Contacts of the helix formed by residues 63 - 71 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LYS* 2.6 37.2 + - - +
355D LYS* 2.8 34.2 + - - +
357D TYR* 2.8 20.4 + - - -
172E GLU* 3.2 18.1 + - - +
62I TYR* 1.3 73.3 - - - +
64I GLN* 1.3 66.3 + - - +
65I GLU* 3.6 13.7 - - + +
66I ARG* 3.1 29.4 + - - +
67I TRP* 3.1 12.3 + - - +
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Residues in contact with GLN 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I TYR* 6.1 0.6 - - - -
62I TYR* 3.2 32.2 + - - +
63I GLU* 1.3 73.5 - - - +
65I GLU* 1.3 58.4 + - - +
67I TRP* 3.3 24.0 + - - +
68I ALA* 2.9 33.7 + - + +
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Residues in contact with GLU 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LYS* 5.5 11.2 - - + -
22D LYS* 4.0 12.9 - - + +
63I GLU* 3.1 19.3 - - + +
64I GLN* 1.3 80.4 - - - +
66I ARG* 1.3 60.9 + - - +
68I ALA* 3.9 4.9 - - - +
69I ASP* 3.0 25.1 + - - +
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Residues in contact with ARG 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LYS* 3.9 13.9 - - - +
130D GLU* 2.8 41.4 + - - +
134D ARG* 4.2 0.2 - - - +
357D TYR* 3.9 9.9 - - - -
167E GLY* 2.9 27.8 + - - +
168E TYR* 3.5 2.4 - - - +
169E SER* 3.7 12.9 - - - -
172E GLU* 3.1 38.1 + - - -
198E TRP* 4.3 7.2 - - + -
199E TYR* 3.8 24.9 - - - +
63I GLU* 3.1 32.4 + - - +
65I GLU* 1.3 78.2 - - - +
67I TRP* 1.3 64.4 + - - +
69I ASP* 3.2 9.2 + - - +
70I LEU* 3.2 33.2 + - + +
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Residues in contact with TRP 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E PRO* 3.4 30.6 - - + +
166E VAL 3.9 4.7 - - - -
167E GLY* 4.1 12.5 + - - +
11I TYR* 3.4 41.5 - + - -
12I TYR* 3.4 21.5 - + - -
52I THR* 3.2 37.9 + - - +
53I GLY* 5.7 0.2 - - - -
62I TYR* 3.6 29.2 - + + -
63I GLU 3.1 4.8 + - - +
64I GLN* 3.6 31.9 - - - +
66I ARG* 1.3 80.1 - - - +
68I ALA* 1.3 82.6 + - + +
70I LEU* 3.3 11.4 + - - +
71I SER* 3.1 18.4 + - - -
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Residues in contact with ALA 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I TYR* 3.2 30.7 + - + +
64I GLN* 2.9 23.3 + - + +
65I GLU* 4.1 4.7 - - - +
67I TRP* 1.3 86.2 - - + +
69I ASP* 1.3 60.6 + - - +
70I LEU 3.4 0.9 + - - -
71I SER* 3.6 9.7 + - - +
73I LYS* 5.8 1.2 + - - -
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Residues in contact with ASP 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D SER* 4.4 3.6 + - - -
22D LYS* 3.5 28.2 - - + +
23D ARG* 2.4 61.6 + - - +
198E TRP* 5.3 1.4 - - - -
65I GLU 3.0 19.4 + - - +
66I ARG* 3.5 6.2 - - - +
67I TRP 3.2 0.8 - - - -
68I ALA* 1.3 78.0 - - - +
70I LEU* 1.3 61.4 + - - +
71I SER 4.8 1.1 - - - +
92I PRO* 3.7 4.7 - - - +
94I HIS* 2.7 26.7 + - - -
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Residues in contact with LEU 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E VAL* 5.4 1.8 - - + -
167E GLY* 3.8 22.2 - - - +
198E TRP* 4.4 6.3 - - + -
199E TYR* 3.7 29.6 - - + -
51I SER* 3.9 4.9 + - - -
52I THR* 4.4 10.8 - - + +
66I ARG* 3.2 25.9 + - + +
67I TRP 3.3 3.8 + - - +
68I ALA 3.2 0.4 - - - -
69I ASP* 1.3 79.9 - - - +
71I SER* 1.3 67.2 + - - +
72I ALA 3.6 0.9 + - - -
91I TYR* 5.6 0.7 - - - +
92I PRO* 3.3 18.5 - - - +
94I HIS* 3.7 35.7 - - + +
95I ALA* 3.9 28.1 - - + +
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Residues in contact with SER 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I TYR* 3.7 30.6 - - - -
12I TYR* 3.8 5.4 - - - -
51I SER* 3.5 5.8 - - - -
52I THR* 2.6 25.1 + - - +
67I TRP* 3.1 16.0 + - - -
68I ALA 3.6 9.2 + - - +
69I ASP 3.5 2.4 - - - +
70I LEU* 1.3 82.3 - - - +
72I ALA* 1.3 64.3 + - - +
73I LYS* 3.9 6.9 - - - +
90I ALA 4.6 0.2 - - - +
92I PRO* 3.9 7.8 - - - +
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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