Contacts of the helix formed by residues 70 - 77 (chain G) in PDB entry 2E9X
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 LEU 70 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G GLU* 4.8 0.2 - - - +
27G MET* 3.4 33.4 - - + -
28G SER* 3.1 17.4 + - - +
30G GLU 2.9 16.5 + - - +
32G LEU* 4.6 6.5 - - + -
68G LEU 3.5 1.5 + - - -
69G PRO* 1.3 69.6 - - - +
71G TRP* 1.3 64.2 + - - +
73G ALA* 3.2 5.2 + - - +
74G LYS* 2.8 35.8 + - + +
119G PHE* 3.9 26.2 - - + +
122G GLN* 4.0 22.4 - - + +
123G LEU 5.3 0.2 - - - +
126G PHE* 3.7 30.5 - - + -
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Residues in contact with TRP 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 5.4 4.5 - - + -
2E PHE* 4.3 7.0 - - + -
3E CYS* 3.6 36.5 - - + +
67E CYS* 3.8 26.8 - - + +
68E SER* 3.8 14.6 - - - -
71E ARG* 3.2 56.7 - - + +
74E ARG* 5.6 1.8 - - - +
28G SER* 3.1 35.6 + - - +
29G HIS* 4.3 6.0 + - - +
69G PRO* 3.5 28.0 - - + +
70G LEU* 1.3 76.8 - - - +
72G LEU* 1.3 97.9 + - + +
74G LYS* 3.4 10.3 + - - +
75G GLY* 3.1 19.8 + - - -
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Residues in contact with LEU 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 3.9 19.5 - - + -
64E PHE* 3.4 41.7 - - + +
67E CYS* 4.4 11.4 - - + -
68G LEU* 4.0 16.6 - - + -
69G PRO* 2.9 23.3 + - + +
71G TRP* 1.3 103.7 - - + +
73G ALA* 1.3 66.0 + - - +
75G GLY* 3.4 1.5 + - - -
76G LEU* 3.1 43.6 + - + +
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Residues in contact with ALA 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G LEU* 3.6 32.8 - - + -
34G VAL* 4.3 14.8 - - + -
68G LEU* 4.6 5.8 - - + +
69G PRO 3.0 11.4 + - - +
70G LEU 3.7 5.6 - - - +
72G LEU* 1.3 76.3 - - - +
74G LYS* 1.3 62.9 + - - +
76G LEU* 3.4 0.9 + - - +
77G PHE* 3.0 27.0 + - - +
84G LEU* 4.2 13.1 - - + +
86G VAL* 4.7 1.1 - - + -
126G PHE* 3.6 6.4 - - + -
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Residues in contact with LYS 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G GLU* 3.1 21.4 + - - +
17G GLU* 3.1 19.4 + - - +
70G LEU* 2.8 27.3 + - + +
71G TRP* 3.6 10.3 - - - +
73G ALA* 1.3 77.6 - - - +
75G GLY* 1.3 64.4 + - - +
77G PHE* 3.2 18.2 + - - +
122G GLN* 2.7 44.0 + - - +
125G HIS* 3.7 20.9 - - + +
126G PHE* 3.9 20.0 - - + -
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Residues in contact with GLY 75 (chain G).
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* 5.4 5.9 - - - +
67E CYS* 3.5 30.5 - - - -
71G TRP 3.1 10.6 + - - -
72G LEU 3.9 1.1 - - - -
74G LYS* 1.3 80.2 - - - +
76G LEU* 1.3 59.7 + - - +
77G PHE 4.3 3.5 - - - +
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Residues in contact with LEU 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E PRO 4.5 3.4 - - - +
63E LYS* 4.1 15.7 - - + -
64E PHE* 4.0 31.4 - - + +
67E CYS* 4.5 3.4 - - - -
40G MET* 4.1 22.9 - - + -
68G LEU* 4.5 5.6 - - + -
72G LEU* 3.1 35.1 + - + +
74G LYS 3.2 0.2 - - - -
75G GLY* 1.3 77.6 - - - +
77G PHE* 1.3 62.4 + - - +
78G ASP* 4.0 4.7 + - - +
83G ILE* 3.7 37.7 - - + +
84G LEU* 3.8 29.2 + - + +
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Residues in contact with PHE 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G ALA 3.0 18.0 + - - +
74G LYS* 3.2 12.5 + - - +
75G GLY 4.3 2.9 - - - +
76G LEU* 1.3 79.6 - - - +
78G ASP* 1.3 92.9 + - - +
79G ASN* 4.2 7.6 - - - -
81G ARG* 4.6 10.5 - - + -
84G LEU* 3.8 30.1 - - + -
86G VAL* 4.1 12.1 - - + -
125G HIS 4.1 6.3 - - - -
126G PHE* 3.5 50.3 - + + -
127G ASP* 3.3 20.6 - - - -
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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