Contacts of the helix formed by residues 74 - 85 (chain N) in PDB entry 5GJQ
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 PHE 74 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69N TYR* 5.3 9.9 - + - -
72N GLY* 3.6 14.5 + - - -
73N ALA* 1.3 81.4 - - - +
75N GLU* 1.3 58.7 + - + +
76N GLU* 2.9 2.2 - - - +
77N SER* 2.6 9.7 + - - +
78N LEU* 2.2 40.9 + - - +
103N LYS* 3.4 47.6 - - + -
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Residues in contact with GLU 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N PHE* 1.3 77.1 - - + +
76N GLU* 1.3 56.7 + - - +
78N LEU* 4.1 7.8 - - - +
79N ASN* 3.0 27.7 + - - +
103N LYS* 5.5 5.1 + - - +
107N HIS* 4.5 23.9 - - + +
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Residues in contact with GLU 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68N PHE* 3.9 8.1 - - + -
73N ALA* 3.7 27.6 - - + -
74N PHE 4.8 0.2 - - - +
75N GLU* 1.3 76.3 - - - +
77N SER* 1.3 64.6 + - - +
79N ASN* 3.1 8.8 + - - +
80N TYR* 3.0 37.6 + - + -
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Residues in contact with SER 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N SER* 2.4 49.0 + - - +
68N PHE* 3.5 13.1 - - - +
69N TYR* 4.2 1.8 - - - -
73N ALA 3.2 20.9 - - - -
74N PHE* 2.6 10.5 + - - -
76N GLU* 1.3 75.8 - - - +
78N LEU* 1.3 51.6 + - - -
80N TYR* 3.0 1.3 + - - -
81N ALA* 2.5 22.3 + - - +
100N ILE* 5.0 12.1 - - - -
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Residues in contact with LEU 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N PHE* 2.2 33.3 + - + +
75N GLU* 4.1 6.1 - - - -
77N SER* 1.3 66.4 - - - +
79N ASN* 1.3 52.7 + - - +
81N ALA* 3.0 3.8 + - - +
82N LEU* 2.3 58.9 + - + +
100N ILE* 5.8 1.0 - - - +
103N LYS* 5.7 1.6 - - + -
104N CYS* 3.3 50.7 - - + +
107N HIS* 5.1 7.9 - - + -
130N LEU* 5.7 2.5 - - + -
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Residues in contact with ASN 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49N TYR* 5.5 1.2 + - - -
75N GLU 3.0 19.7 + - - +
76N GLU* 3.1 6.0 + - - +
78N LEU* 1.3 78.8 - - - +
80N TYR* 1.3 73.3 + - + +
82N LEU* 3.1 17.0 - - - +
83N GLY* 2.5 30.3 + - - -
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Residues in contact with TYR 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46N GLU* 2.6 38.0 + - - -
49N TYR* 3.9 31.7 - + + -
61N ALA* 3.0 45.0 - - + +
62N LEU 3.6 2.9 + - - -
64N ALA* 4.2 15.7 - - + -
65N SER* 3.2 8.1 - - - +
68N PHE* 5.2 1.6 - + - -
76N GLU* 3.0 28.3 + - + -
77N SER* 3.0 3.3 + - - +
79N ASN* 1.3 91.4 - - - +
81N ALA* 1.3 61.3 + - - +
83N GLY* 3.2 1.3 + - - +
84N ALA 2.8 21.8 + - - -
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Residues in contact with ALA 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N LEU* 4.0 17.5 - - + -
65N SER* 2.8 8.7 + - - +
77N SER 2.5 21.9 + - - +
78N LEU* 3.4 7.6 - - - +
80N TYR* 1.3 69.3 - - - +
82N LEU* 1.3 64.3 + - - +
84N ALA* 2.9 23.7 + - - +
85N GLY 3.3 5.9 + - - -
88N PHE* 3.7 15.2 - - + +
100N ILE* 4.2 16.2 - - + -
104N CYS* 5.0 6.1 - - - -
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Residues in contact with LEU 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N LEU* 2.3 57.1 + - + +
79N ASN* 3.1 14.4 - - - +
81N ALA* 1.3 68.7 - - - +
83N GLY* 1.3 63.5 + - - +
85N GLY* 3.8 8.0 + - - -
88N PHE* 6.2 0.2 - - - -
104N CYS* 5.6 3.4 - - + -
127N ASP* 3.4 22.7 - - + +
129N ARG* 3.6 39.1 - - + +
130N LEU* 3.7 24.0 - - + +
133N ILE* 5.5 4.3 - - + -
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Residues in contact with GLY 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49N TYR* 4.0 23.2 + - - -
58N GLN* 3.1 17.7 - - - +
79N ASN 2.5 19.8 + - - -
80N TYR* 3.2 7.4 + - - -
81N ALA 3.1 0.4 - - - -
82N LEU* 1.3 75.5 - - - +
84N ALA* 1.3 65.8 + - - +
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Residues in contact with ALA 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58N GLN* 3.5 25.9 - - - +
62N LEU* 3.8 6.7 - - + -
80N TYR 2.8 16.5 + - - +
81N ALA 2.9 11.0 + - - +
83N GLY* 1.3 77.9 - - - +
85N GLY* 1.3 55.1 + - - +
86N ASP* 2.7 32.3 + - - +
87N LEU* 3.8 3.4 - - + -
88N PHE* 3.4 24.2 - - + +
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Residues in contact with GLY 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81N ALA 3.3 7.6 + - - -
82N LEU 3.8 5.8 + - - -
83N GLY 3.6 1.0 - - - -
84N ALA* 1.3 75.6 - - - +
86N ASP* 1.3 55.6 + - - +
88N PHE* 3.0 26.1 - - - +
89N ASN* 5.5 0.2 - - - +
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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