Contacts of the helix formed by residues 46 - 54 (chain G) in PDB entry 2EHO
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 46 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10G ALA 4.1 3.1 - - - +
11G GLU* 3.0 23.5 + - + +
13G GLU 2.7 20.4 + - - +
15G VAL* 3.6 24.7 - - + -
44G VAL 3.4 0.2 + - - -
45G PRO* 1.3 71.4 - - - +
47G TRP* 1.3 63.7 + - - +
49G ALA* 3.2 2.1 + - + +
50G ILE* 2.9 57.6 + - + +
95G LEU* 3.9 21.5 - - + -
98G LEU* 3.7 28.0 - - + -
99G LEU* 4.1 17.7 - - + -
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Residues in contact with TRP 47 (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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77E ILE* 4.2 8.1 - - + -
80E MSE 3.4 48.0 - - + +
81E GLU* 3.5 41.1 - - + -
84E ARG* 3.6 37.4 - - - +
11G GLU* 3.1 53.1 + - + -
12G LYS* 4.4 2.9 - - - +
28G LEU* 4.7 5.8 - - + -
45G PRO* 3.1 28.5 - - + +
46G LEU* 1.3 79.3 - - - +
48G LEU* 1.3 93.8 + - + +
50G ILE* 3.7 6.2 + - - +
51G ASN* 3.3 20.1 + - - +
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Residues in contact with LEU 48 (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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77E ILE* 3.6 42.6 - - + -
80E MSE 6.3 0.9 - - - -
26G ILE* 4.7 3.1 - - + -
33G LEU* 3.8 20.2 - - + -
36G PHE* 5.1 5.6 - - + -
44G VAL* 3.2 24.5 - - + -
45G PRO* 2.9 9.0 + - + +
47G TRP* 1.3 101.1 - - + +
49G ALA* 1.3 66.5 + - - +
51G ASN* 3.1 7.7 + - + +
52G LEU* 2.9 57.4 + - + +
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Residues in contact with ALA 49 (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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15G VAL* 3.5 18.8 - - + -
17G ILE* 3.9 9.4 - - + -
44G VAL* 3.9 6.1 - - + -
45G PRO 3.1 6.6 + - - +
46G LEU* 3.2 8.7 + - + +
48G LEU* 1.3 79.0 - - - +
50G ILE* 1.3 64.2 + - - +
52G LEU* 3.0 17.8 + - - +
53G LYS 3.0 12.3 + - - -
58G CYS* 3.8 2.9 - - - -
60G LEU* 3.4 33.3 - - + +
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Residues in contact with ILE 50 (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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11G GLU* 6.0 0.2 - - + -
46G LEU* 2.9 52.0 + - + +
47G TRP* 3.7 7.6 - - - +
49G ALA* 1.3 78.1 - - + +
51G ASN* 1.3 61.2 + - - +
53G LYS* 3.8 2.4 + - - +
54G GLN* 3.1 33.2 + - - +
60G LEU* 5.2 6.5 - - + -
98G LEU* 4.2 27.1 - - + +
99G LEU* 4.8 6.5 - - + -
102G HIS* 3.6 40.5 - - + +
103G ALA 5.6 0.4 - - - +
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Residues in contact with ASN 51 (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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77E ILE* 5.8 1.8 - - - +
80E MSE 3.4 30.8 - - + +
145F SER* 3.5 21.9 + - - +
47G TRP 3.3 11.9 + - - +
48G LEU* 3.1 11.1 + - + +
50G ILE* 1.3 80.4 - - - +
52G LEU* 1.3 66.5 + - - +
54G GLN* 3.5 12.1 + - - +
55G ARG* 3.3 54.3 + - - +
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Residues in contact with LEU 52 (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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73E LEU* 5.1 11.2 - - + -
77E ILE* 5.1 9.2 - - + -
17G ILE* 4.3 16.8 - - + -
21G PHE* 4.2 27.4 - - + -
36G PHE* 5.4 2.7 - - + -
48G LEU* 2.9 44.1 + - + +
49G ALA* 3.0 3.3 + - - +
51G ASN* 1.3 77.3 - - - +
53G LYS* 1.3 51.1 + - - +
54G GLN 2.8 3.8 - - - -
55G ARG* 2.5 33.0 + - - +
56G GLN 2.7 12.1 + - - -
57G LYS* 3.2 11.6 + - + +
58G CYS* 3.2 34.3 - - + +
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Residues in contact with LYS 53 (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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49G ALA 3.0 5.4 + - - +
50G ILE* 4.1 2.7 - - - +
52G LEU* 1.3 77.3 - - - +
54G GLN* 1.3 57.7 - - - +
55G ARG 3.2 0.7 - - - -
56G GLN* 3.4 41.4 + - - +
58G CYS* 3.2 15.0 + - - +
59G ARG* 4.9 1.0 - - - +
60G LEU* 3.2 29.8 - - + +
102G HIS* 4.3 9.0 - - + +
103G ALA* 4.2 16.8 - - - +
105G ASP* 3.3 34.2 + - - +
106G ASN* 3.0 37.9 + - - +
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Residues in contact with GLN 54 (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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145F SER* 4.0 19.9 + - - +
50G ILE* 3.1 24.3 + - - +
51G ASN* 3.5 10.5 - - - +
52G LEU 2.7 0.8 + - - -
53G LYS* 1.3 77.9 - - - +
55G ARG* 1.3 60.7 + - + +
56G GLN* 3.2 2.6 - - - +
102G HIS* 2.9 44.8 + - + +
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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