Contacts of the helix formed by residues 70 - 86 (chain B) in PDB entry 3GGJ
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 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B CYS* 4.3 4.0 - - - -
66B VAL* 3.0 27.6 + - - +
69B GLY* 1.3 69.4 - - - +
71B TYR* 1.3 62.8 + - - +
72B LYS 3.2 3.0 + - - -
73B PHE 3.5 2.6 + - - -
74B PHE* 3.4 19.8 + - - +
132B VAL* 5.3 4.4 - - - +
133B GLU* 6.1 0.4 - - - -
134B ASP* 3.1 27.7 + - - +
191B ALA* 6.0 0.2 - - - -
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Residues in contact with TYR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B CYS* 4.1 16.6 - - - -
66B VAL 4.5 0.2 + - - -
67B LEU* 5.3 6.9 - - + +
68B LYS 3.6 15.8 + - - +
69B GLY 3.1 18.1 + - - -
70B GLY* 1.3 75.6 - - - +
72B LYS* 1.3 84.7 + - + +
74B PHE* 3.8 1.3 - - - +
75B ALA* 3.0 28.0 + - + +
191B ALA 5.9 1.3 - - - -
199B ARG* 4.0 36.2 + - - +
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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
----------------------------------------------------------
38B HIS* 5.0 6.0 + - - -
69B GLY 5.5 0.4 - - - +
70B GLY 3.2 1.2 + - - -
71B TYR* 1.3 107.4 - - + +
73B PHE* 1.3 64.4 + - - +
75B ALA* 3.1 6.6 + - - +
76B ASP* 3.0 43.2 + - - +
190B TYR* 3.5 53.6 - - + +
191B ALA* 4.3 11.7 - - + +
202B ASN* 5.9 4.0 - - - -
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Residues in contact with PHE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 3.5 31.0 - - + -
48B LEU* 4.1 17.0 - - + -
70B GLY 3.5 2.6 + - - +
72B LYS* 1.3 74.8 - - - +
74B PHE* 1.3 56.3 + - - +
76B ASP 3.1 0.7 + - - -
77B LEU* 2.7 50.7 + - + +
132B VAL* 3.5 22.9 - - + -
133B GLU 3.3 21.1 - - - -
134B ASP* 3.7 17.2 + - - +
160B ALA* 4.7 2.0 - - + -
161B SER* 4.1 5.8 - - - -
162B LEU* 3.5 48.2 - - + -
190B TYR* 3.8 26.5 - + + -
191B ALA* 4.5 2.4 - - + +
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 3.4 39.0 - - + -
64B LEU 3.4 7.0 - - - -
65B CYS* 3.2 49.1 - - + -
70B GLY 3.4 16.4 + - - +
71B TYR 3.8 3.1 - - - +
73B PHE* 1.3 79.6 - - - +
75B ALA* 1.3 61.0 + - - +
77B LEU* 3.7 2.8 - - - +
78B LEU* 2.8 48.8 + - + +
96B VAL* 3.2 28.5 - - + -
98B PHE* 4.9 2.5 - + - -
132B VAL* 3.6 29.1 - - + +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 3.0 21.3 + - + +
72B LYS* 3.4 7.9 - - - +
74B PHE* 1.3 80.4 - - + +
76B ASP* 1.3 62.6 + - - +
78B LEU* 3.9 4.3 - - - +
79B ASP* 2.9 39.3 + - - +
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Residues in contact with ASP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B HIS* 4.8 0.7 + - - -
42B MET* 3.5 22.9 - - + +
45B THR* 4.1 7.6 - - + -
72B LYS* 3.0 29.1 + - - +
73B PHE 3.8 2.7 - - - +
75B ALA* 1.3 78.6 - - - +
77B LEU* 1.3 66.1 + - - +
79B ASP* 3.2 11.7 + - - +
80B TYR* 3.2 29.9 + - + -
190B TYR* 2.6 40.8 + - - +
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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
----------------------------------------------------------
45B THR* 3.7 33.7 - - + +
48B LEU* 4.3 10.5 - - + -
49B ALA* 4.1 16.2 - - + +
52B VAL* 5.0 4.7 - - + -
73B PHE* 2.7 34.3 + - + +
74B PHE 3.7 2.5 - - - +
76B ASP* 1.3 74.0 - - - +
78B LEU* 1.3 65.1 + - + +
80B TYR* 3.4 5.6 + - - +
81B ILE* 3.2 30.3 + - + +
130B LEU* 4.1 15.0 - - + -
132B VAL* 3.7 34.5 - - + -
160B ALA* 4.6 7.9 - - + -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 3.9 28.7 - - + -
74B PHE* 2.8 39.1 + - + +
75B ALA* 3.9 5.4 - - - +
77B LEU* 1.3 85.2 - - + +
79B ASP* 1.3 60.5 + - - +
81B ILE* 3.3 25.9 + - + +
82B LYS* 2.9 57.2 + - + +
94B MET* 5.8 7.9 - - + -
96B VAL* 4.6 15.7 - - + -
130B LEU* 5.5 0.9 - - + -
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA* 2.9 28.7 + - - +
76B ASP* 3.5 13.7 - - - +
78B LEU* 1.3 76.1 - - - +
80B TYR* 1.3 59.0 + - + +
82B LYS* 3.5 25.7 + - - +
83B ALA* 3.0 26.4 + - - +
86B ARG* 5.1 1.7 + - - -
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Residues in contact with TYR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B MET* 3.4 52.6 + - - +
43B ASP* 5.6 0.7 + - - -
45B THR* 3.9 17.3 - - + +
46B GLU* 3.5 40.1 + - + -
49B ALA* 3.6 21.5 - - + -
76B ASP* 3.2 23.8 + - + -
77B LEU 3.7 2.9 - - - +
78B LEU 3.2 0.4 - - - -
79B ASP* 1.3 79.3 - - + +
81B ILE* 1.3 57.5 + - - +
83B ALA* 3.2 12.6 + - + +
84B LEU* 3.0 29.5 + - - +
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 3.6 24.5 - - + +
52B VAL* 4.1 23.1 - - + -
53B MET* 4.0 16.4 - - + -
61B ILE* 6.5 0.4 - - + -
77B LEU* 3.2 27.7 + - + +
78B LEU* 3.3 32.1 + - + +
80B TYR* 1.3 72.5 - - - +
82B LYS* 1.3 68.1 + - + +
83B ALA 3.0 1.1 - - - -
84B LEU* 2.9 7.6 + - - +
85B ASN* 2.8 46.7 + - - +
130B LEU* 5.1 2.9 - - + -
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 2.9 40.3 + - + +
79B ASP* 3.5 26.8 + - - +
81B ILE* 1.3 77.0 - - + +
83B ALA* 1.3 61.8 + - - +
85B ASN* 3.1 19.7 + - - +
86B ARG* 3.2 32.7 + - - +
96B VAL* 6.2 3.1 - - - +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASP 3.0 15.3 + - - +
80B TYR* 3.2 20.0 - - + +
81B ILE 3.0 0.2 - - - -
82B LYS* 1.3 76.8 - - - +
84B LEU* 1.3 62.1 + - - +
86B ARG* 3.4 35.3 + - - +
87B ASN* 3.9 6.9 - - - +
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Residues in contact with LEU 84 (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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46B GLU 5.3 0.9 - - - +
49B ALA* 3.6 14.1 - - + +
50B ARG* 3.5 39.7 - - + +
53B MET* 4.1 13.7 - - + -
80B TYR 3.0 13.3 + - - +
81B ILE* 2.9 9.7 + - - +
83B ALA* 1.3 78.7 - - + +
85B ASN* 1.3 64.1 + - - +
86B ARG 3.3 1.0 + - - -
87B ASN* 3.7 15.7 + - - +
88B SER* 4.6 1.9 + - - -
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Residues in contact with ASN 85 (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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53B MET* 3.8 21.4 - - - +
61B ILE* 5.9 3.2 - - - +
81B ILE* 2.8 31.0 + - - +
82B LYS* 3.1 11.0 + - - +
84B LEU* 1.3 77.4 - - - +
86B ARG* 1.3 63.2 + - - +
87B ASN 3.2 2.7 - - - -
88B SER* 3.2 21.6 + - - +
91B SER* 5.8 0.3 - - - -
92B ILE* 3.6 38.1 + - + +
94B MET* 5.0 10.9 - - - +
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Residues in contact with ARG 86 (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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79B ASP 5.1 1.8 + - - -
82B LYS* 3.2 29.4 + - - +
83B ALA* 3.4 36.8 - - - +
84B LEU 3.2 1.0 - - - -
85B ASN* 1.3 76.9 - - - +
87B ASN* 1.3 66.7 + - - +
88B SER 3.7 4.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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