Contacts of the helix formed by residues 71 - 83 (chain B) in PDB entry 1JUO
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 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ARG* 4.9 6.2 - - - +
55B GLN* 4.1 3.4 - - - +
69B PRO 3.6 1.8 + - - -
70B PHE* 1.3 76.6 - - - +
72B LEU* 1.3 59.9 + - - +
73B GLU* 2.6 37.6 + - - +
74B THR* 2.7 35.2 + - - +
75B CYS* 3.2 8.8 + - - -
157B ASP* 2.6 29.5 + - - +
158B ASP* 3.7 14.3 + - - -
161B ALA* 5.5 1.2 - - - +
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Residues in contact with LEU 72 (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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51B ALA* 4.7 6.7 - - + +
52B ASP* 3.4 35.2 - - - +
55B GLN* 3.8 32.5 - - + +
71B ASN* 1.3 72.6 - - - +
73B GLU* 1.3 60.0 + - - +
75B CYS* 3.7 5.0 - - + +
76B ARG* 2.9 27.2 + - - +
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Residues in contact with GLU 73 (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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73A GLU* 3.9 44.6 - - + +
147A ARG* 4.2 4.4 + - - -
71B ASN* 2.6 18.4 + - - +
72B LEU* 1.3 73.3 - - - +
74B THR* 1.3 57.3 + - - +
76B ARG* 2.5 51.6 + - - +
77B LEU* 2.9 38.4 + - + +
147B ARG* 5.4 0.9 - - - +
161B ALA* 5.8 2.0 - - + -
165B LYS* 5.7 1.4 - - - +
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Residues in contact with THR 74 (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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70B PHE* 3.9 4.7 - - + +
71B ASN* 2.7 39.3 + - - +
73B GLU* 1.3 73.6 - - - +
75B CYS* 1.3 54.9 + - - -
77B LEU* 3.4 12.6 + - - +
78B MET* 3.1 42.2 + - - +
157B ASP* 2.7 34.3 + - - +
160B ILE* 4.3 2.8 - - - +
161B ALA* 3.7 24.1 + - - -
164B VAL* 5.4 0.2 - - - +
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Residues in contact with CYS 75 (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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51B ALA* 3.7 20.4 - - + +
54B LEU* 3.9 5.7 - - + +
55B GLN* 3.6 39.3 - - - -
58B LEU* 5.2 0.2 - - - -
70B PHE* 3.9 17.7 - - - -
71B ASN 3.2 17.8 + - - -
72B LEU* 3.7 9.9 - - - +
73B GLU 3.1 0.4 - - - -
74B THR* 1.3 74.6 - - - +
76B ARG* 1.3 67.6 + - - +
78B MET* 3.2 13.5 + - - +
79B VAL* 2.9 30.6 + - - +
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Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ARG* 3.1 41.7 - - - +
51B ALA* 4.2 12.0 - - + +
72B LEU 2.9 14.5 + - - +
73B GLU* 2.5 48.2 + - - +
75B CYS* 1.3 78.2 - - - +
77B LEU* 1.3 69.2 + - - +
79B VAL* 3.4 4.0 + - - +
80B SER* 3.0 36.9 + - - -
165B LYS* 5.8 0.4 - - - +
197B SER 5.3 0.4 + - - -
198B VAL* 3.2 26.9 + - - -
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 2.9 27.2 + - + +
74B THR* 3.5 7.2 - - - +
75B CYS 3.1 0.2 - - - -
76B ARG* 1.3 101.8 - - - +
78B MET* 1.3 56.9 + - - +
80B SER* 3.3 6.9 + - - -
81B MET* 2.9 28.8 + - - +
148B TYR* 5.1 1.3 - - - +
161B ALA* 3.6 42.2 - - + +
164B VAL* 3.6 20.6 - - + +
165B LYS* 4.0 25.4 - - + -
198B VAL* 3.8 15.5 - - + +
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Residues in contact with MET 78 (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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54B LEU* 4.0 7.4 - - + -
58B LEU* 3.6 30.1 - - + -
70B PHE* 3.7 16.2 - - + -
74B THR* 3.1 37.0 + - - +
75B CYS* 3.2 10.7 + - - +
77B LEU* 1.3 72.6 - - - +
79B VAL* 1.3 66.8 + - - +
80B SER 3.4 0.3 + - - -
81B MET* 3.4 16.2 + - + +
82B LEU* 3.4 12.5 + - - +
90B MET* 3.6 8.7 - - - +
98B LEU* 4.0 18.4 - - + -
102B LEU* 3.9 26.9 - - + -
160B ILE* 4.3 5.6 - - + -
164B VAL* 4.2 17.5 - - + -
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Residues in contact with VAL 79 (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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49B ILE 5.2 2.0 - - - +
50B ASP 4.4 2.9 - - - -
51B ALA* 3.8 25.4 - - + +
54B LEU* 3.8 18.4 - - + -
75B CYS 2.9 21.2 + - - +
76B ARG* 3.7 5.4 - - - +
78B MET* 1.3 75.9 - - - +
80B SER* 1.3 59.0 + - - +
82B LEU* 3.3 2.8 + - - +
83B ASP* 2.9 28.0 + - + +
88B GLY* 3.7 34.5 - - - +
89B THR 4.1 12.2 - - - +
90B MET* 3.6 12.5 - - + +
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Residues in contact with SER 80 (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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76B ARG* 3.0 31.4 + - - -
77B LEU* 3.5 9.0 - - - -
78B MET 3.2 0.2 - - - -
79B VAL* 1.3 76.4 - - - +
81B MET* 1.3 64.1 + - - +
82B LEU 3.1 1.0 + - - -
83B ASP* 3.4 16.8 + - - +
197B SER 5.0 7.1 + - - -
198B VAL* 5.0 2.9 + - - -
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Residues in contact with MET 81 (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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77B LEU 2.9 17.2 + - - +
78B MET* 3.7 5.4 - - - +
80B SER* 1.3 76.4 - - - +
82B LEU* 1.3 70.8 + - + +
84B ARG* 5.2 5.7 + - - +
98B LEU* 3.6 30.7 - - + -
101B VAL* 4.6 9.9 - - + -
105B TRP* 3.8 33.7 - - + -
164B VAL* 3.9 20.4 - - + -
167B ARG* 4.3 23.3 - - + -
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Residues in contact with LEU 82 (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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78B MET 3.4 8.0 + - - +
79B VAL 3.3 3.3 + - - -
80B SER 3.1 0.6 - - - -
81B MET* 1.3 107.8 - - + +
83B ASP* 1.3 57.9 + - - +
84B ARG* 2.9 33.4 + - - +
85B ASP* 5.4 0.2 - - - +
89B THR 5.5 0.7 - - - -
90B MET* 4.4 9.7 - - + +
94B GLU* 3.7 41.0 - - + +
97B GLU* 3.2 39.3 - - + +
98B LEU* 3.8 34.5 - - + -
101B VAL* 5.8 1.1 - - + -
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Residues in contact with ASP 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL* 2.9 20.9 + - + +
80B SER* 3.4 14.3 + - - +
82B LEU* 1.3 72.3 - - - +
84B ARG* 1.3 60.7 + - - +
85B ASP* 3.3 8.0 - - - +
86B MET* 3.0 18.7 + - - +
87B SER* 2.7 27.2 + - - -
88B GLY* 2.5 33.6 + - - -
89B THR 3.8 10.8 - - - +
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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