Contacts of the helix formed by residues 78 - 90 (chain B) in PDB entry 1A4I
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 GLU 78 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B THR* 1.3 74.1 - - - +
79B SER* 1.4 63.6 + - - +
81B VAL* 3.1 4.3 + - - +
82B MET* 2.9 33.8 + - + +
107B ASN* 5.3 0.4 - - - +
108B SER 4.2 7.3 + - - +
109B ILE* 3.5 34.5 - - + +
110B ASN* 2.8 34.0 + - - +
113B GLU* 3.6 19.8 - - - +
114B VAL* 4.7 4.3 - - + -
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR* 3.1 14.5 + - - -
78B GLU* 1.4 80.0 - - - +
80B GLU* 1.3 62.8 + - - +
82B MET* 3.6 9.2 - - - +
83B LYS* 3.0 23.4 + - - +
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 5.3 0.4 - - + -
75B THR 4.1 2.3 - - - +
76B THR* 3.4 21.6 + - + +
77B THR* 2.9 41.9 + - - +
79B SER* 1.3 78.6 + - - +
81B VAL* 1.3 67.0 + - - +
83B LYS* 3.2 7.0 + - - +
84B TYR* 3.1 35.8 + - + -
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 4.2 12.1 - - + -
43B VAL* 3.6 27.8 - - + -
72B LEU* 4.4 7.9 - - + -
76B THR* 3.7 11.2 - - + -
77B THR 3.1 13.4 + - - +
78B GLU* 3.6 7.4 - - - +
80B GLU* 1.3 76.1 - - - +
82B MET* 1.3 63.4 + - - +
84B TYR* 3.2 4.4 + - - +
85B ILE* 3.0 27.2 + - + +
99B VAL* 5.5 0.7 - - + -
103B LEU* 5.3 2.7 - - + -
109B ILE* 4.1 15.0 - - + -
114B VAL* 3.8 35.7 - - + -
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Residues in contact with MET 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU* 2.9 33.6 + - + +
79B SER* 3.6 8.3 - - - +
81B VAL* 1.3 76.8 - - - +
83B LYS* 1.3 57.4 + - - +
85B ILE* 3.3 5.7 + - - +
86B THR* 3.0 35.5 + - - +
113B GLU* 4.2 9.9 - - + +
114B VAL* 4.0 23.6 - - + -
117B ALA* 3.5 33.2 - - + -
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Residues in contact with LYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER 3.0 17.4 + - - +
80B GLU* 3.2 8.0 + - - +
82B MET* 1.3 76.0 - - - +
84B TYR* 1.3 62.3 + - + +
86B THR* 3.4 9.9 + - + -
87B SER* 2.9 32.9 + - - -
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Residues in contact with TYR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 4.1 15.0 - - + -
70B ILE* 3.9 34.5 - - + +
72B LEU* 3.5 37.1 - - + +
80B GLU* 3.1 29.1 + - + -
81B VAL* 3.2 6.7 + - - +
83B LYS* 1.3 78.0 - - + +
85B ILE* 1.3 63.7 + - - +
87B SER* 2.5 26.3 + - - -
88B LEU* 3.0 15.6 + - + +
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Residues in contact with ILE 85 (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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41B LEU* 4.0 13.0 - - + -
81B VAL* 3.0 20.3 + - + +
82B MET* 3.7 9.4 - - - +
84B TYR* 1.3 74.6 - - - +
86B THR* 1.3 58.8 + - - +
88B LEU* 3.2 2.9 + - - +
89B ASN* 2.8 33.6 + - - +
97B PHE* 3.7 17.0 - - + -
99B VAL* 4.0 10.1 - - + -
114B VAL* 3.3 45.1 - - + +
117B ALA* 3.6 38.1 - - + +
118B ILE* 3.9 9.6 - - + +
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Residues in contact with THR 86 (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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82B MET* 3.0 20.4 + - - +
83B LYS* 3.6 12.3 - - + +
85B ILE* 1.3 76.6 - - - +
87B SER* 1.3 57.8 + - - +
89B ASN* 3.2 13.3 + - - +
90B GLU* 2.9 43.9 + - + +
117B ALA* 6.0 1.2 - - - +
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Residues in contact with SER 87 (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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83B LYS* 2.9 19.1 + - - -
84B TYR* 2.5 34.0 + - - +
86B THR* 1.3 77.6 - - - +
88B LEU* 1.3 60.3 + - - +
90B GLU* 3.2 7.2 + - - +
91B ASP* 2.9 30.4 + - - +
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Residues in contact with LEU 88 (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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39B ALA* 3.8 24.7 - - + -
41B LEU* 4.6 17.5 - - + +
68B THR* 6.3 0.4 - - + -
70B ILE* 4.2 25.1 - - + -
84B TYR* 3.0 19.6 + - + +
85B ILE* 3.6 3.8 - - - +
87B SER* 1.3 80.2 + - - +
89B ASN* 1.3 68.0 + - - +
91B ASP* 3.3 12.7 + - + +
94B VAL* 4.2 18.6 - - + +
97B PHE* 3.6 40.6 - - + -
122B LYS* 2.9 20.1 + - - +
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Residues in contact with ASN 89 (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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85B ILE* 2.8 20.7 + - - +
86B THR* 3.2 14.9 + - - +
88B LEU* 1.3 77.7 - - - +
90B GLU* 1.3 65.9 + - - +
97B PHE* 3.1 18.4 - - - -
117B ALA 2.9 25.5 + - - -
119B ALA* 2.9 34.4 + - + +
121B GLU* 4.5 4.9 - - - +
122B LYS* 3.1 23.7 + - - +
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B THR* 2.9 36.1 + - + +
87B SER* 3.7 6.7 - - - +
88B LEU 3.2 0.2 - - - -
89B ASN* 1.3 81.4 - - - +
91B ASP* 1.3 58.5 + - - +
92B SER* 3.2 10.2 + - - -
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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