Contacts of the helix formed by residues 59 - 69 (chain E) in PDB entry 2KVQ
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 THR 59 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E THR 3.7 13.8 + - - +
33E GLY* 4.7 7.9 - - - +
57E GLU 4.0 8.1 - - - +
58E PRO* 1.3 76.8 - - - +
60E GLU* 1.3 64.7 + - - +
61E LYS* 2.9 23.0 + - - +
62E THR* 2.7 31.0 + - - +
63E VAL* 3.1 16.7 + - - +
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Residues in contact with GLU 60 (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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59E THR* 1.3 72.7 - - - +
61E LYS* 1.3 65.2 + - + +
63E VAL* 2.8 35.2 - - - +
64E ASP* 3.0 31.0 + - - +
139G GLY* 5.6 7.0 - - - -
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Residues in contact with LYS 61 (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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32E THR* 3.8 14.8 - - - +
59E THR* 2.9 10.5 + - - +
60E GLU* 1.3 79.5 - - + +
62E THR* 1.3 56.0 + - - +
64E ASP* 3.4 7.2 + - - +
65E ALA* 2.9 31.4 + - - +
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Residues in contact with THR 62 (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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6E ILE* 4.6 6.5 - - + -
28E THR* 5.1 1.5 - - + +
29E ALA* 4.3 8.3 - - + -
32E THR* 2.5 42.2 + - + +
34E ALA* 4.0 10.3 - - + -
55E ILE* 4.1 15.3 - - + -
58E PRO* 3.7 8.5 - - + +
59E THR* 2.7 33.5 + - - -
61E LYS* 1.3 75.6 - - - +
63E VAL* 1.3 62.8 + - - +
65E ALA* 3.3 2.6 + - - +
66E LEU* 2.9 24.5 + - + +
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Residues in contact with VAL 63 (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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6E ILE* 4.4 19.3 - - + -
58E PRO* 4.9 2.9 - - + -
59E THR 3.5 11.2 - - - +
60E GLU* 2.8 46.7 - - - +
62E THR* 1.3 75.6 - - - +
64E ASP* 1.3 66.5 + - - +
66E LEU* 3.3 6.5 + - - +
67E MET* 3.0 27.4 + - - +
81E LEU* 4.5 9.4 - - + -
139G GLY* 5.0 0.9 - - - -
140G PRO* 3.5 43.1 - - + +
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Residues in contact with ASP 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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60E GLU* 3.0 41.8 + - - +
61E LYS* 3.7 6.6 - - - +
63E VAL* 1.3 82.3 - - - +
65E ALA* 1.3 60.5 + - - +
67E MET* 3.3 9.7 + - - +
68E ARG* 3.0 23.9 + - - +
140G PRO* 5.3 3.1 - - - +
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Residues in contact with ALA 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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28E THR* 3.3 26.2 - - + +
32E THR* 4.0 9.0 - - - +
61E LYS 2.9 18.3 + - - +
62E THR 3.7 2.9 - - - +
64E ASP* 1.3 76.7 - - - +
66E LEU* 1.3 62.6 + - - +
68E ARG* 3.3 7.2 + - - +
69E LEU* 3.0 22.7 + - - +
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Residues in contact with LEU 66 (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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6E ILE* 4.7 19.1 - - + -
8E ILE* 4.4 18.6 - - + -
25E ILE* 4.5 22.4 - - + -
28E THR* 4.0 6.7 - - + +
62E THR* 2.9 19.4 + - + +
63E VAL* 3.3 7.6 + - - +
65E ALA* 1.3 74.1 - - - +
67E MET* 1.3 69.2 + - + +
69E LEU* 3.4 36.4 + - + +
71E LEU* 5.6 5.8 - - + -
79E ILE* 4.5 23.3 - - + -
140G PRO* 5.9 4.7 - - + -
141G PHE* 5.9 1.8 - - + -
164G ILE* 5.5 0.2 - - - +
165G PHE* 4.2 6.5 - - + -
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Residues in contact with MET 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 VAL 3.0 12.4 + - - +
64E ASP* 3.7 9.2 - - - +
65E ALA 3.3 0.2 - - - -
66E LEU* 1.3 81.7 - - - +
68E ARG* 1.3 63.3 + - - +
79E ILE* 5.6 2.0 - - - -
140G PRO* 3.0 55.2 - - + +
141G PHE* 4.8 10.5 - - + -
144G PHE* 3.5 29.8 - - + -
162G VAL* 6.3 0.4 - - + -
164G ILE* 3.7 28.3 - - + -
165G PHE* 3.6 21.1 - - - -
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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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64E ASP 3.0 16.4 + - - +
65E ALA* 3.8 8.5 - - - +
66E LEU 3.3 0.2 - - - -
67E MET* 1.3 74.7 - - - +
69E LEU* 1.3 66.0 + - - +
70E ASP* 3.2 5.5 + - - +
165G PHE* 5.6 0.2 - - - -
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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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24E GLU* 4.0 30.7 - - + +
25E ILE* 4.1 13.9 - - + -
28E THR* 3.6 23.8 - - + +
65E ALA 3.0 14.9 + - - +
66E LEU* 3.5 20.2 - - + +
67E MET 3.2 0.4 - - - -
68E ARG* 1.3 75.4 - - - +
70E ASP* 1.3 71.8 + - - +
71E LEU* 3.6 26.6 + - + -
165G PHE* 3.0 28.5 - - - -
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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