Contacts of the strand formed by residues 105 - 115 (chain B) in PDB entry 1JC0
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 ASN 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B THR* 4.7 1.1 - - + -
98B ILE 3.0 16.4 - - - +
99B PHE* 4.1 25.7 - - + -
104B GLY* 1.3 80.1 - - - +
106B TYR* 1.3 62.5 + - - +
107B LYS* 4.1 16.0 - - - +
126B LYS 5.1 0.5 - - - +
127B GLY* 3.1 1.0 - - - -
128B ILE* 3.0 50.0 + - - +
129B ASP* 4.1 7.9 + - - -
130B PHE* 2.9 21.5 - - - -
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Residues in contact with TYR 106 (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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22B VAL* 4.0 16.4 - - + -
55B VAL* 3.5 19.9 - - + +
59B THR* 2.9 45.5 + - - +
60B LEU* 4.3 4.5 - - + -
63B THR* 4.9 0.2 - - - -
96B ARG 4.4 0.2 - - - -
97B THR* 3.2 6.2 - - - +
98B ILE* 2.6 62.5 + - + -
100B PHE* 3.5 16.6 - + - -
105B ASN* 1.3 77.1 - - - +
107B LYS* 1.3 66.8 + - - +
108B THR* 4.3 7.4 - - + -
125B LEU* 4.0 21.5 - - + -
126B LYS 3.7 3.1 - - - +
127B GLY* 3.9 6.3 - - - -
130B PHE* 3.2 30.1 - + - -
136B ILE* 4.3 2.1 - - - +
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Residues in contact with LYS 107 (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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96B ARG 3.2 5.8 - - - +
97B THR* 3.0 34.1 - - + -
99B PHE* 5.7 1.4 - - - -
105B ASN* 4.1 12.6 - - - +
106B TYR* 1.3 80.9 - - - +
108B THR* 1.3 61.8 + - - +
124B GLU 4.0 0.3 - - - +
125B LEU* 3.7 0.5 - - - -
126B LYS* 3.0 41.9 + - + +
128B ILE* 6.3 1.3 - - + -
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Residues in contact with THR 108 (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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63B THR* 4.0 29.0 + - + +
94B GLN 4.5 2.1 + - - -
95B GLU* 2.9 9.5 - - - +
96B ARG* 2.7 57.8 + - + +
98B ILE* 4.9 0.7 - - + -
106B TYR* 4.5 6.5 - - + -
107B LYS* 1.3 82.5 - - - +
109B ARG* 1.3 62.4 + - - +
110B ALA* 6.0 0.2 - - - +
123B ILE* 4.6 3.6 - - - -
124B GLU 3.3 8.3 - - - +
125B LEU* 3.9 23.3 - - + -
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Residues in contact with ARG 109 (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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93B VAL* 3.5 31.6 - - + +
94B GLN 3.5 2.9 - - - -
95B GLU* 4.0 16.4 + - + +
108B THR* 1.3 75.1 - - - +
110B ALA* 1.3 63.6 + - - +
111B GLU* 3.1 39.3 + - - +
122B ARG 4.1 0.3 - - - +
123B ILE* 3.4 2.4 - - - +
124B GLU* 3.0 41.5 + - + +
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Residues in contact with ALA 110 (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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63B THR 5.8 0.9 - - - +
93B VAL* 3.1 9.5 - - - +
94B GLN* 2.6 56.5 + - + +
108B THR* 6.0 0.2 - - - +
109B ARG* 1.3 78.1 - - - +
111B GLU* 1.3 64.6 + - - +
112B VAL* 4.4 2.2 - - + -
121B ASN* 3.7 20.4 - - - +
122B ARG 3.3 8.3 - - - +
123B ILE* 3.9 11.0 - - + -
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Residues in contact with GLU 111 (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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92B TYR 3.6 1.6 - - - -
93B VAL* 3.3 24.7 - - + +
109B ARG* 3.1 30.9 + - - +
110B ALA* 1.3 74.1 - - - +
112B VAL* 1.3 60.1 + - - +
113B LYS* 2.7 34.3 + - - +
120B VAL 3.6 2.8 - - - +
121B ASN* 3.8 0.5 - - - -
122B ARG* 3.0 39.9 + - + +
188B ILE* 3.8 17.8 - - + +
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Residues in contact with VAL 112 (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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66B CRO 3.8 15.7 - - - +
68B VAL* 4.6 2.7 - - + -
70B CYS* 4.3 8.7 - - - -
88B MET* 3.4 4.0 - - + +
91B GLY* 3.2 2.6 - - - -
92B TYR* 2.9 72.1 + - + +
94B GLN* 4.6 3.6 - - + +
110B ALA* 4.4 9.2 - - + -
111B GLU* 1.3 70.5 - - - +
113B LYS* 1.3 60.5 + - - +
119B LEU* 4.1 22.4 - - + -
120B VAL 3.4 6.7 - - - +
121B ASN* 3.4 23.3 - - - +
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Residues in contact with LYS 113 (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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88B MET* 4.4 1.3 - - - -
89B PRO 3.8 0.4 - - - +
90B GLU 3.2 27.4 - - - +
91B GLY* 3.7 4.9 - - - -
111B GLU* 2.7 34.9 + - - +
112B VAL* 1.3 76.7 - - - +
114B PHE* 1.3 63.8 + - - +
115B GLU* 3.5 27.1 + - + -
119B LEU* 3.6 6.5 - - - +
120B VAL* 2.9 32.9 + - + +
122B ARG* 4.6 16.3 - - + +
188B ILE* 4.2 12.1 - - + -
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Residues in contact with PHE 114 (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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7B LEU* 4.0 28.0 - - + -
8B PHE* 3.0 38.4 - + - -
12B VAL* 3.6 32.3 - - + -
88B MET* 3.9 17.2 - - + -
89B PRO* 3.4 31.9 + - + +
113B LYS* 1.3 75.5 - - - +
115B GLU* 1.3 64.6 + - - +
116B GLY 3.9 10.3 + - - +
117B ASP* 3.8 15.5 - - - -
118B THR 3.5 11.4 - - - -
119B LEU* 3.6 18.2 - - + -
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Residues in contact with GLU 115 (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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113B LYS* 3.5 28.6 + - + -
114B PHE* 1.3 75.4 - - - +
116B GLY* 1.3 56.7 + - - +
117B ASP 2.8 0.3 + - - -
118B THR* 2.5 43.9 + - - +
120B VAL* 2.8 51.2 - - + +
122B ARG* 3.3 21.7 + - - -
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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