Contacts of the helix formed by residues 63 - 71 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LYS* 2.7 35.5 + - - +
355C LYS* 2.6 37.6 + - - +
357C TYR* 2.9 18.3 + - - -
167D GLY 4.4 1.4 - - - +
172D GLU* 2.9 20.1 + - - +
62J TYR* 1.3 72.7 - - - +
64J GLN* 1.3 64.9 + - - +
65J GLU* 3.3 23.0 - - - +
66J ARG* 3.3 21.5 + - - +
67J TRP* 3.2 20.3 + - - +
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Residues in contact with GLN 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J PRO* 4.3 16.7 - - + +
62J TYR* 3.1 32.7 + - - +
63J GLU* 1.3 71.0 - - - +
65J GLU* 1.3 77.8 + - - +
67J TRP* 3.1 31.5 + - - +
68J ALA* 2.9 27.0 + - - +
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Residues in contact with GLU 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LYS* 5.3 14.8 - - + +
22C LYS* 3.9 15.4 - - + +
63J GLU* 3.3 28.0 - - - +
64J GLN* 1.3 85.7 + - - +
66J ARG* 1.3 61.8 + - - +
68J ALA* 3.6 4.1 + - - +
69J ASP* 3.1 25.5 + - - +
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Residues in contact with ARG 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LYS* 3.9 12.8 - - - +
130C GLU* 3.1 39.1 + - - +
357C TYR* 4.2 4.0 - - - -
167D GLY 2.9 19.8 + - - +
168D TYR* 3.3 6.3 - - - +
169D SER* 3.0 19.2 - - - +
172D GLU* 2.3 43.6 + - - -
198D TRP* 4.3 6.3 - - + -
199D TYR* 4.1 18.6 - - - +
63J GLU* 3.3 39.3 + - - +
64J GLN 3.2 0.6 - - - -
65J GLU* 1.3 76.4 - - - +
67J TRP* 1.3 66.3 + - - +
69J ASP* 3.3 4.5 + - + +
70J LEU* 3.3 40.6 + - + +
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Residues in contact with TRP 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D PRO* 3.3 34.8 - - + +
166D VAL 4.2 1.8 - - - -
167D GLY* 4.1 13.8 + - - +
11J TYR* 3.6 43.7 - + + -
12J TYR* 3.5 22.6 + + - -
52J THR* 3.2 26.8 + - - +
62J TYR* 3.7 31.0 - + + -
63J GLU 3.2 2.2 + - - -
64J GLN* 3.1 29.7 + - - +
66J ARG* 1.3 78.9 - - - +
68J ALA* 1.3 81.5 + - + +
70J LEU* 3.1 11.4 + - - +
71J SER* 2.8 25.1 + - - -
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Residues in contact with ALA 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J TYR* 3.4 22.8 + - - +
64J GLN* 2.9 17.0 + - - +
65J GLU* 4.1 4.7 - - - +
67J TRP* 1.3 90.2 - - + +
69J ASP* 1.3 62.1 + - - +
70J LEU 3.2 0.7 + - - -
71J SER* 3.3 17.6 + - - +
73J LYS* 5.4 5.4 - - - -
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Residues in contact with ASP 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C SER* 4.2 3.8 + - - -
22C LYS* 3.6 28.3 - - + +
23C ARG* 2.6 49.6 + - - +
198D TRP* 5.4 1.6 - - - -
65J GLU 3.1 19.2 + - - +
66J ARG* 3.6 6.1 - - - +
67J TRP 3.2 0.2 - - - -
68J ALA* 1.3 77.2 - - - +
70J LEU* 1.3 62.2 + - - +
71J SER 3.5 1.4 - - - +
92J PRO* 3.7 6.4 - - - +
94J HIS* 2.7 26.9 + - - -
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Residues in contact with LEU 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D VAL* 5.3 2.6 - - + +
167D GLY* 3.9 22.4 - - - +
198D TRP* 4.6 4.3 - - + -
199D TYR* 3.9 25.6 - - + -
51J SER* 4.4 5.0 - - - -
52J THR* 3.9 14.9 - - + +
66J ARG* 3.3 27.1 + - + +
67J TRP* 3.1 5.6 + - - +
68J ALA 3.1 0.6 - - - -
69J ASP* 1.3 79.7 - - - +
71J SER* 1.3 62.7 + - - +
72J ALA 3.8 1.0 + - - -
92J PRO* 3.9 13.7 - - - +
94J HIS* 3.6 49.1 - - + +
95J ALA* 3.8 20.5 - - + +
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Residues in contact with SER 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J TYR* 4.1 14.4 - - - -
12J TYR* 3.7 12.3 - - - -
52J THR* 2.7 27.3 + - - -
67J TRP* 2.8 30.1 + - - -
68J ALA* 3.3 13.7 + - - +
69J ASP 4.8 1.4 - - - +
70J LEU* 1.3 79.9 - - - +
72J ALA* 1.3 64.9 + - - +
73J LYS* 4.2 12.9 - - - +
90J ALA 4.7 0.2 - - - +
92J PRO* 4.2 8.3 - - - +
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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