Contacts of the helix formed by residues 69 - 82 (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 GLY 69 (chain B).
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Specific contacts
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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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Residues in contact with ILE 70 (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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62A ASP* 3.6 39.0 - - + +
65A ILE* 3.8 31.5 - - + +
66A ARG* 3.5 33.2 - - + +
65B ILE* 3.7 28.4 - - + +
69B GLY* 1.3 73.4 - - - -
71B ASP* 1.3 64.1 + - - +
73B ILE* 3.5 7.3 - - + +
74B ASN* 2.9 35.9 + - - +
107B LYS* 4.1 15.7 - - - +
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Residues in contact with ASP 71 (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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66A ARG* 2.6 50.6 + - - +
69B GLY 3.3 0.8 - - - -
70B ILE* 1.3 79.0 - - - +
72B LYS* 1.3 59.6 + - + +
74B ASN* 3.3 7.9 + - - +
75B GLU* 2.9 28.3 + - - +
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Residues in contact with LYS 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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68B TYR* 3.4 35.9 - - + +
69B GLY 3.3 1.8 + - - -
70B ILE 3.3 0.4 - - - -
71B ASP* 1.3 73.8 - - + +
73B ILE* 1.3 67.1 + - - +
75B GLU* 3.1 30.9 + - - +
76B ILE* 2.9 35.1 + - + +
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Residues in contact with ILE 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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64B ALA* 3.6 10.3 - - + +
65B ILE* 2.4 61.0 - - + +
68B TYR* 3.9 17.0 - - + -
69B GLY 3.0 15.7 + - - +
70B ILE* 3.5 11.9 - - + +
72B LYS* 1.3 75.9 - - - +
74B ASN* 1.3 65.7 + - - +
76B ILE* 3.2 9.1 + - - +
77B VAL* 2.9 24.8 + - + +
104B ILE* 5.2 5.8 - - + -
107B LYS* 3.8 40.8 - - + -
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Residues in contact with ASN 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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62A ASP* 3.1 30.6 + - - +
66A ARG* 4.4 11.5 - - - +
70B ILE* 2.9 30.3 + - - +
71B ASP* 3.7 6.6 - - - +
73B ILE* 1.3 80.3 - - - +
75B GLU* 1.3 58.4 + - - +
77B VAL* 3.8 6.5 - - - +
78B GLU* 2.9 29.8 + - - +
107B LYS* 4.5 9.2 + - - -
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Residues in contact with GLU 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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71B ASP 2.9 16.0 + - - +
72B LYS* 3.1 41.9 + - + +
74B ASN* 1.3 75.6 - - - +
76B ILE* 1.3 60.5 + - + +
78B GLU* 3.4 6.3 + - - +
79B ALA* 2.9 30.8 + - + +
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Residues in contact with ILE 76 (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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68B TYR* 4.1 20.6 - - + -
72B LYS* 2.9 25.7 + - + +
73B ILE* 3.6 6.1 - - - +
75B GLU* 1.3 77.2 - - + +
77B VAL* 1.3 67.3 + - + +
79B ALA* 3.2 7.1 + - - +
80B MSE 2.9 35.6 + - + +
87B ILE* 5.5 3.8 - - + -
104B ILE* 3.8 44.6 - - + -
108B ILE* 4.4 2.5 - - + -
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Residues in contact with VAL 77 (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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73B ILE* 2.9 22.7 + - + +
74B ASN* 3.8 8.1 - - - +
76B ILE* 1.3 75.6 - - + +
78B GLU* 1.3 58.3 + - - +
80B MSE 3.0 3.3 + - - +
81B SER* 2.9 27.9 + - - -
104B ILE* 6.2 0.7 - - + -
107B LYS* 3.6 33.7 - - + -
108B ILE* 4.1 23.0 - - + +
111B HIS* 3.4 45.3 - - + +
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Residues in contact with GLU 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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74B ASN 2.9 18.8 + - - +
75B GLU* 3.7 7.0 - - - +
77B VAL* 1.3 77.8 - - - +
79B ALA* 1.3 61.7 + - - +
81B SER* 3.2 24.2 + - - -
82B GLU* 4.6 2.6 + - - +
111B HIS* 5.8 3.7 - - - -
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Residues in contact with ALA 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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75B GLU* 2.9 20.5 + - + +
76B ILE* 3.6 7.6 - - - +
78B GLU* 1.3 77.1 - - - +
80B MSE 1.3 62.6 + - + +
81B SER 3.7 0.3 + - - -
82B GLU* 4.8 2.3 + - - +
84B ASP* 5.3 1.9 + - - +
85B HIS* 3.3 34.7 + - + +
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Residues in contact with MSE 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 ILE* 2.9 25.4 + - + +
77B VAL 3.0 4.2 + - - +
79B ALA* 1.3 78.6 - - + +
81B SER* 1.3 65.4 + - - +
82B GLU 3.3 1.8 - - - -
83B GLY* 3.0 16.7 + - - -
85B HIS* 3.3 42.2 - - - +
86B TYR 4.4 1.6 - - - +
87B ILE* 3.8 28.5 - - + -
108B ILE* 3.8 26.5 - - + -
112B TRP* 3.4 14.2 - - + -
124B SER* 4.0 10.1 - - - +
125B LEU* 3.8 28.0 - - + +
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Residues in contact with SER 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 VAL 2.9 10.9 + - - -
78B GLU* 3.2 25.2 + - - -
80B MSE 1.3 77.6 - - - +
82B GLU* 1.3 66.6 + - - +
108B ILE* 6.0 0.2 - - - -
111B HIS* 3.1 26.5 + - - -
112B TRP* 2.9 27.4 + - - +
115B LYS* 3.7 15.1 + - - -
117B ILE* 5.7 1.0 - - - +
121B ARG* 3.0 12.1 + - - -
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Residues in contact with GLU 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 GLU 4.6 3.0 + - - +
79B ALA 4.8 1.9 + - - +
80B MSE 3.3 0.8 - - - -
81B SER* 1.3 83.7 + - - +
83B GLY* 1.3 61.5 + - - +
84B ASP* 3.3 25.0 + - + +
115B LYS* 5.0 6.2 + - - -
121B ARG* 3.3 29.6 + - - +
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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