEU 3.5 2.0 - - - +
123C ARG* 3.3 2.2 - - - -
124C PHE* 3.0 64.4 + - + -
154C ILE* 4.3 12.6 - - + -
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Residues in contact with GLU 82 (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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334A VAL* 3.5 14.6 - - - +
14C ARG* 5.1 5.4 + - - -
38C VAL* 3.9 16.4 - - + +
39C VAL 2.8 16.6 + - - +
40C GLU* 3.4 21.2 - - + +
41C PHE 3.0 23.7 + - - +
80C TYR 3.7 0.2 + - - -
81C LEU* 1.3 73.2 - - - +
83C LEU* 1.3 61.2 + - - +
84C THR* 4.0 0.8 + - - +
121C ILE* 3.5 30.0 - - + +
122C LEU 3.4 2.7 - - - +
123C ARG* 3.3 34.6 + - + +
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Residues in contact with LEU 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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41C PHE* 3.1 31.9 - - + +
43C MET* 3.9 36.3 - - + +
73C MET* 4.6 4.0 - - - -
81C LEU* 3.7 17.4 - - + +
82C GLU* 1.3 76.1 - - - +
84C THR* 1.3 66.4 + - - +
85C LEU* 3.5 14.1 + - + +
97C ILE* 4.0 21.1 - - + -
99C PHE* 3.9 29.2 - - + -
120C THR* 3.8 0.3 - - - +
121C ILE* 3.6 1.8 - - - -
122C LEU* 3.0 35.6 + - + +
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Residues in contact with THR 84 (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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41C PHE 3.0 8.3 + - - -
42C THR* 3.1 39.6 + - + +
43C MET 3.2 6.9 + - - -
82C GLU* 4.0 1.3 + - - +
83C LEU* 1.3 71.1 - - - +
85C LEU* 1.3 59.1 + - - +
86C ILE* 4.1 21.1 - - + -
119C LYS* 4.3 13.2 - - + +
120C THR 3.3 13.0 - - - +
121C ILE* 2.9 32.6 - - + +
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Residues in contact with LEU 85 (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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43C MET* 2.8 35.4 - - + +
45C ILE* 3.2 24.5 - - + -
64C PHE* 3.2 36.6 - - + -
83C LEU* 3.5 15.7 + - + +
84C THR* 1.3 70.9 - - - +
86C ILE* 1.3 72.5 + - - +
96C ASN* 4.9 8.1 - - - -
97C ILE* 4.7 14.4 - - + +
112C THR* 5.0 3.8 - - + +
114C ILE* 3.7 19.3 - - + -
119C LYS* 3.1 13.9 - - - +
120C THR* 3.0 22.3 + - + +
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Residues in contact with ILE 86 (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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42C THR* 3.9 25.8 - - + -
43C MET 3.3 4.6 + - - -
44C VAL* 3.4 21.7 - - + -
45C ILE* 3.1 26.9 + - - -
84C THR* 4.1 5.6 - - + -
85C LEU* 1.3 87.5 - - - +
87C ASN* 1.3 69.5 + - - +
88C PRO* 3.1 10.0 - - + +
114C ILE* 4.2 1.1 - - - -
118C GLU 4.7 0.9 - - - +
119C LYS* 3.3 35.9 - - + +
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Residues in contact with ASN 87 (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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45C ILE* 4.4 5.2 - - + +
86C ILE* 1.3 74.3 - - - +
88C PRO* 1.3 55.2 - - - +
91C ASN* 2.5 36.2 + - - +
93C LEU 3.0 26.3 + - - -
95C HIS* 3.6 13.3 - - - -
114C ILE* 3.3 32.9 + - + +
115C ASN 4.2 1.6 - - - +
116C PRO* 3.4 16.9 - - - +
117C GLY* 2.8 31.9 + - - -
118C GLU 3.2 21.4 + - - +
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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