Contacts of the helix formed by residues 89 - 97 (chain B) in PDB entry 1YCH
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 ALA 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B THR* 3.5 16.1 + - - +
53B VAL 3.0 20.2 + - - +
55B GLU* 4.7 2.2 - - - +
58B LYS* 3.8 32.3 - - + -
61B LEU* 4.2 10.5 - - + -
87B ALA 3.2 0.8 - - - -
88B GLY* 1.3 74.8 - - - +
90B PHE* 1.3 64.4 + - - +
91B PRO* 3.4 2.2 - - - -
92B ALA* 3.4 6.3 + - + +
93B ILE* 3.0 25.3 + - + +
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Residues in contact with PHE 90 (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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52B THR* 3.8 8.8 + - + -
77B LEU* 3.8 14.4 - - + -
79B VAL* 4.7 11.4 - - + -
87B ALA* 3.0 22.4 + - + +
89B ALA* 1.3 74.2 - - - +
91B PRO* 1.4 74.2 - - + +
93B ILE* 3.1 1.9 + - - +
94B MET* 2.8 64.0 + - + +
102B VAL* 4.1 9.4 - - + -
112B LEU* 3.8 34.1 - - + -
116B TYR* 3.8 26.9 - + + -
119B ILE* 4.2 20.0 - - + -
121B PHE* 4.1 18.4 - + - -
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Residues in contact with PRO 91 (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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87B ALA 4.2 1.1 - - - +
88B GLY 3.6 14.8 - - - +
89B ALA 3.6 0.7 - - - -
90B PHE* 1.4 93.9 - - + +
92B ALA* 1.3 56.6 + - - +
94B MET* 3.6 2.5 - - + +
95B GLU* 2.8 32.9 + - - +
116B TYR* 3.9 23.6 - - + -
119B ILE* 3.6 33.3 - - + +
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Residues in contact with ALA 92 (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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58B LYS* 4.0 33.0 - - + +
62B ILE* 4.5 15.6 - - + +
89B ALA* 3.4 10.2 + - + +
90B PHE 3.2 0.6 - - - -
91B PRO* 1.3 81.6 - - - +
93B ILE* 1.3 63.5 + - + +
95B GLU* 3.4 8.6 + - - +
96B LEU* 3.1 22.2 + - - +
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Residues in contact with ILE 93 (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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49B LEU* 4.4 3.1 - - + -
52B THR* 4.2 7.4 - - + -
61B LEU* 3.9 22.9 - - + -
62B ILE* 4.2 17.0 - - + -
65B LEU* 3.8 28.7 - - + -
72B VAL* 5.7 0.9 - - + -
74B LEU* 3.7 22.4 - - + -
77B LEU* 3.5 31.0 - - + -
89B ALA* 3.0 19.3 + - + +
90B PHE 3.9 2.0 - - - +
92B ALA* 1.3 73.9 - - + +
94B MET* 1.3 63.1 + - + +
96B LEU* 2.9 25.6 + - + +
97B CYS* 2.9 14.8 + - + +
100B ALA* 5.6 0.4 - - + -
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Residues in contact with MET 94 (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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77B LEU* 3.1 24.9 - - + -
90B PHE* 2.8 59.6 + - + +
91B PRO* 3.6 4.0 - - + +
93B ILE* 1.3 80.0 - - - +
95B GLU* 1.3 55.8 + - - +
97B CYS 3.1 15.4 - - - +
98B PRO* 3.0 40.4 - - + +
100B ALA* 4.1 17.7 - - + +
102B VAL* 3.9 11.7 - - + -
119B ILE* 4.0 27.4 - - + -
120B ASP 4.6 2.9 - - - +
121B PHE* 4.3 14.4 - - + -
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Residues in contact with GLU 95 (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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91B PRO 2.8 18.2 + - - +
92B ALA* 3.5 9.2 - - - +
93B ILE 3.1 0.2 - - - -
94B MET* 1.3 76.7 - - - +
96B LEU* 1.3 61.4 + - - +
97B CYS 3.7 0.2 + - - -
98B PRO* 3.8 14.3 - - - +
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Residues in contact with LEU 96 (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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62B ILE* 5.1 18.6 - - + -
66B LYS* 4.7 17.7 - - - +
72B VAL* 3.7 31.0 - - + +
92B ALA 3.1 12.7 + - - +
93B ILE* 2.9 18.6 + - + +
95B GLU* 1.3 80.6 - - - +
97B CYS* 1.3 70.7 + - - +
98B PRO* 3.7 3.4 - - - +
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Residues in contact with CYS 97 (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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72B VAL* 3.3 27.8 - - - -
73B LYS 3.7 4.9 - - - +
74B LEU* 3.6 33.9 - - + +
93B ILE 2.9 6.9 + - - +
94B MET* 3.1 10.7 - - - +
96B LEU* 1.3 94.3 - - - +
98B PRO* 1.4 65.1 - - - +
99B ASP* 3.0 7.1 + - + +
100B ALA* 3.1 29.8 + - + +
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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