Contacts of the helix formed by residues 72 - 83 (chain B) in PDB entry 4GTU
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 SER 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B LEU* 3.8 32.2 - - - +
16B ILE* 4.4 7.0 - - - +
60B PRO* 4.2 10.5 - - - +
71B GLN* 1.3 74.7 + - - +
73B ASN* 1.3 61.9 + - - +
75B ILE* 3.4 14.2 + - - +
76B LEU* 3.2 28.3 + - - +
104B MET* 3.6 27.3 - - - +
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Residues in contact with ASN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ASN* 6.0 0.2 - - - +
97A ASP* 5.4 0.2 - - - -
101A ASN* 2.9 28.6 + - - +
71B GLN 2.9 3.0 + - - -
72B SER* 1.3 76.4 - - - +
74B ALA* 1.3 64.3 + - - +
76B LEU* 4.0 13.6 - - - +
77B CYS* 3.1 33.0 + - - -
100B GLU* 2.9 43.3 + - + +
101B ASN* 4.5 6.9 + - - +
104B MET* 3.8 31.3 - - - +
154B PHE* 5.5 1.7 - - + -
158B LEU* 4.6 2.4 - - - +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ILE* 6.3 0.2 - - + -
97A ASP* 3.6 36.7 - - + +
98A ILE* 3.4 33.0 - - + -
101A ASN* 4.5 2.0 + - - -
69B ILE* 4.2 5.6 - - + +
70B THR 3.4 0.9 - - - +
71B GLN* 2.7 20.0 + - + +
73B ASN* 1.3 74.0 - - - +
75B ILE* 1.3 55.6 + - - +
78B TYR* 3.1 30.0 + - - +
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 5.7 1.8 - - + -
16B ILE* 3.5 31.0 - - + -
60B PRO* 3.6 44.9 - - + +
61B TYR* 3.9 11.0 - - - -
62B LEU* 3.7 31.6 - - + +
69B ILE* 4.3 12.3 - - + +
70B THR 3.6 16.8 - - - +
71B GLN 4.1 1.8 - - - +
72B SER* 3.4 9.4 + - - +
73B ASN 3.3 0.4 - - - -
74B ALA* 1.3 74.5 - - - +
76B LEU* 1.3 67.9 + - - +
78B TYR* 3.5 2.8 + - - +
79B ILE* 3.2 20.5 + - + +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ALA* 3.9 13.0 - - + +
16B ILE* 3.7 37.0 - - + +
19B LEU* 3.4 31.7 - - + +
72B SER* 3.2 19.3 + - - +
73B ASN* 4.0 11.2 - - - +
75B ILE* 1.3 79.3 - - - +
77B CYS* 1.3 66.3 + - - +
79B ILE* 3.1 1.6 + - - -
80B ALA* 3.0 19.5 + - - +
104B MET* 6.0 0.2 - - - -
154B PHE* 3.9 21.8 - - + +
157B PHE* 5.3 1.6 - - + -
158B LEU* 3.9 38.8 - - + -
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Residues in contact with CYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASP* 3.4 14.6 - - - +
73B ASN* 3.1 26.5 + - - +
74B ALA 3.8 0.4 - - - +
76B LEU* 1.3 78.1 - - - +
78B TYR* 1.3 56.0 + - - +
80B ALA* 2.9 12.3 + - - +
81B ARG* 2.8 49.4 + - - +
86B CYS* 4.6 6.5 - - - -
100B GLU* 5.2 6.5 - - - -
154B PHE* 4.1 27.3 - - - -
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Residues in contact with TYR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLU* 3.5 28.5 - - + -
94A ILE* 3.7 21.3 - - + -
97A ASP* 5.3 0.2 - - - +
2B MET* 5.2 2.0 - - + -
62B LEU* 3.9 16.4 - - + -
64B ASP* 3.4 19.1 + - + -
67B HIS* 2.7 52.8 + + + -
69B ILE* 3.5 22.0 - - + -
74B ALA 3.1 16.3 + - - +
75B ILE 3.7 3.6 - - - +
76B LEU 3.3 0.2 - - - -
77B CYS* 1.3 79.2 - - - +
79B ILE* 1.3 63.3 + - + +
81B ARG* 3.1 25.4 - - + +
82B LYS* 3.8 23.2 + - - +
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B MET* 5.1 1.8 - - + -
16B ILE* 3.7 24.2 - - + -
19B LEU* 3.9 27.1 - - + -
20B LEU* 3.6 37.9 - - + -
23B THR* 4.1 4.9 - - - +
25B SER* 4.5 0.9 - - - +
62B LEU* 4.3 11.7 - - + -
75B ILE* 3.2 21.8 - - + +
76B LEU* 3.1 3.9 + - - +
78B TYR* 1.3 75.6 - - + +
80B ALA* 1.3 62.8 + - - +
81B ARG 3.4 0.3 + - - -
82B LYS* 3.4 13.9 - - + +
83B HIS* 2.7 48.2 - - + +
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 4.4 1.7 - - + +
76B LEU 3.0 11.2 + - - +
77B CYS* 2.9 14.0 + - - +
79B ILE* 1.3 77.5 - - - +
81B ARG* 1.3 49.1 - - - +
83B HIS* 2.9 4.6 + - - -
84B ASN* 2.7 33.4 + - - -
85B LEU* 3.0 41.3 + - + +
86B CYS* 3.9 11.9 - - - -
154B PHE* 4.0 12.6 - - + -
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLU* 3.2 31.9 - - - +
93A LYS* 3.4 42.8 - - + +
94A ILE* 5.8 1.3 - - - +
97A ASP* 3.0 40.1 + - - -
77B CYS* 2.8 32.5 + - - +
78B TYR* 3.1 24.6 - - + +
79B ILE 3.2 0.2 - - - -
80B ALA* 1.3 76.3 - - - +
82B LYS* 1.3 58.3 + - - +
83B HIS 2.8 6.2 + - - -
84B ASN* 3.2 16.1 + - - +
86B CYS* 4.6 12.3 - - - -
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B MET* 6.0 1.4 - - - +
64B ASP* 3.8 23.4 + - - -
67B HIS* 5.9 0.4 - - - -
78B TYR* 3.8 26.0 + - - +
79B ILE* 3.4 20.8 + - + +
81B ARG* 1.3 76.0 - - - +
83B HIS* 1.3 83.9 + - + +
84B ASN 3.9 0.2 - - - -
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Residues in contact with HIS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B THR* 3.5 44.6 + - + +
25B SER* 4.0 6.5 + - - -
79B ILE* 2.7 34.7 + - + +
80B ALA* 2.9 7.8 + - - +
82B LYS* 1.3 107.5 + - + +
84B ASN* 1.3 73.9 + - - +
85B LEU* 3.4 24.2 + - + +
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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