Contacts of the helix formed by residues 100 - 109 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195B THR* 3.4 24.9 + - - +
231B THR 3.5 10.3 + - - -
232B ALA* 3.4 18.5 - - + +
233B ASP* 4.2 3.1 - - - -
236B GLU* 6.6 0.2 - - + -
96G PHE* 5.9 0.5 - - - +
97G GLU* 3.2 41.1 + - + +
98G GLU 3.2 7.3 - - - +
99G ALA* 1.3 78.3 - - - +
101G LEU* 1.3 61.6 + - - +
102G PRO* 3.3 9.0 - - - +
103G GLY* 2.8 17.3 + - - -
104G LEU* 3.0 18.7 + - - +
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Residues in contact with LEU 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ASP* 4.5 3.6 + - - +
99G ALA 3.9 1.0 - - - -
100G ASN* 1.3 69.8 - - - +
102G PRO* 1.3 66.7 - - + +
104G LEU* 3.0 12.8 + - + -
105G LEU* 2.7 58.8 + - + +
128G PHE* 4.3 15.7 - - + -
136G PHE* 4.1 30.4 - - + -
261G TRP* 4.1 22.4 - - + -
304G LEU* 4.1 30.5 - - + -
308G ILE* 4.2 13.0 - - + -
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Residues in contact with PRO 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B THR* 4.0 20.1 - - + +
232B ALA* 3.7 23.8 - - - +
233B ASP* 3.7 17.0 - - - +
258B ILE* 3.7 25.0 - - + +
259B THR* 6.0 0.7 - - - -
100G ASN* 3.3 9.2 - - - +
101G LEU* 1.3 96.1 - - + +
103G GLY* 1.3 55.6 + - - +
105G LEU* 3.4 4.8 + - + -
106G ALA* 3.0 27.7 + - - +
261G TRP* 4.2 21.8 - - + +
262G GLY* 4.5 2.2 - - - -
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Residues in contact with GLY 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B ASN* 4.7 6.3 - - - +
195B THR* 3.7 26.0 - - - -
231B THR* 4.5 2.9 - - - +
96G PHE* 4.9 4.3 - - - -
100G ASN* 2.8 23.7 + - - -
102G PRO* 1.3 72.5 - - - +
104G LEU* 1.3 62.1 + - - +
106G ALA* 3.2 19.2 + - - +
107G SER* 3.5 7.8 + - - -
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Residues in contact with LEU 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G ILE* 5.1 6.1 - - + -
96G PHE* 4.3 31.7 - - + +
100G ASN 3.0 11.1 + - - +
101G LEU* 3.0 15.6 + - + +
103G GLY* 1.3 74.1 - - - +
105G LEU* 1.3 70.3 + - + +
107G SER* 3.0 13.9 + - - -
108G ILE* 3.0 38.3 + - + +
126G LEU* 4.6 7.9 - - + -
128G PHE* 3.5 34.1 - - + -
132G LEU* 4.1 17.3 - - + -
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Residues in contact with LEU 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ILE* 4.1 5.3 - - + +
284B MET* 4.1 13.0 - - + -
101G LEU* 2.7 41.3 + - + +
102G PRO* 3.7 5.2 - - + +
104G LEU* 1.3 73.0 - - + +
106G ALA* 1.3 58.0 + - - +
108G ILE* 3.9 19.3 - - + -
109G ALA* 3.0 40.3 + - + +
123G LEU* 5.8 0.7 - - + -
126G LEU* 4.6 4.7 - - + -
261G TRP* 3.5 52.0 - - + +
300G VAL* 5.7 1.3 - - + -
304G LEU* 3.8 22.0 - - + -
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Residues in contact with ALA 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B GLU* 3.4 42.8 - - + +
193B ASN* 4.2 3.6 - - - +
255B ASP* 3.5 13.7 - - - +
258B ILE* 3.4 14.5 - - + +
283B ALA* 5.1 0.4 - - - -
102G PRO 3.0 12.9 + - - +
103G GLY* 3.3 14.1 - - - +
104G LEU 3.1 0.4 - - - -
105G LEU* 1.3 76.4 - - - +
107G SER* 1.3 60.5 + - - +
110G GLY* 3.8 14.0 - - - -
111G ASN 4.7 1.0 + - - -
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Residues in contact with SER 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LYS* 6.4 0.2 - - - +
193B ASN* 3.0 33.8 + - - +
49G GLU 4.7 1.1 - - - +
50G SER* 3.2 40.3 + - - +
51G SER* 4.9 0.7 - - - -
96G PHE* 3.5 28.1 - - - -
103G GLY 3.5 2.8 + - - -
104G LEU 3.0 9.2 + - - -
106G ALA* 1.3 82.1 - - - +
108G ILE* 1.3 61.0 + - - +
109G ALA 3.3 2.8 + - - -
110G GLY* 4.1 4.0 + - - -
111G ASN 5.6 0.2 + - - -
112G ILE* 4.5 2.9 - - - +
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Residues in contact with ILE 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G ILE* 5.1 2.2 - - + -
27G ALA* 4.5 7.0 - - + -
29G PHE* 3.2 25.1 - - - -
50G SER* 4.5 4.5 - - - -
91G TYR* 3.6 44.0 - - + -
96G PHE* 4.6 4.3 - - + -
104G LEU* 3.0 33.4 - - + +
105G LEU* 3.9 8.5 - - + -
107G SER* 1.3 80.7 - - - +
109G ALA* 1.3 71.9 + - + +
110G GLY 3.9 0.2 - - - -
112G ILE* 3.6 4.8 - - - +
123G LEU* 4.0 6.7 - - + +
126G LEU* 3.5 36.8 - - + -
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Residues in contact with ALA 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B MET* 3.2 41.6 - - + +
105G LEU* 3.0 17.7 + - + +
108G ILE* 1.3 91.5 - - + +
110G GLY* 1.3 58.5 + - - +
112G ILE* 4.4 1.8 - - - -
113G PHE* 3.4 25.3 - - + -
123G LEU* 4.1 11.4 - - + -
296G ILE* 4.4 4.0 - - + -
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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