Contacts of the helix formed by residues 100 - 109 (chain B) in PDB entry 3KDO
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 ASN 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B PHE* 6.0 0.5 - - - +
97B GLU* 2.9 50.2 + - + +
98B GLU 3.2 0.8 - - - -
99B ALA* 1.3 77.2 - - - +
101B LEU* 1.3 61.0 + - - +
102B PRO* 3.4 3.1 - - - +
103B GLY* 2.8 17.3 + - - -
104B LEU* 3.1 17.4 + - - +
195G THR* 3.5 13.3 + - - +
231G THR 3.4 19.8 + - - -
232G ALA* 3.4 23.6 - - + +
233G ASP* 4.1 2.9 - - - -
236G GLU* 6.6 0.2 - - + -
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Residues in contact with LEU 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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99B ALA 3.9 1.6 + - - -
100B ASN* 1.3 70.7 - - - +
102B PRO* 1.3 77.9 - - + +
104B LEU* 2.9 11.5 + - + +
105B LEU* 2.9 43.6 + - + +
128B PHE* 4.6 12.8 - - + -
136B PHE* 4.2 27.3 - - + -
261B TRP* 4.0 25.1 - - + -
265B ARG* 6.2 0.2 - - - +
304B LEU* 4.1 28.9 - - + -
308B ILE* 4.2 17.0 - - + -
233G ASP* 4.3 5.1 + - - +
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Residues in contact with PRO 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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100B ASN* 3.4 8.1 - - - +
101B LEU* 1.3 97.7 - - + +
103B GLY* 1.3 61.5 + - - +
105B LEU* 3.3 1.9 + - + -
106B ALA* 3.0 22.2 + - - +
261B TRP* 4.1 27.6 - - + +
262B GLY* 4.6 1.8 - - - -
231G THR* 3.9 20.7 - - + +
232G ALA 3.6 23.6 - - - +
233G ASP* 3.8 13.7 - - - +
258G ILE* 3.7 25.5 - - + +
259G THR* 6.0 0.4 - - - -
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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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96B PHE* 5.1 2.8 - - - -
100B ASN* 2.8 20.1 + - - -
102B PRO* 1.3 76.4 - - - +
104B LEU* 1.3 61.5 + - - +
106B ALA* 3.2 19.9 - - - +
107B SER* 3.5 8.3 + - - -
193G ASN* 4.5 6.4 - - - +
195G THR* 3.7 25.8 - - - -
231G THR* 4.5 3.5 - - - +
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Residues in contact with LEU 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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25B ILE* 4.7 5.4 - - + -
96B PHE* 4.1 37.6 - - + +
100B ASN 3.1 11.3 + - - +
101B LEU* 2.9 14.4 + - + +
103B GLY* 1.3 74.8 - - - +
105B LEU* 1.3 63.2 + - + +
107B SER* 3.0 17.7 + - - -
108B ILE* 3.0 38.1 + - + -
126B LEU* 4.4 12.1 - - + -
128B PHE* 3.9 28.0 - - + -
132B LEU* 3.9 17.9 - - + -
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Residues in contact with LEU 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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101B LEU* 2.9 34.1 + - + +
102B PRO 3.8 4.3 - - - +
104B LEU* 1.3 73.6 - - + +
106B ALA* 1.3 60.5 + - - +
108B ILE* 3.6 22.4 - - + -
109B ALA* 2.9 39.8 + - + +
123B LEU* 5.7 0.9 - - + -
126B LEU* 4.5 5.6 - - + -
261B TRP* 3.5 52.3 - - + +
296B ILE* 6.3 0.2 - - + -
300B VAL* 5.6 1.8 - - + -
304B LEU* 4.0 19.1 - - + -
258G ILE* 3.8 6.5 - - + +
284G MET* 4.0 13.9 - - + -
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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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102B PRO 3.0 12.7 + - - +
103B GLY* 3.2 15.9 - - - +
105B LEU* 1.3 76.8 - - - +
107B SER* 1.3 57.3 + - - +
110B GLY* 3.7 15.2 - - - -
111B ASN 4.7 1.2 + - - -
192G GLU* 3.4 42.2 - - + +
193G ASN* 4.0 5.8 - - - +
255G ASP* 3.4 13.5 - - - +
258G ILE* 3.3 13.8 - - + +
283G ALA* 5.0 0.9 - - + -
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Residues in contact with SER 107 (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 GLU 4.6 0.9 - - - +
50B SER* 3.1 39.6 + - - +
51B SER* 5.1 0.3 - - - -
96B PHE* 3.7 24.7 - - - -
103B GLY 3.5 3.4 + - - -
104B LEU 3.0 9.5 + - - -
106B ALA* 1.3 81.3 - - - +
108B ILE* 1.3 61.4 + - - +
109B ALA 3.3 3.3 + - - -
110B GLY* 4.2 3.3 + - - -
111B ASN 5.6 0.2 + - - -
112B ILE* 4.5 2.8 - - - +
193G ASN* 3.0 35.4 + - - +
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Residues in contact with ILE 108 (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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25B ILE* 5.1 2.0 - - + -
27B ALA* 4.6 12.1 - - + -
29B PHE* 3.4 24.4 - - - -
50B SER* 4.5 4.3 - - - -
91B TYR* 3.7 43.3 - - + +
96B PHE* 4.6 4.0 - - + -
104B LEU* 3.1 28.7 - - + +
105B LEU* 3.6 23.8 - - + -
107B SER* 1.3 78.4 - - - +
109B ALA* 1.3 72.9 + - + +
110B GLY 3.9 0.4 - - - -
112B ILE* 3.7 6.0 - - - +
123B LEU* 4.1 9.2 - - + +
126B LEU* 3.8 20.6 - - + -
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Residues in contact with ALA 109 (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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105B LEU* 2.9 16.6 + - + +
108B ILE* 1.3 92.4 - - + +
110B GLY* 1.3 58.0 + - - +
112B ILE* 4.5 1.3 - - - -
113B PHE* 3.3 29.9 - - + -
123B LEU* 4.3 7.2 - - + -
296B ILE* 4.2 7.6 - - + -
284G MET* 3.2 39.4 - - + +
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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