Contacts of the helix formed by residues 100 - 106 (chain B) in PDB entry 1WKJ
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 THR 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B ARG* 3.7 1.8 - - - -
86B LYS 3.6 19.5 - - - +
87B MET* 3.2 12.8 - - - +
88B MET 3.7 1.7 + - - -
89B GLY* 3.6 20.1 - - - -
96B ALA* 3.8 2.1 - - - +
97B LEU* 2.7 33.4 + - + +
98B PRO 4.7 0.7 - - - +
99B GLY* 1.3 80.3 - - - +
101B ILE* 1.3 60.8 + - - +
103B GLY* 3.0 15.4 + - - -
104B ASP* 2.9 31.2 + - - -
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Residues in contact with ILE 101 (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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21B ILE* 4.2 27.1 - - + -
24B ARG* 3.7 31.4 - - + +
25B PHE* 3.6 33.9 - - + -
87B MET* 2.9 23.7 + - + +
88B MET* 4.0 10.5 - - - -
100B THR* 1.3 72.8 - - - +
102B ARG* 1.3 59.1 + - - +
105B PHE* 2.9 47.3 + - + +
113B VAL* 4.5 5.4 - - + -
114B ILE* 4.1 27.8 - - + -
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Residues in contact with ARG 102 (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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85B ARG* 5.1 6.3 + - - +
88B MET* 2.9 39.9 + - - +
89B GLY 2.7 22.6 + - - -
90B ALA 3.0 21.9 + - - +
91B THR* 3.7 24.1 + - - +
93B PRO* 4.1 6.2 - - + +
96B ALA* 4.0 5.2 - - + -
101B ILE* 1.3 74.4 - - + +
103B GLY* 1.3 62.0 + - - +
106B ALA* 3.0 41.9 + - + +
112B ASN* 3.1 48.5 - - - +
113B VAL* 5.2 1.1 - - + -
114B ILE* 2.8 40.8 + - + +
115B HIS* 4.5 2.4 - - - +
116B GLY 5.3 0.2 - - - +
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Residues in contact with GLY 103 (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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93B PRO 4.7 2.7 - - - -
96B ALA* 3.5 19.4 - - - +
97B LEU 3.7 8.3 - - - -
98B PRO* 4.7 5.3 - - - +
100B THR* 3.0 20.9 + - - -
102B ARG* 1.3 80.3 - - - +
104B ASP* 1.3 63.4 + - - +
106B ALA 4.8 3.6 - - - +
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Residues in contact with ASP 104 (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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24B ARG* 2.9 39.2 + - - +
98B PRO* 3.7 5.4 - - - +
99B GLY* 2.9 29.2 + - - -
100B THR 2.9 14.9 + - - +
103B GLY* 1.3 81.2 - - - +
105B PHE* 1.3 70.2 + - + +
106B ALA 3.9 0.2 - - - -
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Residues in contact with PHE 105 (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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15B ARG* 2.8 37.6 + - - +
17B LEU* 3.7 33.7 - - + -
20B GLU* 3.7 44.6 - - + -
21B ILE* 4.8 9.6 - - + -
24B ARG* 3.6 37.2 - - - -
101B ILE* 2.9 38.3 + - + +
104B ASP* 1.3 84.9 - - + +
106B ALA* 1.3 58.4 + - - +
107B THR* 5.5 1.3 - - - +
113B VAL* 4.4 7.6 - - + -
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Residues in contact with ALA 106 (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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15B ARG* 4.6 2.0 - - - +
93B PRO* 3.4 29.1 - - + +
102B ARG* 3.0 23.7 + - - +
103B GLY 4.8 3.6 - - - +
104B ASP 5.4 0.2 - - - -
105B PHE* 1.3 79.7 - - - +
107B THR* 1.3 66.8 + - - +
111B GLU 4.0 2.9 - - - +
112B ASN* 3.9 21.1 - - - -
113B VAL* 4.0 11.2 - - + -
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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