Contacts of the helix formed by residues 63 - 71 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A TYR* 1.3 74.8 - - - +
64A GLN* 1.3 67.4 + - - +
65A GLU* 3.4 20.4 - - - +
66A ARG* 3.0 30.3 + - - +
67A TRP 3.3 8.7 + - - -
22G LYS* 2.7 36.2 + - - +
355G LYS* 2.7 27.2 + - - +
357G TYR* 2.6 27.6 + - - -
172H GLU* 3.1 18.7 + - - +
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Residues in contact with GLN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PRO* 4.0 21.2 - - + +
62A TYR* 3.1 41.9 + - - +
63A GLU* 1.3 69.9 - - - +
65A GLU* 1.3 73.2 + - - +
67A TRP* 3.3 16.7 + - - +
68A ALA* 3.1 25.2 + - - +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLU* 3.1 24.7 + - - +
64A GLN* 1.3 83.4 + - - +
66A ARG* 1.3 62.8 + - - +
68A ALA* 3.5 4.5 + - - +
69A ASP* 3.0 24.0 + - - +
21G LYS* 4.1 31.7 + - - +
22G LYS* 4.3 14.1 - - + +
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLU* 3.0 35.1 + - - +
65A GLU* 1.3 77.6 - - - +
67A TRP* 1.3 66.1 + - - +
69A ASP* 3.1 12.9 + - + +
70A LEU* 3.2 23.8 + - + +
22G LYS* 3.9 14.6 - - - +
130G GLU* 2.8 41.1 + - - +
357G TYR* 4.0 6.3 - - - -
167H GLY* 2.8 39.4 + - - +
168H TYR* 3.6 2.0 - - - +
169H SER* 3.9 14.3 + - - -
172H GLU* 3.1 37.5 + - - -
198H TRP* 4.5 5.6 - - + -
199H TYR* 4.0 20.0 - - - +
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Residues in contact with TRP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.1 40.8 - + + -
12A TYR* 3.3 22.1 + + - -
52A THR* 2.8 33.5 + - + +
62A TYR* 3.7 29.3 + + + -
63A GLU 3.3 2.8 + - - -
64A GLN* 3.3 21.5 + - - +
66A ARG* 1.3 77.0 - - - +
68A ALA* 1.3 89.7 + - + +
70A LEU* 3.0 4.7 + - - +
71A SER* 2.9 32.5 + - - -
164H PRO* 3.6 25.5 - - + +
166H VAL 4.3 1.1 - - - -
167H GLY* 4.2 12.7 + - - +
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.5 23.9 + - + +
64A GLN 3.1 11.9 + - - +
65A GLU* 4.0 4.5 - - - +
67A TRP* 1.3 101.4 - - + +
69A ASP* 1.3 62.3 + - - +
70A LEU 3.4 0.7 + - - -
71A SER* 3.8 9.9 + - - +
73A LYS* 4.9 2.4 + - - -
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Residues in contact with ASP 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLU 3.0 18.9 + - - +
66A ARG* 3.1 6.6 + - - +
68A ALA* 1.3 76.9 - - - +
70A LEU* 1.3 61.9 + - - +
71A SER 4.6 1.1 - - - +
92A PRO* 3.7 5.2 - - - +
94A HIS* 2.8 24.7 + - - -
20G SER* 4.5 2.3 + - - -
22G LYS* 3.4 33.1 - - + +
23G ARG* 2.5 64.8 + - - +
198H TRP* 5.3 2.1 - - - -
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A SER* 5.0 2.9 - - - -
52A THR* 4.6 10.3 - - + -
66A ARG* 3.5 18.6 - - + +
67A TRP 3.0 6.1 + - - +
69A ASP* 1.3 81.3 - - - +
71A SER* 1.3 70.0 + - - +
72A ALA* 3.4 1.0 + - - +
91A TYR* 5.8 0.3 - - - -
92A PRO* 3.0 19.3 - - - +
94A HIS* 3.2 50.0 - - + +
95A ALA* 3.8 17.7 - - + +
166H VAL* 5.1 2.9 - - + -
167H GLY* 3.9 23.6 - - - +
198H TRP* 4.6 2.9 - - + -
199H TYR* 3.7 32.3 - - + +
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.8 17.0 - - - -
12A TYR* 3.6 13.0 - - - -
51A SER* 4.2 1.1 - - - -
52A THR* 2.5 33.8 + - - +
67A TRP* 2.9 28.8 + - - -
68A ALA 4.1 9.6 - - - +
69A ASP 3.7 1.8 - - - +
70A LEU* 1.3 80.1 - - - +
72A ALA* 1.3 62.9 + - - +
73A LYS* 4.4 7.0 + - - +
92A PRO* 4.1 5.5 - - - +
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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