Contacts of the helix formed by residues 62 - 67 (chain E) in PDB entry 5LSJ
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 TYR 62 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C MET* 6.1 0.7 - - + -
39C VAL* 4.6 3.4 - - + +
40C GLU* 4.5 4.0 - - - -
43C ILE* 3.4 34.2 - - + +
60C ILE* 4.2 18.6 + - + +
63C CYS* 3.5 24.5 - - + -
64C THR* 2.9 38.4 - - + +
67C PHE* 4.8 4.9 - + + -
58E PHE* 3.1 51.6 - + + +
59E THR* 2.6 14.6 + - - +
61E CYS* 1.3 77.0 - - - +
63E LYS* 1.3 63.7 + - - +
64E CYS 2.8 20.6 - - - +
65E PHE* 4.7 8.3 - + + -
66E TYR* 3.2 14.9 + - + +
73E THR* 5.6 3.4 - - + -
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Residues in contact with LYS 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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59E THR* 2.8 23.5 + - - +
60E ASP* 3.4 37.2 - - - +
61E CYS 3.3 3.6 + - - -
62E TYR* 1.3 74.8 - - - +
64E CYS* 1.3 54.2 + - - +
66E TYR* 2.7 45.3 + - + -
67E GLN* 2.8 37.0 + - - +
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Residues in contact with CYS 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ILE* 5.4 13.2 - - + +
59C GLN* 5.7 4.0 - - - -
60C ILE* 5.3 11.0 - - - +
63C CYS* 4.5 20.2 - - - -
61E CYS 4.6 2.9 - - - -
62E TYR* 2.8 25.4 - - - +
63E LYS* 1.3 75.5 - - - +
65E PHE* 1.3 63.5 + - - +
66E TYR 3.2 0.2 - - - -
67E GLN* 3.9 7.1 + - - +
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Residues in contact with PHE 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ILE* 3.6 52.7 - - + -
46C LYS* 5.2 11.0 - - + -
47C LEU* 3.8 21.3 - - + -
55C ILE* 5.0 6.7 + - + +
60C ILE* 4.8 6.7 - - + -
62E TYR* 4.7 9.4 - + + -
63E LYS 3.1 1.0 + - - -
64E CYS* 1.3 75.3 - - - +
66E TYR* 1.3 59.5 + - - +
67E GLN 3.5 1.3 - - - -
68E LEU* 2.7 58.5 - - + +
69E GLN* 4.7 8.1 - - - -
72E MET* 4.8 20.4 - - + -
73E THR* 3.2 32.8 + - + -
76E ILE* 5.6 2.5 - - + -
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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
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55E TYR* 3.7 22.1 + - - -
59E THR* 3.9 34.7 - - + +
62E TYR 3.2 22.4 + - - +
63E LYS* 2.7 38.0 + - + +
65E PHE* 1.3 73.7 - - - +
67E GLN* 1.3 67.2 + - + +
68E LEU 3.3 0.5 + - - -
70E PRO* 3.3 40.4 - - + +
73E THR* 3.9 19.7 - - + +
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Residues in contact with GLN 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 LYS* 2.8 52.6 + - - +
64E CYS* 3.9 6.8 - - - +
65E PHE 3.5 2.0 + - - -
66E TYR* 1.3 79.7 - - + +
68E LEU* 1.3 65.9 - - + +
69E GLN 4.0 1.2 + - - -
70E PRO* 4.1 9.4 - - - +
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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