Contacts of the helix formed by residues 73 - 90 (chain B) in PDB entry 1Z0X
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 GLU 73 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B CYS* 3.4 26.7 - - - +
72B GLY* 1.3 79.8 - - - +
74B TRP* 1.3 65.7 + - - +
75B TYR* 4.5 3.2 - - + +
76B SER* 3.0 23.0 + - - +
77B ASP* 2.9 27.1 + - - -
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Residues in contact with TRP 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLY 3.7 4.0 + - - -
73B GLU* 1.3 71.0 - - - +
75B TYR* 1.3 95.4 + + + +
78B LEU* 3.1 27.9 + - + +
119B ILE* 3.8 22.8 - - + +
120B LEU* 3.8 15.5 - - + -
123B ALA* 3.7 34.9 + - + -
125B PHE* 3.8 21.7 - + - -
208B LEU* 3.8 20.0 - - + -
211B LEU* 4.0 20.4 - - + -
212B GLN* 3.8 40.8 - - + -
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Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 3.2 3.5 - - + +
74B TRP* 1.3 110.1 - + + +
76B SER* 1.3 70.8 + - - +
78B LEU 3.9 0.2 - - - -
79B LEU* 3.0 37.4 + - + +
205B LYS* 3.1 29.2 + - + +
208B LEU* 3.4 42.2 - - + +
209B ASP* 2.8 31.3 + - - -
212B GLN* 4.5 12.6 - - - -
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B CYS* 4.1 16.3 - - - -
73B GLU* 3.0 26.8 + - - +
75B TYR* 1.3 83.4 - - - +
77B ASP* 1.3 54.3 - - - +
79B LEU* 2.9 13.0 + - - +
80B ALA* 2.7 36.5 + - - +
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Residues in contact with ASP 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PRO* 5.1 0.2 - - - +
69B ALA 4.5 1.6 - - - +
70B LEU* 3.5 21.8 - - + +
71B CYS* 2.9 28.6 + - - -
72B GLY* 3.0 24.8 + - - -
73B GLU 2.9 25.6 + - - +
74B TRP* 4.1 2.4 - - - +
76B SER* 1.3 75.0 - - - +
78B LEU* 1.3 62.9 + - - +
80B ALA* 3.0 9.2 + - - +
81B PHE* 3.0 27.4 + - - -
119B ILE* 3.9 23.8 - - + +
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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
----------------------------------------------------------
74B TRP 3.1 16.5 + - - +
75B TYR 4.0 2.0 - - - +
77B ASP* 1.3 78.9 - - - +
79B LEU* 1.3 61.9 + - - +
81B PHE* 3.3 5.1 + - + +
82B MSE 3.2 24.9 + - + +
116B MSE 3.8 48.0 - - + +
119B ILE* 4.7 5.7 - - + +
120B LEU* 3.7 35.0 - - + -
134B VAL* 4.8 4.5 - - + -
137B LEU* 3.7 30.1 - - + -
208B LEU* 4.0 17.0 - - + -
211B LEU* 5.0 2.0 - - + -
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TYR* 3.0 27.0 + - + +
76B SER* 2.9 15.7 + - - +
78B LEU* 1.3 75.3 - - - +
80B ALA* 1.3 62.8 + - - +
82B MSE 3.3 4.3 + - + -
83B GLU* 3.0 32.2 + - - +
201B ILE* 4.2 26.7 - - + -
204B VAL* 4.8 11.0 - - + -
205B LYS* 3.9 32.8 - - + -
208B LEU* 4.0 16.8 - - + +
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PRO* 3.7 21.5 - - + -
69B ALA 4.9 9.2 - - - +
70B LEU* 5.4 0.7 - - + -
76B SER 2.7 15.2 + - - +
77B ASP* 3.0 13.0 + - - +
79B LEU* 1.3 72.6 - - - +
81B PHE* 1.3 62.1 + - - +
83B GLU* 3.4 9.5 + - - +
84B ASN* 3.0 30.4 + - - +
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Residues in contact with PHE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 3.8 31.3 - + - -
68B PRO* 3.7 20.9 - - + -
70B LEU* 4.1 5.6 - - + -
77B ASP 3.0 21.5 + - - -
78B LEU* 3.4 10.3 - - - +
80B ALA* 1.3 76.5 - - - +
82B MSE 1.3 57.2 + - - +
84B ASN* 3.2 3.8 + - - +
85B TYR* 3.0 36.0 + + - -
112B HIS* 4.3 15.5 - - + -
115B GLN* 3.2 37.9 - - + -
116B MSE 3.5 37.7 - - + -
119B ILE* 3.8 25.8 - - + -
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Residues in contact with MSE 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 LEU* 3.2 16.2 + - + +
79B LEU* 3.3 4.2 + - + +
81B PHE* 1.3 73.1 - - - +
83B GLU* 1.3 60.6 + - - +
85B TYR* 3.3 5.6 + - + +
86B TYR 3.0 22.3 + - - -
116B MSE 4.1 19.1 - - - +
134B VAL* 5.5 0.9 - - - +
137B LEU* 3.4 55.0 - - + +
138B GLN* 3.5 26.2 - - - +
141B LEU* 3.9 20.2 - - + -
200B PHE* 3.4 29.3 - - + -
204B VAL* 4.4 14.1 - - + -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 3.0 26.4 + - - +
80B ALA* 3.6 9.2 - - - +
82B MSE 1.3 78.4 - - - +
84B ASN* 1.3 70.0 + - - +
86B TYR* 3.1 7.7 + - - +
87B ASP* 3.1 24.8 + - - +
197B LYS* 3.6 30.1 + - - +
200B PHE* 4.4 0.2 - - - -
201B ILE* 3.9 29.6 - - + +
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Residues in contact with ASN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 3.5 22.4 - - + -
66B GLN* 2.9 33.2 + - + +
67B GLU 4.0 0.6 + - - -
68B PRO* 3.3 29.9 - - - +
80B ALA* 3.0 14.3 + - - +
81B PHE 3.7 0.7 - - - +
83B GLU* 1.3 82.2 - - - +
85B TYR* 1.3 61.2 + - - +
87B ASP* 3.4 15.5 + - - +
88B LEU* 3.0 26.3 + - - +
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Residues in contact with TYR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU* 2.9 25.3 + - - -
65B PHE* 3.6 27.8 - + - -
81B PHE* 3.0 28.9 + + - +
82B MSE 3.7 7.2 - - - +
83B GLU 3.2 0.2 - - - -
84B ASN* 1.3 75.7 - - - +
86B TYR* 1.3 60.2 + - - +
88B LEU* 3.6 8.5 - - + +
89B TYR* 2.9 53.3 + + + -
109B ARG* 3.6 28.7 + - - -
112B HIS* 3.1 19.9 - - - +
116B MSE 3.9 28.6 - - + +
138B GLN* 4.1 13.2 - - - +
141B LEU* 3.8 16.4 - - + -
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Residues in contact with TYR 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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82B MSE 3.0 14.3 + - - +
83B GLU* 3.1 9.6 + - - +
85B TYR* 1.3 78.0 - - - +
87B ASP* 1.3 65.7 + - - +
89B TYR* 3.7 2.5 + - - +
90B GLN* 3.1 48.2 + - + +
141B LEU* 3.7 25.1 - - + +
144B MSE 3.7 20.2 - - + -
145B ILE* 3.7 17.4 - - + +
196B GLN* 2.7 34.7 + - - +
197B LYS* 3.5 43.8 + - + +
200B PHE* 3.9 23.8 - + + -
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLN* 6.6 0.2 - - + -
83B GLU* 3.1 12.0 + - - +
84B ASN* 3.7 18.9 - - - +
86B TYR* 1.3 80.1 - - - +
88B LEU* 1.3 63.1 + - - +
90B GLN* 3.1 14.9 + - - +
91B GLN* 3.2 27.7 + - - +
197B LYS* 2.6 40.2 + - - +
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Residues in contact with LEU 88 (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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61B ILE* 3.5 42.8 - - + +
62B GLU* 4.4 3.6 - - - +
64B HIS* 3.6 26.7 - - + +
65B PHE* 3.8 29.6 - - + -
84B ASN 3.0 18.1 + - - +
85B TYR* 3.3 18.8 + - + +
87B ASP* 1.3 76.9 - - - +
89B TYR* 1.3 63.1 + - + +
91B GLN* 2.8 33.9 + - - +
92B PHE* 3.5 18.1 - - + -
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Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 4.7 1.3 - - + -
85B TYR* 2.9 40.6 + + + +
86B TYR 4.3 3.1 - - - +
88B LEU* 1.3 82.0 - - + +
90B GLN* 1.3 64.3 + - - +
91B GLN 3.2 0.2 - - - -
92B PHE 3.4 15.9 - - - +
95B ALA* 3.6 25.2 - - + +
96B VAL* 4.5 17.3 - - + -
99B GLU* 3.4 32.8 + - + +
109B ARG* 2.7 31.6 + - - -
138B GLN* 3.7 9.4 + - - -
141B LEU* 3.4 33.0 - - + -
142B PHE* 4.0 15.6 - + - -
145B ILE* 4.6 13.3 - - + +
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Residues in contact with GLN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B TYR* 3.1 48.1 + - + +
87B ASP* 3.1 9.4 + - - +
88B LEU 3.0 0.8 - - - -
89B TYR* 1.3 77.5 + - - +
91B GLN* 1.3 61.9 + - + +
92B PHE 3.5 2.1 + - - +
145B ILE* 3.2 34.3 + - + +
149B THR* 5.5 2.2 + - - -
196B GLN* 3.5 13.9 + - - +
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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
------------------------------------------------------------
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