Contacts of the helix formed by residues 58 - 66 (chain E) in PDB entry 5TWV
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 ASP 58 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54E ARG 2.9 15.9 + - - +
55E PHE* 3.2 16.3 + - - +
57E GLN* 1.3 73.7 - - - +
59E VAL* 1.3 60.8 + - - +
60E PHE 3.6 2.5 - - - -
61E THR* 3.7 23.4 - - + +
62E THR* 3.9 4.7 - - - +
176G ARG* 4.0 33.4 - - + +
177G ARG* 5.9 2.0 - - - -
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Residues in contact with VAL 59 (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 PHE 5.1 0.2 - - - -
56E LEU* 3.3 22.2 - - + +
57E GLN 2.9 15.5 + - - +
58E ASP* 1.3 70.6 - - - +
60E PHE* 1.3 89.8 + - + +
62E THR* 2.5 25.0 + - - -
63E LEU* 3.0 25.5 + - + +
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Residues in contact with PHE 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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58E ASP 3.6 1.0 - - - -
59E VAL* 1.3 91.7 - - + +
61E THR* 1.3 66.3 + - - +
63E LEU* 3.2 9.9 + - + +
64E VAL* 2.9 33.7 + - + +
162E ILE* 5.3 16.6 - - + -
166E CYS* 5.2 16.6 - - + -
169E MET* 6.5 0.7 - - + -
68G TRP* 4.1 30.1 - + - -
170G LYS 4.6 2.7 - - - -
171G THR* 3.3 53.6 - - - +
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Residues in contact with THR 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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58E ASP* 3.7 22.8 + - + +
60E PHE* 1.3 76.3 - - - +
62E THR* 1.3 82.3 + - + +
64E VAL* 3.2 8.1 + - - +
65E ASP* 2.9 24.2 + - - +
177G ARG* 3.9 38.8 + - - -
206G ARG* 4.1 13.9 + - - +
208G SER* 5.3 1.0 + - - -
293G THR* 3.9 22.5 + - - +
294G THR* 6.5 1.1 - - - -
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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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55E PHE* 4.6 9.0 - - + +
58E ASP 3.9 13.2 - - - +
59E VAL* 2.5 25.1 + - - +
61E THR* 1.3 83.5 - - + +
63E LEU* 1.3 74.0 + - - +
65E ASP* 3.2 7.7 + - - +
66E LEU* 3.0 29.2 + - - +
49F ILE* 5.8 1.0 - - - +
53F SER* 3.8 23.3 - - - +
206G ARG* 3.9 27.6 - - - +
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Residues in contact with LEU 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 VAL* 3.0 31.9 + - + +
60E PHE* 3.2 14.3 + - + +
62E THR* 1.3 93.1 + - - +
64E VAL* 1.3 64.0 + - - +
66E LEU* 3.2 21.0 + - + +
71E THR* 4.6 8.8 + - - +
74E ILE* 5.0 20.1 - - + +
75E PHE* 5.5 8.3 - - + -
166E CYS* 3.9 26.9 - - - -
49F ILE* 4.8 18.2 - - + -
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Residues in contact with VAL 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 PHE* 2.9 25.5 + - + +
61E THR* 3.6 6.3 - - - +
63E LEU* 1.3 76.2 - - - +
65E ASP* 1.3 64.6 + - - +
66E LEU 3.9 4.9 - - - +
166E CYS* 4.7 12.1 - - - +
169E MET* 3.7 51.6 - - + +
170E LYS* 4.7 15.2 - - - +
173E GLN* 5.0 13.5 + - + +
293G THR* 4.5 23.3 - - + +
294G THR* 5.6 2.5 - - + -
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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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61E THR* 2.9 17.5 + - - +
62E THR* 3.6 8.7 - - - +
64E VAL* 1.3 80.1 - - - +
66E LEU* 1.3 67.9 + - + +
67E LYS* 3.5 2.8 + - - +
173E GLN* 5.6 2.3 - - - +
56F SER* 6.1 2.1 - - - -
57F LYS* 4.1 22.6 - - - +
206G ARG* 5.0 7.3 + - - +
208G SER* 4.3 14.1 + - - +
293G THR* 5.2 11.2 - - + +
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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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62E THR 3.0 21.2 + - - +
63E LEU* 3.2 12.8 + - + +
64E VAL 3.9 6.1 - - - +
65E ASP* 1.3 82.2 - - + +
67E LYS* 1.3 70.4 + - - +
68E TRP* 5.9 0.5 - - - -
70E HIS* 4.9 13.0 - - + +
71E THR* 3.0 13.2 + - - +
74E ILE* 4.3 22.7 - - + -
49F ILE* 4.4 9.2 - - + +
52F GLY* 3.6 31.4 - - - +
53F SER* 3.8 27.4 - - - +
56F SER* 4.6 12.8 - - - -
57F LYS 5.8 0.7 - - - +
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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