Contacts of the helix formed by residues 63 - 73 (chain E) in PDB entry 3KZ1
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 GLN 63 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E GLY* 4.3 4.7 - - - -
34E TYR* 4.9 3.2 + - - -
36E PRO* 4.4 26.6 - - - +
37E THR 5.5 0.8 - - - +
61E ALA* 3.6 1.0 - - + +
62E GLY* 1.3 79.5 - - - +
64E GLU* 1.3 64.8 + - - +
65E ASP* 3.8 17.5 - - - +
66E TYR* 3.4 38.7 + - + +
67E ASP* 4.6 0.7 - - - -
70E ARG* 3.8 13.9 + - - -
538E GSP 4.2 14.2 - - - -
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Residues in contact with GLU 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E GLY 3.9 2.6 + - - +
63E GLN* 1.3 69.9 - - - +
65E ASP* 1.3 71.2 + - - +
66E TYR 3.0 2.5 - - - -
67E ASP* 2.9 40.9 + - - +
98E LYS* 4.1 17.2 - - + +
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Residues in contact with ASP 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E GLN* 3.3 16.9 - - - +
64E GLU* 1.3 81.5 + - - +
66E TYR* 1.3 74.8 + - + +
67E ASP* 3.3 3.6 + - - +
68E ARG* 4.2 15.8 - - - +
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Residues in contact with TYR 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E PRO* 6.0 2.0 - - + -
37E THR 4.2 4.9 - - - -
38E VAL* 3.8 37.1 - - + +
61E ALA* 3.5 32.8 - - + +
63E GLN* 3.4 30.3 + - + +
64E GLU 3.0 1.0 - - - -
65E ASP* 1.3 86.8 - - + +
67E ASP* 1.3 64.1 + - - +
68E ARG* 3.1 5.6 - - - +
69E LEU* 3.1 37.6 + - + +
70E ARG* 3.5 15.9 + - - -
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Residues in contact with ASP 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E GLN 4.1 0.2 - - - +
64E GLU* 2.9 39.2 + - - +
65E ASP 3.2 1.4 - - - -
66E TYR* 1.3 76.9 - - - +
68E ARG* 1.3 58.1 + - + +
70E ARG* 2.6 38.1 + - - +
71E PRO* 3.0 24.4 - - - +
98E LYS* 2.8 23.4 + - - -
102E GLU* 5.2 4.1 - - - +
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Residues in contact with ARG 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048B THR* 3.8 19.3 + - - +
1049B SER 4.4 1.2 + - - -
1050B LYS* 3.2 41.8 - - - +
1052B GLY 4.2 16.4 + - - -
1054B PRO* 3.1 41.1 - - + +
65E ASP 4.2 16.6 - - - +
66E TYR* 5.1 2.7 - - - +
67E ASP* 1.3 79.1 - - + +
69E LEU* 1.3 80.6 + - - +
70E ARG 3.5 0.4 - - - -
71E PRO* 3.7 12.2 - - - +
72E LEU* 5.0 0.3 - - - +
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Residues in contact with LEU 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032B LEU* 4.4 12.1 - - + -
1046B ILE* 4.7 4.7 - - + -
1048B THR* 4.0 22.2 - - + -
1054B PRO* 4.0 23.6 - - + -
38E VAL* 4.0 33.7 - - + +
39E PHE* 5.1 9.9 - - + -
66E TYR* 3.1 26.0 + - + +
68E ARG* 1.3 95.1 - - - +
70E ARG* 1.3 64.4 + - - +
71E PRO 3.5 0.9 - - - -
72E LEU* 3.4 30.1 + - + +
73E SER* 4.3 4.0 + - - -
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Residues in contact with ARG 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E VAL* 4.3 2.2 - - - -
60E THR* 3.5 34.1 - - + -
61E ALA* 2.7 40.6 + - + +
63E GLN 3.8 8.1 + - - -
66E TYR 3.5 15.3 + - - +
67E ASP* 2.6 34.8 + - - +
69E LEU* 1.3 75.7 - - - +
71E PRO* 1.4 64.2 - - + +
72E LEU 2.9 11.2 + - - -
73E SER* 3.1 15.3 + - - -
74E TYR* 3.4 25.4 - - + +
98E LYS* 3.7 5.3 - - - +
99E TRP* 3.3 36.7 - - - -
102E GLU* 3.4 17.1 + - - +
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Residues in contact with PRO 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054B PRO* 6.3 0.4 - - + -
67E ASP 3.0 19.5 - - - +
68E ARG* 3.7 11.4 - - - +
69E LEU 3.7 2.9 - - - -
70E ARG* 1.4 86.8 - - + +
72E LEU* 1.3 62.2 + - + +
73E SER 3.4 0.2 - - - -
74E TYR* 3.4 19.1 + - + +
75E PRO* 3.5 15.8 - - - +
102E GLU* 5.1 2.2 - - - +
106E PHE* 3.8 38.9 - - + -
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Residues in contact with LEU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046B ILE* 3.7 29.4 - - + -
1054B PRO* 3.1 47.1 - - + +
1055B GLN* 4.0 10.3 - - + +
1056B ILE* 3.9 36.2 - - + +
7E LYS* 5.2 0.3 + - - -
39E PHE* 5.2 4.0 - - + -
58E TRP* 4.6 2.4 - - - -
68E ARG 5.0 0.7 - - - +
69E LEU* 3.4 20.1 + - + +
70E ARG 2.9 1.2 + - - -
71E PRO* 1.3 80.3 - - + +
73E SER* 1.3 58.0 + - - +
74E TYR 3.3 0.2 - - - -
75E PRO* 3.3 17.8 - - + +
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Residues in contact with SER 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E LYS* 3.0 28.2 + - - -
9E VAL* 3.4 15.0 - - - +
39E PHE* 3.3 25.6 - - - -
58E TRP* 3.8 18.2 - - - +
59E ASP 4.6 1.9 + - - -
60E THR* 3.7 26.1 - - - +
69E LEU 4.8 1.6 + - - -
70E ARG* 3.1 11.1 + - - -
72E LEU* 1.3 77.0 - - - +
74E TYR* 1.3 59.9 + - - +
75E PRO* 3.5 1.3 - - - -
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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