Contacts of the helix formed by residues 83 - 96 (chain J) in PDB entry 5A0Q
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 PRO 83 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48J LEU* 3.7 26.5 - - + -
81J ILE 4.1 1.3 - - - +
82J LYS* 1.3 85.4 - - + +
84J TYR* 1.4 56.2 - - - +
86J LEU* 3.4 1.0 + - - +
87J MET* 3.1 21.3 + - - +
108J ILE* 3.2 14.5 - - + +
111J LEU 3.5 20.9 - - - +
112J ASP* 3.7 30.7 - - + +
113J PRO* 3.9 3.8 - - + -
119J PHE* 3.4 35.9 - - + -
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Residues in contact with TYR 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TYR* 5.6 1.7 + - - -
101B GLN* 3.4 39.8 + - + +
82J LYS* 3.3 15.5 - - + -
83J PRO* 1.4 76.3 - - - +
85J THR* 1.3 67.0 + - - +
87J MET* 3.2 35.4 + - + +
88J SER* 3.0 22.2 + - - -
119J PHE* 4.2 24.5 - + + -
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Residues in contact with THR 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B TYR* 3.2 52.8 + - + +
101B GLN 4.5 1.7 + - - -
102B GLU* 3.9 21.7 + - - +
73J TYR* 5.4 1.3 - - + -
79J ARG* 5.3 2.7 - - - +
81J ILE* 3.5 23.3 - - + -
82J LYS* 3.2 20.8 + - - +
84J TYR* 1.3 78.4 - - - +
86J LEU* 1.4 55.5 + - - +
88J SER* 3.2 3.5 + - - -
89J MET* 2.9 25.6 + - + +
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Residues in contact with LEU 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48J LEU* 3.8 30.3 - - + +
49J TYR 5.2 0.4 - - - +
50J ILE* 5.3 2.5 - - + -
66J LEU* 3.8 33.7 - - + -
70J LEU* 3.8 37.9 - - + -
81J ILE* 3.8 7.4 - - + +
82J LYS 3.1 12.6 + - - +
83J PRO 3.6 8.1 - - - +
84J TYR 3.3 0.2 - - - -
85J THR* 1.4 72.1 - - - +
87J MET* 1.4 66.0 + - - +
89J MET* 3.0 16.7 + - - +
90J VAL* 3.1 16.3 + - + +
108J ILE* 3.9 26.0 - - + -
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Residues in contact with MET 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLN* 5.6 0.7 - - + -
83J PRO 3.1 12.1 + - - +
84J TYR* 3.3 41.3 - - + +
85J THR 3.2 0.4 - - - -
86J LEU* 1.4 76.1 - - - +
88J SER* 1.3 80.6 + - - +
90J VAL* 3.5 6.2 - - - +
91J ALA* 2.9 32.2 + - + +
108J ILE* 4.2 4.9 - - - +
119J PHE* 4.2 10.5 - - + -
121J CYS* 3.6 29.4 - - - -
122J SER 5.3 0.7 - - - +
123J LEU* 3.5 14.0 - - + +
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Residues in contact with SER 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU 5.4 0.7 - - - -
99B VAL 3.5 17.0 - - - +
100B TYR 3.8 6.1 - - - -
101B GLN* 3.1 33.9 - - - +
84J TYR* 3.0 12.5 + - - -
85J THR 3.2 7.6 + - - -
87J MET* 1.3 88.0 - - - +
89J MET* 1.3 62.1 + - - +
91J ALA* 3.7 6.9 - - - +
92J ASN* 3.0 26.9 + - - +
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Residues in contact with MET 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 4.2 8.9 + - + -
100B TYR* 3.7 36.8 - - + -
66J LEU* 3.8 22.7 - - + -
69J ARG* 3.2 37.3 + - - +
70J LEU* 4.0 32.8 - - + -
73J TYR* 5.2 3.8 - - + -
81J ILE* 4.2 23.1 - - + -
85J THR 2.9 9.1 + - - +
86J LEU* 3.0 12.5 + - - +
88J SER* 1.3 77.1 - - - +
90J VAL* 1.4 57.9 + - - +
92J ASN* 4.0 0.3 - - - +
93J LEU* 3.0 22.8 + - - +
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Residues in contact with VAL 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J ILE* 4.5 9.6 - - + -
62J VAL* 4.3 20.6 - - + -
66J LEU* 3.6 36.6 - - + -
86J LEU* 3.1 14.6 + - + +
87J MET* 3.5 10.5 - - - +
89J MET* 1.4 74.8 - - - +
91J ALA* 1.3 64.0 + - - +
93J LEU* 3.6 7.0 - - + -
94J LEU* 3.1 29.2 + - + +
106J PRO* 4.7 11.0 - - + -
108J ILE* 5.3 3.6 - - + -
123J LEU* 3.6 26.5 - - + -
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Residues in contact with ALA 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I MET* 3.5 22.2 - - + +
57I GLN* 6.1 0.2 - - - +
87J MET* 2.9 24.1 + - + +
88J SER* 3.7 9.2 - - - +
89J MET 3.3 0.4 - - - -
90J VAL* 1.3 76.9 - - - +
92J ASN* 1.3 62.2 + - - +
94J LEU* 4.1 2.4 - - - +
95J TYR* 3.2 24.6 + - - +
123J LEU* 3.3 17.7 - - + +
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Residues in contact with ASN 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 3.9 25.1 - - - +
99B VAL* 4.2 25.3 - - + +
54I MET* 4.0 15.3 - - + +
57I GLN* 5.5 0.2 - - - +
69J ARG* 4.2 10.8 - - - +
88J SER 3.0 16.9 + - - +
89J MET 4.0 3.1 - - - +
91J ALA* 1.3 74.7 - - - +
93J LEU* 1.4 63.4 + - - +
95J TYR* 3.4 12.0 + - - +
96J GLU* 3.4 34.1 + - - +
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Residues in contact with LEU 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62J VAL* 4.2 21.3 - - + -
65J ARG* 4.0 33.9 - - + +
66J LEU* 4.1 18.4 - - + +
69J ARG* 3.5 36.1 - - - +
89J MET 3.0 19.8 + - - +
90J VAL* 3.7 9.4 - - + +
91J ALA 3.3 0.4 - - - -
92J ASN* 1.4 76.0 - - - +
94J LEU* 1.3 65.4 + - + +
96J GLU* 4.0 16.3 - - - +
97J LYS* 4.8 6.4 + - - +
102J TYR* 5.9 1.2 - - - -
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Residues in contact with LEU 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62J VAL* 3.6 36.1 - - + -
90J VAL* 3.1 18.2 + - + +
91J ALA* 4.3 2.0 - - - +
93J LEU* 1.3 82.7 - - + +
95J TYR* 1.3 60.9 + - - +
96J GLU 3.1 2.6 + - - -
97J LYS* 2.9 27.6 + - - +
101J PRO* 5.0 2.1 - - - +
102J TYR* 4.9 22.8 + - + +
104J THR* 4.2 11.2 - - + +
106J PRO* 4.0 33.9 - - + -
123J LEU* 5.0 1.6 - - + -
124J ASP 4.2 17.9 - - - +
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Residues in contact with TYR 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I ALA* 3.8 17.7 - - + -
51I ASP* 3.6 22.4 + - - -
54I MET* 3.4 50.0 - - + +
55I THR* 3.9 5.9 + - - -
94I ILE* 3.5 26.3 - - + +
91J ALA 3.2 18.9 + - - +
92J ASN* 3.4 4.4 + - - +
94J LEU* 1.3 74.7 - - - +
96J GLU* 1.3 64.7 + - + +
97J LYS 3.2 2.4 + - - -
98J ARG* 3.4 33.4 + - + +
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Residues in contact with GLU 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J ARG* 3.2 30.0 + - - -
92J ASN* 3.4 24.4 + - - +
93J LEU* 4.0 13.8 - - - +
94J LEU 3.1 0.4 - - - -
95J TYR* 1.3 77.6 - - + +
97J LYS* 1.3 71.5 + - + +
98J ARG 3.5 3.6 + - - -
99J PHE* 4.9 1.6 + - - +
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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