Contacts of the helix formed by residues 84 - 90 (chain B) in PDB entry 2O1X
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 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ILE* 4.0 5.2 - - - -
78B PHE* 4.0 29.2 - - + -
81B GLY 3.5 16.1 + - - +
82B HIS 3.2 5.3 + - - -
83B GLN* 1.3 78.7 - - - +
85B TYR* 1.3 66.5 + - - +
86B ALA 3.4 2.0 - - - -
87B HIS* 3.1 25.2 - - + +
88B LYS* 3.2 12.9 + - + +
110B THR* 4.1 10.1 - - + -
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Residues in contact with TYR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 4.1 15.0 - - + -
44B VAL* 4.6 6.7 - - + -
45B CYS* 3.9 23.8 - - - -
50B LEU* 3.6 13.6 - - + +
51B HIS* 3.2 46.4 + + + -
55B SER* 3.4 22.6 + - - +
81B GLY 5.2 0.2 - - - -
82B HIS 3.7 11.9 - - - -
83B GLN 3.7 0.8 + - - -
84B ALA* 1.3 77.0 - - - +
86B ALA* 1.3 60.8 + - - +
88B LYS* 3.2 9.1 + - + +
89B ILE* 2.9 34.6 + - - +
97B MET* 3.8 20.1 - - + +
100B ILE* 3.6 31.3 - - + +
101B LYS* 4.8 2.1 - - - +
108B GLY 3.7 16.3 + - - -
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.0 21.5 - - + -
41B ILE* 3.8 16.7 - - + +
55B SER* 5.3 1.1 - - - +
59B VAL* 4.3 16.4 - - + +
62B ILE* 4.0 20.8 - - + +
84B ALA 3.4 0.2 - - - -
85B TYR* 1.3 72.9 - - - +
87B HIS* 1.3 56.2 + - - +
89B ILE* 3.2 12.4 + - - +
90B LEU* 2.8 39.4 + - - +
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Residues in contact with HIS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 3.6 13.1 - - + +
66B HIS* 2.9 35.8 + + - -
76B ILE* 5.2 4.3 - - + -
78B PHE* 3.5 38.7 - + + -
84B ALA 3.1 14.4 + - - +
86B ALA* 1.3 77.7 - - - +
88B LYS* 1.3 58.9 + - + +
90B LEU* 3.1 10.1 + - - -
91B THR* 2.5 31.6 + - + +
93B ARG* 3.5 8.0 + - - -
110B THR* 4.2 12.0 - - + +
117B HIS* 3.3 25.7 + - + -
118B ASP* 2.9 27.9 + - - -
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Residues in contact with LYS 88 (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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81B GLY 6.0 0.2 - - - -
84B ALA* 3.2 15.0 + - - +
85B TYR* 3.2 11.3 + - + +
87B HIS* 1.3 76.1 - - + +
89B ILE* 1.3 64.3 - - - +
91B THR* 3.0 18.5 + - - -
93B ARG* 3.2 57.9 + - + +
97B MET* 3.9 15.7 - - - -
100B ILE* 5.0 3.4 - - + -
106B ILE* 4.2 11.0 - - + -
107B SER 2.8 19.4 + - - +
108B GLY 5.4 1.3 - - - -
109B PHE* 2.7 35.5 + - - +
110B THR* 4.2 6.1 - - - +
114B GLU* 3.1 19.2 + - - +
118B ASP* 3.8 7.1 + - - -
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Residues in contact with ILE 89 (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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13B LEU* 3.7 27.2 - - + +
16B ILE 4.8 5.2 - - - +
17B HIS 6.0 0.3 - - - -
37B LEU* 3.3 28.7 - - + -
40B GLU* 4.3 16.8 - - + -
41B ILE* 3.6 31.6 - - + +
44B VAL* 5.2 0.7 - - + -
85B TYR 2.9 23.1 + - - +
86B ALA* 3.5 7.9 - - - +
88B LYS* 1.3 74.9 - - - +
90B LEU* 1.3 59.9 + - - +
91B THR 3.6 0.5 + - - -
92B GLY 4.5 3.5 + - - -
94B ARG* 4.2 25.1 + - + +
97B MET* 4.1 26.7 - - + -
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Residues in contact with LEU 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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13B LEU* 4.7 6.1 - - + -
16B ILE* 4.4 19.0 - - + +
17B HIS 5.2 0.2 - - - -
18B GLY* 3.4 21.8 - - - -
19B PRO* 3.4 11.5 - - + +
22B LEU* 4.6 16.4 - - + -
33B LEU* 4.3 16.2 - - + -
37B LEU* 3.9 35.2 - - + -
62B ILE* 4.4 18.2 - - + +
63B THR* 4.4 17.3 - - + +
66B HIS* 4.8 8.7 - - + -
86B ALA 2.8 22.2 + - - +
87B HIS* 3.1 4.0 + - - +
89B ILE* 1.3 75.8 - - - +
91B THR* 1.3 61.4 + - + +
92B GLY 3.8 1.8 - - - -
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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