Contacts of the helix formed by residues 86 - 95 (chain J) in PDB entry 3J7Y
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 86 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2171A U 3.5 38.8 - - + +
2172A A 4.8 3.4 - - - +
2174A G 4.0 21.8 + - - +
23J ILE* 3.5 33.6 - - + +
65J PRO* 4.9 1.9 + - - +
67J PRO* 3.7 8.6 - - + +
85J PRO* 1.3 70.9 - - - +
87J VAL* 1.3 66.5 + - - +
88J SER* 4.3 2.5 - - - -
89J TYR* 2.9 22.4 + - - +
90J PHE* 2.8 19.9 + - - +
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Residues in contact with VAL 87 (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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2170A G 3.8 21.1 - - + +
2171A U 3.4 18.3 + - - +
85J PRO 3.4 2.6 + - - -
86J THR* 1.3 70.4 - - - +
88J SER* 1.3 56.9 + - - +
90J PHE* 3.2 1.8 + - - +
91J LEU* 2.6 54.8 + - + +
120J ILE* 3.6 30.7 - - + -
124J LYS* 3.5 22.6 - - - +
144J ILE* 3.9 12.8 - - + -
147J SER* 3.9 21.8 - - - +
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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
----------------------------------------------------------
2171A U 5.8 2.5 - - - -
2173A G 3.8 10.8 - - - -
2174A G 3.0 36.8 + - - -
86J THR* 3.1 0.4 - - - -
87J VAL* 1.3 86.8 - - - +
89J TYR* 1.3 62.5 + - - +
91J LEU* 3.4 2.3 + - - +
92J LYS* 3.0 29.9 + - - +
147J SER* 5.9 1.6 - - - -
151J LEU* 3.2 33.5 - - - +
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Residues in contact with TYR 89 (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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2174A G 4.6 1.7 + - - +
63J GLY 5.6 1.3 - - - -
64J ILE* 3.8 24.0 - - + -
65J PRO* 3.4 39.8 - - + +
85J PRO* 5.0 0.7 - - + -
86J THR* 2.9 25.7 + - - +
88J SER* 1.3 80.4 - - - +
90J PHE* 1.3 58.9 + - - +
92J LYS* 3.2 8.7 + - + +
93J ALA* 2.9 30.1 + - + +
98J GLU 6.2 0.2 - - - -
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Residues in contact with PHE 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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64J ILE* 4.2 18.5 - - + +
84J GLN* 5.3 0.2 - - - -
85J PRO* 4.3 12.8 - - + -
86J THR 2.8 12.3 + - - +
87J VAL* 3.6 9.4 - - - +
89J TYR* 1.3 77.7 - - - +
91J LEU* 1.3 57.4 + - - +
93J ALA* 3.2 12.0 + - + +
94J ALA* 2.9 32.7 + - + +
120J ILE* 3.4 39.9 - - + -
123J ILE* 3.3 41.5 - - + -
124J LYS* 4.1 9.2 - - - +
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Residues in contact with LEU 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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87J VAL* 2.6 44.0 + - + +
88J SER 3.7 4.5 - - - +
90J PHE* 1.3 72.8 - - - +
92J LYS* 1.3 58.4 + - - +
94J ALA* 3.2 7.6 + - + +
95J ALA* 2.9 29.3 + - - +
112J VAL* 4.9 20.0 - - + +
117J VAL* 5.3 7.0 - - + -
120J ILE* 4.2 28.9 - - + -
144J ILE* 4.3 7.4 - - + +
147J SER* 4.4 3.1 - - - -
148J ALA* 4.0 34.1 - - + +
151J LEU* 4.2 13.9 - - + -
153J ILE* 4.3 11.2 - - + +
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Residues in contact with LYS 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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2174A G 4.1 0.9 - - - -
2175A C 3.4 23.6 - - - +
88J SER* 3.0 22.4 + - - +
89J TYR* 3.4 13.2 - - + +
91J LEU* 1.3 76.3 - - - +
93J ALA* 1.3 56.3 + - - +
95J ALA* 3.2 7.2 + - - -
97J ILE* 2.7 72.0 + - + +
98J GLU 4.4 11.7 - - - +
100J GLY* 3.4 20.2 - - - -
101J ALA 4.5 0.2 - - - +
109J ALA* 5.2 0.2 - - - +
151J LEU* 3.7 37.8 - - + +
152J GLY* 4.2 8.3 - - - +
153J ILE* 4.5 6.6 - - + +
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Residues in contact with ALA 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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64J ILE* 4.6 12.1 - - + -
89J TYR* 2.9 17.2 + - + +
90J PHE* 3.3 18.2 - - + +
92J LYS* 1.3 76.6 - - - +
94J ALA* 1.3 57.9 + - - +
96J GLY* 2.9 20.8 + - - -
97J ILE 3.8 7.2 + - - -
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Residues in contact with ALA 94 (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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90J PHE* 2.9 17.7 + - + +
91J LEU* 3.3 14.4 - - + +
93J ALA* 1.3 73.2 - - - +
95J ALA* 1.3 57.9 + - - +
96J GLY 2.8 10.8 + - - -
112J VAL* 5.6 0.7 - - + -
116J HIS* 3.3 39.7 + - + +
120J ILE* 5.0 9.0 - - + -
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Residues in contact with ALA 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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91J LEU 2.9 12.4 + - - +
92J LYS* 3.2 8.9 + - - +
94J ALA* 1.3 73.7 - - - +
96J GLY* 1.3 58.9 + - - +
97J ILE* 3.3 33.5 - - + +
110J GLY* 4.8 9.1 - - - -
111J LEU 5.4 2.9 - - - -
112J VAL* 4.5 18.5 - - + +
153J ILE* 5.0 4.3 - - + -
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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