Contacts of the helix formed by residues 77 - 91 (chain A) in PDB entry 1DIA
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 THR 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A THR 4.1 4.7 - - - +
76A THR* 1.3 78.7 - - - +
78A GLU* 1.3 64.7 + - - +
79A SER* 3.6 10.4 + - - -
80A GLU* 3.2 32.1 + - + +
81A VAL* 3.0 25.1 + - - +
107A ASN* 4.0 18.8 - - + +
109A ILE* 3.9 4.9 - - - -
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A THR* 1.3 73.6 - - - +
79A SER* 1.3 57.6 + - - +
81A VAL* 3.3 4.5 + - - +
82A MET* 3.0 45.4 + - + +
107A ASN* 5.7 0.2 - - - +
108A SER 4.5 5.8 + - - +
109A ILE* 3.8 34.4 - - + +
110A ASN* 2.9 32.9 + - - +
113A GLU* 2.7 29.9 - - - +
114A VAL* 4.0 8.1 - - + -
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Residues in contact with SER 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A THR* 3.8 9.4 - - - -
78A GLU* 1.3 79.5 - - - +
80A GLU* 1.3 61.4 + - - +
82A MET* 3.4 10.2 + - - +
83A LYS* 3.3 34.9 + - - +
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PRO* 5.6 1.9 - - - +
75A THR* 4.5 2.8 + - - +
76A THR* 3.5 32.7 + - + +
77A THR* 3.2 21.4 + - - +
78A GLU 3.3 0.2 - - - -
79A SER* 1.3 74.6 - - - +
81A VAL* 1.3 65.8 + - - +
83A LYS* 3.1 23.2 + - + +
84A TYR* 3.2 28.2 + - + -
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.4 12.8 - - + -
43A VAL* 3.9 22.4 - - + -
72A LEU* 4.4 8.7 - - + -
76A THR* 3.5 16.2 - - + -
77A THR 3.0 17.2 + - - +
78A GLU* 3.3 7.8 + - - +
80A GLU* 1.3 75.8 - - - +
82A MET* 1.3 56.7 + - - +
84A TYR* 3.2 4.2 + - - +
85A ILE* 3.0 32.2 + - + +
99A VAL* 5.5 0.7 - - + -
103A LEU* 5.4 2.7 - - + -
109A ILE* 4.1 14.1 - - + -
114A VAL* 3.6 32.5 - - + -
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Residues in contact with MET 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 3.0 41.1 + - + +
79A SER* 3.4 12.1 - - - +
81A VAL* 1.3 78.3 - - - +
83A LYS* 1.3 56.5 + - + +
85A ILE* 3.8 5.9 - - - +
86A THR* 2.9 34.1 + - - +
113A GLU* 3.6 27.6 - - + +
114A VAL* 4.0 19.1 - - - -
117A ALA* 3.9 24.0 - - + +
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Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A SER* 3.3 24.7 + - - +
80A GLU* 3.1 16.4 + - + +
82A MET* 1.3 75.6 - - + +
84A TYR* 1.3 65.2 + - + +
86A THR* 3.5 5.3 + - - -
87A SER* 2.8 28.0 + - - -
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.1 15.9 - - + -
70A ILE* 4.1 27.8 - - + -
72A LEU* 3.5 40.4 - - + +
80A GLU* 3.2 29.3 + - + -
81A VAL* 3.2 7.6 + - - +
83A LYS* 1.3 77.8 - - + +
85A ILE* 1.3 60.1 + - - +
87A SER* 3.1 9.6 + - - -
88A LEU* 2.9 36.6 + - + +
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.0 14.6 - - + -
81A VAL* 3.0 20.0 + - + +
82A MET* 3.8 8.5 - - - +
83A LYS 3.3 0.2 - - - -
84A TYR* 1.3 77.4 - - - +
86A THR* 1.3 56.8 + - - +
88A LEU* 3.2 3.6 + - - +
89A ASN* 2.9 30.8 + - - +
97A PHE* 3.8 19.9 - - + -
99A VAL* 4.2 8.7 - - + -
114A VAL* 3.1 47.1 - - + +
117A ALA* 3.8 36.8 - - + +
118A ILE* 3.9 4.3 - - + +
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Residues in contact with THR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A MET* 2.9 19.2 + - - +
83A LYS* 3.8 6.9 - - - -
84A TYR 3.3 0.2 - - - -
85A ILE* 1.3 76.7 - - - +
87A SER* 1.3 63.4 + - - +
89A ASN* 3.2 11.6 + - + +
90A GLU* 3.1 46.2 + - - +
117A ALA* 6.0 1.4 - - - +
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LYS 2.8 20.1 + - - -
84A TYR* 3.4 14.6 - - - -
86A THR* 1.3 77.8 - - - +
88A LEU* 1.3 57.9 + - - +
90A GLU* 3.3 7.8 + - - +
91A ASP* 2.9 30.3 + - - +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA* 3.8 25.4 - - + -
41A LEU* 4.5 17.0 - - + -
68A THR* 6.4 0.2 - - + -
70A ILE* 4.2 25.1 - - + -
84A TYR* 2.9 24.9 + - + +
85A ILE 3.2 4.7 + - - +
87A SER* 1.3 75.7 - - - +
89A ASN* 1.3 59.9 + - - +
90A GLU 3.5 0.2 + - - -
91A ASP* 3.6 11.7 + - + +
94A VAL* 4.2 18.6 - - + +
97A PHE* 3.6 39.8 - - + -
122A LYS* 3.0 24.9 + - - +
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Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ILE* 2.9 21.4 + - - +
86A THR* 3.2 13.1 + - + +
88A LEU* 1.3 77.3 - - - +
90A GLU* 1.3 62.7 + - + +
97A PHE* 3.1 19.3 - - - -
117A ALA 2.9 26.5 + - - -
119A ALA* 3.0 34.5 + - + +
122A LYS* 3.2 20.7 + - - +
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 3.1 35.9 + - + +
87A SER* 3.6 6.3 - - - +
89A ASN* 1.3 81.6 - - + +
91A ASP* 1.3 57.4 + - - +
92A SER* 3.0 12.0 + - - -
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Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 4.1 6.6 + - - -
87A SER 2.9 16.9 + - - +
88A LEU* 3.6 7.8 + - + +
89A ASN 3.5 1.2 - - - -
90A GLU* 1.3 72.1 - - - +
92A SER* 1.3 58.7 + - - +
93A THR* 2.7 32.8 + - - +
94A VAL* 2.9 35.8 + - + +
122A LYS* 3.1 14.7 + - - -
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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