Contacts of the helix formed by residues 59 - 69 (chain B) in PDB entry 3JRV
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 LYS 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LYS* 6.1 1.2 - - - +
55B LYS* 3.3 19.6 + - - +
56B GLU* 3.2 43.3 + - - +
57B LEU 3.1 0.6 - - - -
58B MSE 1.3 78.2 - - - +
60B PHE* 1.3 58.6 + - + +
61B ASP 3.0 1.3 - - - -
62B ASP* 3.0 32.0 + - - +
63B VAL* 3.4 11.2 + - + +
66B ARG* 5.2 0.3 + - - -
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Residues in contact with PHE 60 (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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56B GLU 4.1 10.3 - - - -
57B LEU* 3.0 40.0 + - + +
59B LYS* 1.3 76.0 - - + +
61B ASP* 1.3 64.9 + - - +
63B VAL* 3.6 12.3 - - + +
64B ALA 3.0 17.8 + - - -
99B PHE* 3.4 62.4 - + + +
102B ILE* 3.9 27.4 - - + -
103B GLY* 3.6 17.8 - - - +
140B LEU* 3.7 21.8 - - + -
143B PHE* 3.7 20.4 - + - -
144B LEU* 4.9 1.8 - - + -
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Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TYR* 4.2 1.7 + - - -
37B ARG* 3.1 41.4 + - - -
57B LEU 4.8 0.3 - - - +
58B MSE 3.0 18.3 + - - +
59B LYS 3.0 0.6 - - - -
60B PHE* 1.3 79.9 - - - +
62B ASP* 1.3 62.3 + - - +
64B ALA* 3.4 4.8 + - - +
65B ILE* 3.0 34.7 + - + +
103B GLY* 4.1 9.7 - - - +
106B ALA* 3.9 13.0 - - - +
107B LYS* 5.0 8.5 + - + -
110B GLU* 5.2 0.5 - - - +
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Residues in contact with ASP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.4 30.8 - - + +
74A ASN* 3.0 22.6 + - - +
58B MSE 5.7 0.2 - - - -
59B LYS* 3.0 19.1 + - - +
61B ASP* 1.3 83.8 - - - +
63B VAL* 1.3 60.3 + - - +
65B ILE* 3.3 8.6 + - - +
66B ARG* 2.9 46.5 + - - +
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Residues in contact with VAL 63 (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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59B LYS* 3.9 11.4 - - + +
60B PHE* 3.3 25.2 + - + +
62B ASP* 1.3 75.0 - - - +
64B ALA* 1.3 64.6 + - - +
66B ARG* 3.2 25.9 + - - +
67B TYR* 2.9 22.5 + - - +
96B GLU* 3.8 24.5 - - + +
99B PHE* 3.8 12.8 - - + -
100B ALA* 3.6 23.6 - - + +
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Residues in contact with ALA 64 (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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60B PHE 3.0 11.8 + - - +
61B ASP* 3.6 9.4 - - - +
63B VAL* 1.3 77.1 - - - +
65B ILE* 1.3 58.7 + - + +
68B TYR* 2.9 40.6 + - + +
73B ILE* 3.6 12.3 - - + +
100B ALA* 3.5 32.5 - - - +
103B GLY 4.2 2.7 - - - -
104B ILE* 4.1 12.3 - - + +
107B LYS* 6.4 0.4 - - + -
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Residues in contact with ILE 65 (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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65A ILE* 3.5 38.8 - - + -
70A ILE* 4.4 15.3 - - + +
61B ASP* 3.0 20.5 + - + +
62B ASP* 3.7 10.1 - - - +
63B VAL 3.3 0.2 - - - -
64B ALA* 1.3 76.3 - - + +
66B ARG* 1.3 57.8 + - - +
69B GLY* 2.8 30.5 + - - -
70B ILE* 3.7 25.4 - - + +
73B ILE* 2.4 46.4 - - + -
107B LYS* 5.1 7.9 - - + +
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Residues in contact with ARG 66 (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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70A ILE* 3.4 22.5 - - + +
71A ASP* 2.8 45.5 + - - +
74A ASN* 5.0 3.6 - - - +
59B LYS 5.2 0.4 + - - -
62B ASP* 2.9 31.6 + - - +
63B VAL* 3.2 35.1 + - - +
65B ILE* 1.3 78.5 - - - +
67B TYR* 1.3 62.4 + - - +
69B GLY* 4.4 1.7 + - - -
96B GLU* 5.1 7.1 + - - +
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Residues in contact with TYR 67 (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 VAL 2.9 16.8 + - - +
64B ALA 3.7 1.1 - - - +
66B ARG* 1.3 80.2 - - - +
68B TYR* 1.3 102.2 + + - +
93B HIS* 4.1 13.1 - + - -
94B ASP* 5.3 1.1 - - - -
96B GLU* 3.6 38.8 - - + +
97B SER* 3.5 31.4 - - - -
100B ALA* 3.7 16.2 - - + -
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Residues in contact with TYR 68 (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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64B ALA* 2.9 24.8 + - + +
67B TYR* 1.3 108.7 - + - +
69B GLY* 1.3 68.7 + - - +
72B LYS* 3.4 30.5 + - + +
73B ILE* 3.9 8.1 - - + +
76B ILE* 4.1 16.2 - - + -
100B ALA* 3.8 10.5 - - + -
101B THR* 3.7 17.5 + - - +
104B ILE* 2.7 44.9 - - + +
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Residues in contact with GLY 69 (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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65B ILE* 2.8 20.1 + - - -
66B ARG 4.4 1.6 + - - -
67B TYR 3.6 1.0 - - - -
68B TYR* 1.3 80.1 - - - +
70B ILE* 1.3 67.1 + - - -
71B ASP 3.3 2.9 - - - -
72B LYS 3.3 1.3 + - - -
73B ILE* 3.0 24.2 + - - +
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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