Contacts of the helix formed by residues 63 - 71 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A GLU* 3.0 20.0 + - - +
22E LYS* 2.5 38.5 + - - +
355E LYS* 2.5 38.5 + - - +
357E TYR* 2.9 13.6 + - - -
62H TYR* 1.3 72.6 - - - +
64H GLN* 1.3 69.3 + - - +
65H GLU* 3.0 13.5 + - + +
66H ARG* 3.0 33.0 + - - +
67H TRP 3.3 8.3 + - - -
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Residues in contact with GLN 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H PRO* 5.1 8.9 - - - +
62H TYR* 2.9 35.5 + - - +
63H GLU* 1.3 72.1 - - - +
65H GLU* 1.3 62.3 + - - +
67H TRP* 3.3 28.6 + - + +
68H ALA* 3.1 24.0 + - + +
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Residues in contact with GLU 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E LYS* 6.0 7.6 - - + -
22E LYS* 4.2 12.0 - - + +
63H GLU* 3.0 18.9 + - + +
64H GLN* 1.3 80.6 - - - +
66H ARG* 1.3 62.1 + - - +
68H ALA* 3.4 6.2 + - - +
69H ASP* 3.1 23.0 + - - +
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Residues in contact with ARG 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLY* 2.9 32.2 + - - +
168A TYR* 3.5 2.4 - - - +
169A SER* 3.6 14.7 + - - -
172A GLU* 3.0 36.5 + - - -
198A TRP* 4.7 4.9 - - + -
199A TYR* 4.1 19.4 - - - +
22E LYS* 4.0 12.1 - - - +
130E GLU* 2.8 41.3 + - - +
355E LYS* 5.4 0.2 - - - +
357E TYR* 3.9 11.5 - - - -
63H GLU* 3.0 29.5 + - - +
65H GLU* 1.3 77.1 - - - +
67H TRP* 1.3 64.7 + - - +
69H ASP* 3.1 14.4 + - + +
70H LEU* 3.2 26.0 + - + +
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Residues in contact with TRP 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A PRO* 3.5 32.2 - - + +
166A VAL 4.3 0.7 - - - -
167A GLY* 4.0 13.1 + - - +
8H ILE* 5.2 10.8 - - + +
11H TYR* 3.3 52.3 - + + -
12H TYR* 3.6 19.5 + + - -
52H THR* 3.2 26.8 + - + +
58H LEU* 5.8 1.2 - - - +
62H TYR* 3.5 33.6 + + + -
63H GLU 3.3 2.4 + - - -
64H GLN* 3.5 34.5 - - + +
66H ARG* 1.3 79.8 - - - +
68H ALA* 1.3 75.8 + - + +
70H LEU* 3.3 4.2 + - - +
71H SER* 2.9 31.6 + - - -
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Residues in contact with ALA 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H TYR* 3.6 20.8 + - - +
64H GLN* 3.1 14.4 + - + +
65H GLU* 3.8 6.1 - - - +
67H TRP* 1.3 91.3 - - + +
69H ASP* 1.3 63.5 + - - +
70H LEU 3.2 0.5 + - - -
71H SER* 3.3 16.7 + - - +
73H LYS* 4.9 7.6 + - - -
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Residues in contact with ASP 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A TRP* 5.5 1.4 - - - -
20E SER* 4.2 4.4 + - - -
22E LYS* 3.4 31.4 - - + +
23E ARG* 2.6 58.2 + - - +
65H GLU 3.1 13.9 + - - +
66H ARG* 3.1 9.5 + - - +
68H ALA* 1.3 77.2 - - - +
70H LEU* 1.3 61.1 + - - +
71H SER 4.7 1.4 - - - +
92H PRO* 3.7 6.4 - - - +
94H HIS* 2.6 26.7 + - - -
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Residues in contact with LEU 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A VAL* 5.2 1.8 - - + +
167A GLY* 3.9 22.2 - - - +
198A TRP* 4.8 2.9 - - + -
199A TYR* 3.6 34.3 - - + +
51H SER* 4.6 4.3 - - - -
52H THR* 4.1 15.6 - - + +
66H ARG* 3.2 22.5 + - + +
67H TRP 3.3 3.6 + - - +
68H ALA 3.1 0.8 - - - -
69H ASP* 1.3 79.4 - - - +
71H SER* 1.3 64.5 + - - +
72H ALA 3.8 0.7 + - - -
91H TYR* 5.9 0.9 - - - -
92H PRO* 3.9 13.1 - - - +
94H HIS* 3.4 50.0 - - + +
95H ALA* 3.7 19.7 - - + +
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Residues in contact with SER 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H TYR* 4.2 13.7 - - - -
12H TYR* 3.9 11.1 - - - -
51H SER* 4.3 0.2 - - - -
52H THR* 2.6 29.1 + - - -
67H TRP* 2.9 28.9 + - - -
68H ALA 3.3 13.0 + - - +
69H ASP 4.7 1.6 - - - +
70H LEU* 1.3 79.6 - - - +
72H ALA* 1.3 65.9 + - - +
73H LYS* 4.2 14.1 + - - +
90H ALA 4.6 0.2 - - - +
92H PRO* 4.2 7.7 - - - +
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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