Contacts of the helix formed by residues 90 - 97 (chain N) in PDB entry 3O3U
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 90 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89N LEU* 1.3 73.2 - - - +
91N PRO* 1.3 75.8 - - + +
92N PHE* 3.8 29.8 - + + -
93N THR* 2.7 28.5 + - + -
94N TRP* 3.4 4.2 + - - -
302N VAL 3.9 4.5 - - - -
303N ALA* 3.1 27.0 + - - -
305N LYS* 3.8 37.0 + - + +
308N GLU* 2.5 51.5 + - + +
309N GLU* 4.3 7.2 + - - +
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Residues in contact with PRO 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89N LEU 3.4 6.0 - - - +
90N TYR* 1.3 88.5 - - + +
92N PHE* 1.3 63.2 + - + +
94N TRP* 3.1 14.9 + - + +
95N ASP* 3.1 29.4 + - - +
305N LYS* 4.5 9.6 - - - +
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Residues in contact with PHE 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90N TYR* 3.3 29.4 - + + -
91N PRO* 1.3 80.1 - - + +
93N THR* 1.3 66.9 + - + +
95N ASP* 3.4 15.3 + - + +
96N ALA* 3.3 19.1 + - - +
110N VAL* 3.7 40.6 - - + -
259N VAL* 5.3 2.5 - - + -
261N VAL* 5.2 4.0 - - + -
321N MET* 5.7 5.2 - - - -
329N ILE* 5.1 14.2 - - + +
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Residues in contact with THR 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89N LEU* 4.2 2.4 - - - +
90N TYR* 2.7 26.8 + - + +
92N PHE* 1.3 92.9 - - + +
94N TRP* 1.3 64.6 + - - +
96N ALA* 3.2 20.0 + - - +
97N VAL* 3.6 4.5 + - - +
107N PRO* 3.6 34.3 - - - +
110N VAL* 3.7 30.3 - - + -
261N VAL* 4.4 5.6 - - + -
303N ALA* 3.7 20.1 - - + +
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Residues in contact with TRP 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79N ILE* 3.9 21.5 - - + -
81N PRO* 3.9 16.6 - - + -
85N PHE* 4.0 15.9 - + - -
86N GLN* 2.9 54.0 + - + +
89N LEU* 3.5 27.5 - - + +
90N TYR 3.4 17.0 + - - -
91N PRO* 3.1 11.7 + - + +
93N THR* 1.3 78.4 + - - +
95N ASP* 1.3 66.3 + - - +
97N VAL* 3.1 18.2 + - + +
98N ARG* 3.3 29.1 + - - +
103N LEU* 3.9 26.7 - - + +
105N ALA 3.9 0.9 - - - -
106N TYR* 4.1 5.4 - + - -
107N PRO* 3.4 26.2 - - + -
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Residues in contact with ASP 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91N PRO* 3.1 18.1 + - - +
92N PHE* 3.6 17.0 - - + +
93N THR 3.2 0.2 - - - -
94N TRP* 1.3 76.7 - - - +
96N ALA* 1.3 62.3 + - - +
97N VAL 3.2 0.9 + - - -
98N ARG* 2.7 52.0 + - - +
332N ASN* 4.7 1.2 + - - -
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Residues in contact with ALA 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64N HIS* 3.4 40.8 - - + +
67N PHE* 6.1 0.3 - - - +
92N PHE 3.3 7.2 + - - +
93N THR 3.2 10.9 + - - +
94N TRP 3.1 0.8 - - - -
95N ASP* 1.3 80.5 - - - +
97N VAL* 1.3 57.6 + - + +
98N ARG 3.5 0.2 - - - -
261N VAL* 3.8 24.5 - - + -
329N ILE* 4.6 9.0 - - + -
332N ASN* 3.2 18.2 + - - +
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Residues in contact with VAL 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64N HIS* 4.3 5.6 - - + -
67N PHE* 5.9 0.9 - - + -
93N THR 3.7 11.9 - - - +
94N TRP* 3.3 27.8 - - + +
96N ALA* 1.3 79.7 - - + +
98N ARG* 1.3 59.0 + - - +
103N LEU* 3.6 3.7 - - + -
104N ILE* 3.0 37.7 + - + +
105N ALA* 3.2 35.2 - - + +
107N PRO* 3.9 7.2 - - + -
263N SER* 3.2 34.3 - - - +
332N ASN* 4.5 0.4 - - - +
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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