Contacts of the helix formed by residues 72 - 83 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.7 30.4 - - - +
16D ILE* 4.6 15.3 - - - +
60D PRO* 4.1 10.9 - - - +
71D GLN* 1.3 69.5 - - - +
73D ASN* 1.3 60.1 + - - +
75D ILE* 2.9 18.1 + - - +
76D LEU* 2.9 30.9 + - - +
104D MET* 3.7 22.4 - - - +
158D LEU* 6.4 0.2 - - - -
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Residues in contact with ASN 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLU* 5.7 0.4 - - - +
101C ASN* 3.5 26.9 + - - +
71D GLN* 3.4 1.0 - - - +
72D SER* 1.3 71.4 - - - +
74D ALA* 1.3 64.3 + - - +
76D LEU* 3.4 21.0 - - - +
77D CYS* 2.9 33.0 + - - -
100D GLU* 3.4 36.9 + - - +
101D ASN* 5.4 0.8 - - - +
104D MET* 3.5 41.8 - - - +
158D LEU* 4.2 2.3 - - - +
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Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ASP* 3.6 35.1 - - + +
98C ILE* 4.0 9.2 - - - +
101C ASN* 3.7 10.8 - - - +
69D ILE* 3.7 11.0 - - + +
70D THR 3.3 22.2 - - - +
71D GLN* 3.0 4.3 + - + +
73D ASN* 1.3 76.1 - - - +
75D ILE* 1.3 63.4 + - - +
77D CYS* 3.3 3.9 + - - +
78D TYR* 3.0 22.5 + - - +
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Residues in contact with ILE 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 5.5 1.3 - - + -
16D ILE* 4.0 26.0 - - + -
60D PRO* 3.9 33.9 - - + +
61D TYR* 4.2 3.1 - - - +
62D LEU* 3.8 31.4 - - + +
69D ILE* 3.9 35.9 - - + +
70D THR 4.3 0.2 - - - -
71D GLN 3.1 20.4 - - - +
72D SER* 3.1 8.7 - - - +
74D ALA* 1.3 76.3 - - - +
76D LEU* 1.3 62.8 + - - +
78D TYR* 3.0 15.8 + - - +
79D ILE* 3.1 14.2 + - + +
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ALA* 4.2 8.7 - - + -
16D ILE* 3.9 39.0 - - + +
19D LEU* 3.9 20.2 - - + +
72D SER* 2.9 16.3 + - - +
73D ASN* 3.4 33.9 - - - +
74D ALA 3.3 0.2 - - - -
75D ILE* 1.3 75.2 - - - +
77D CYS* 1.3 58.3 + - - +
79D ILE* 3.0 6.2 + - + +
80D ALA* 2.9 31.5 + - - +
154D PHE* 4.2 18.4 - - + +
157D PHE* 5.8 1.8 - - + -
158D LEU* 3.8 30.7 - - + -
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Residues in contact with CYS 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ASP* 3.3 26.5 - - - +
100C GLU* 5.9 2.7 - - - -
101C ASN* 6.0 0.9 - - - -
73D ASN* 2.9 29.3 + - - +
74D ALA* 3.6 0.7 - - - +
75D ILE 3.3 0.2 - - - -
76D LEU* 1.3 75.6 - - - +
78D TYR* 1.3 56.3 + - - +
80D ALA* 4.7 4.9 - - - -
81D ARG* 3.0 37.6 + - - +
86D CYS* 4.3 9.2 - - - -
100D GLU* 4.0 22.2 - - - -
154D PHE* 4.0 15.0 - - - -
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Residues in contact with TYR 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLU* 3.9 8.3 - - - -
94C ILE* 3.6 36.1 - - + -
2D MET* 5.2 1.1 - - + -
62D LEU* 4.8 11.0 - - + -
64D ASP* 3.0 30.2 + - + -
67D HIS* 2.7 40.6 + + + -
69D ILE* 3.8 23.8 - - + -
74D ALA 3.0 12.1 + - - +
75D ILE* 3.0 11.5 + - + +
77D CYS* 1.3 76.8 - - - +
79D ILE* 1.3 66.4 + - + +
81D ARG* 3.2 28.2 + - - +
82D LYS* 3.2 33.4 + - + +
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Residues in contact with ILE 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D MET* 5.3 3.4 - - + -
16D ILE* 3.9 17.5 - - + +
19D LEU* 3.6 32.3 - - + -
20D LEU* 3.4 41.1 - - + -
23D THR* 4.4 13.5 - - - +
25D SER* 5.0 2.9 - - - +
62D LEU* 4.5 10.1 - - + -
75D ILE* 3.6 19.5 - - + +
76D LEU* 3.0 5.5 + - - +
78D TYR* 1.3 79.6 - - + +
80D ALA* 1.3 65.1 + - - +
82D LYS* 3.1 16.7 + - - +
83D HIS* 3.5 18.0 + - + -
85D LEU* 5.8 0.4 - - + -
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Residues in contact with ALA 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 4.3 2.0 - - + +
76D LEU 2.9 13.1 + - - +
79D ILE* 1.3 77.2 - - - +
81D ARG* 1.3 57.7 + - - +
83D HIS 3.3 0.8 + - - -
84D ASN* 2.9 8.1 + - - -
85D LEU* 2.7 49.2 + - + -
86D CYS* 3.8 5.7 + - - -
154D PHE* 3.5 42.8 - - + -
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Residues in contact with ARG 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLU* 3.0 41.5 + - - +
93C LYS* 3.5 42.4 + - + +
94C ILE* 4.9 0.8 - - - +
97C ASP* 3.4 22.6 + - - -
74D ALA 4.6 0.2 + - - -
77D CYS* 3.0 33.5 + - - +
78D TYR* 3.2 35.6 + - - +
79D ILE 3.2 0.8 - - - -
80D ALA* 1.3 75.5 - - - +
82D LYS* 1.3 57.4 + - - +
83D HIS 3.1 4.4 + - - -
84D ASN* 3.5 18.0 + - - +
86D CYS* 3.9 14.3 - - - -
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Residues in contact with LYS 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLU* 4.2 22.2 + - - +
64D ASP* 4.6 9.8 + - - +
67D HIS* 4.7 7.1 - - - -
78D TYR* 3.2 41.0 + - + +
79D ILE* 3.1 11.0 + - - +
81D ARG* 1.3 78.1 - - - +
83D HIS* 1.3 72.3 + - + +
84D ASN* 3.7 1.8 - - - -
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Residues in contact with HIS 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D THR* 3.5 48.8 + - + +
25D SER* 3.8 9.4 + - - -
79D ILE* 3.5 22.8 + - + +
80D ALA 3.3 1.0 + - - -
82D LYS* 1.3 90.4 + - + +
84D ASN* 1.3 71.2 + - - +
85D LEU* 3.0 30.2 + - + +
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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