Contacts of the helix formed by residues 63 - 70 (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 GLU 63 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LYS* 2.6 34.1 + - - +
355A LYS* 2.9 32.7 + - - +
357A TYR* 3.1 15.5 + - - -
172B GLU* 2.9 20.4 + - - +
62G TYR* 1.3 77.1 - - - +
64G GLN* 1.3 65.8 + - - +
65G GLU* 3.4 29.9 + - - +
66G ARG* 3.5 15.9 + - - +
67G TRP 3.4 15.4 + - - -
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Residues in contact with GLN 64 (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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58G LEU* 5.9 0.2 - - - +
60G PRO* 5.2 12.3 - - + +
62G TYR* 3.3 37.8 + - - +
63G GLU* 1.3 72.9 - - - +
65G GLU* 1.3 72.7 + - + +
67G TRP* 3.4 26.4 + - - +
68G ALA* 3.0 27.5 + - - +
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Residues in contact with GLU 65 (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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21A LYS* 4.8 25.3 + - + +
22A LYS* 4.2 14.8 - - + +
63G GLU* 3.3 22.4 - - - +
64G GLN* 1.3 87.7 + - + +
66G ARG* 1.3 61.7 + - - +
68G ALA* 3.6 5.0 + - - +
69G ASP* 3.1 24.3 + - - +
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Residues in contact with ARG 66 (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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22A LYS* 4.0 19.5 - - - +
130A GLU* 2.7 41.2 + - - +
357A TYR* 3.9 5.9 - - - -
167B GLY* 2.9 29.3 + - - +
168B TYR* 3.6 3.2 - - - +
169B SER* 3.9 9.9 - - - -
172B GLU* 3.1 38.7 + - - -
198B TRP* 4.2 7.2 - - + -
199B TYR* 3.8 25.2 - - - +
63G GLU* 3.5 25.2 + - - +
64G GLN 3.3 0.2 - - - -
65G GLU* 1.3 76.7 - - - +
67G TRP* 1.3 66.1 + - - +
69G ASP* 2.9 15.8 + - + +
70G LEU* 3.1 27.7 + - + +
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Residues in contact with TRP 67 (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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164B PRO* 3.2 38.0 - - + +
166B VAL 4.2 1.8 - - - -
167B GLY* 3.9 13.5 + - - +
11G TYR* 3.7 46.0 - + + -
12G TYR* 3.7 18.2 + + - -
52G THR* 3.4 23.0 + - - +
62G TYR* 3.3 34.9 + + + -
63G GLU 3.4 2.4 + - - -
64G GLN* 3.5 28.9 - - - +
66G ARG* 1.3 80.7 - - - +
68G ALA* 1.3 81.6 + - + +
69G ASP 3.3 0.3 + - - -
70G LEU* 3.3 7.8 + - - -
71G SER* 3.0 23.1 + - - -
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Residues in contact with ALA 68 (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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11G TYR* 3.3 25.8 + - - +
64G GLN* 3.0 18.6 + - - +
65G GLU* 4.1 4.7 - - - +
67G TRP* 1.3 90.8 - - + +
69G ASP* 1.3 59.9 + - - +
70G LEU 3.3 0.6 + - - -
71G SER* 3.8 11.4 + - - +
73G LYS* 5.5 2.3 - - - -
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Residues in contact with ASP 69 (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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20A SER* 4.6 3.3 + - - -
22A LYS* 3.7 27.5 - - + +
23A ARG* 2.5 61.0 + - - +
198B TRP* 5.2 1.4 - - - -
65G GLU 3.1 18.2 + - - +
66G ARG* 2.9 8.6 + - - +
68G ALA* 1.3 79.6 - - - +
70G LEU* 1.3 60.7 + - - +
71G SER 3.4 1.7 + - - +
92G PRO* 3.7 4.9 - - - +
94G HIS* 2.6 27.9 + - - -
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Residues in contact with LEU 70 (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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166B VAL* 5.3 2.5 - - + +
167B GLY* 3.9 21.8 - - - -
198B TRP* 4.3 4.5 - - + -
199B TYR* 3.8 31.0 - - + -
51G SER* 4.4 5.4 - - - -
52G THR* 4.0 15.1 - - + +
66G ARG* 3.1 25.3 + - + +
67G TRP 3.3 4.0 + - - +
69G ASP* 1.3 79.7 - - - +
71G SER* 1.3 63.5 + - - +
72G ALA 3.8 1.0 + - - -
91G TYR* 5.8 0.7 - - - -
92G PRO* 4.0 8.7 - - - +
94G HIS* 3.1 49.8 - - + +
95G ALA* 3.9 23.5 - - + +
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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