Contacts of the helix formed by residues 68 - 84 (chain B) in PDB entry 1Z83
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 PRO 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 4.7 6.7 - - + -
60B ILE* 4.2 17.3 - - + -
66B LEU 3.9 1.1 - - - +
67B VAL* 1.3 91.8 - - + +
69B LEU* 1.3 66.0 + - - +
70B GLU* 3.3 4.3 + - + +
71B THR* 3.3 24.2 + - - +
72B VAL* 3.4 10.7 + - - +
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Residues in contact with LEU 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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67B VAL 3.6 2.1 + - - -
68B PRO* 1.3 72.3 - - - +
70B GLU* 1.3 67.4 + - - +
72B VAL* 3.2 10.0 - - - +
73B LEU* 2.8 50.5 + - + +
95B TYR* 4.3 2.7 - - - +
98B GLU* 4.4 8.5 - - - +
100B GLN* 4.0 12.3 - - + +
101B GLN* 3.9 43.2 - - + +
104B GLU* 3.6 28.9 - - + +
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU* 3.4 8.5 - - - +
74A ASP* 3.2 9.3 - - - +
107A ARG* 5.7 4.5 - - - +
108A ARG* 3.3 37.6 + - - +
68B PRO* 3.3 2.5 - - + +
69B LEU* 1.3 84.0 - - - +
71B THR* 1.3 57.7 + - - +
73B LEU* 4.7 1.8 - - - +
74B ASP* 2.9 39.0 + - - +
104B GLU* 3.5 2.6 - - - +
108B ARG* 2.9 27.0 + - - -
642B ZN 2.1 29.0 - - - -
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 4.6 10.0 + - - -
702A SO4 4.4 9.1 + - - +
43B LEU* 4.9 1.6 - - + -
53B ARG* 3.9 25.9 + - - +
57B LEU* 4.1 23.5 - - + +
67B VAL* 5.2 0.7 - - - -
68B PRO* 3.3 22.8 + - - +
69B LEU 3.2 0.4 - - - -
70B GLU* 1.3 81.0 - - - +
72B VAL* 1.3 62.8 + - - +
74B ASP* 3.6 5.5 + - - +
75B MET* 3.3 38.6 + - + +
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B THR* 3.4 35.7 - - + -
42B LEU* 6.3 0.2 - - + -
43B LEU* 4.4 15.0 - - + -
67B VAL* 4.1 12.7 - - + +
68B PRO 3.4 9.1 + - - +
69B LEU* 3.2 15.5 - - - +
71B THR* 1.3 80.1 - - - +
73B LEU* 1.3 60.1 + - - +
75B MET* 3.3 8.2 + - + +
76B LEU* 2.9 27.4 + - - +
95B TYR* 3.9 17.0 - - + -
101B GLN* 4.3 0.9 - - - +
632B AP5 3.9 26.5 - - + +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 2.8 36.0 + - + +
70B GLU* 4.4 3.1 - - - +
72B VAL* 1.3 72.4 - - - +
74B ASP* 1.3 60.3 + - - +
76B LEU* 4.3 7.4 - - + -
77B ARG* 2.9 32.8 + - + +
95B TYR* 3.7 32.3 - - + +
104B GLU* 3.8 19.3 - - + +
105B PHE* 4.1 20.2 - - + -
108B ARG* 3.6 33.9 - - + +
109B ILE* 4.3 12.3 - - + -
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Residues in contact with ASP 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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77A ARG* 3.7 34.0 + - - +
78A ASP* 5.3 0.7 - - - +
108A ARG* 2.9 50.6 + - - +
70B GLU* 2.9 25.4 + - - +
71B THR* 3.7 6.2 - - - +
73B LEU* 1.3 74.9 - - - +
75B MET* 1.3 63.6 + - + +
77B ARG* 4.3 2.4 - - - +
78B ASP* 3.0 32.9 + - - +
108B ARG* 4.0 9.7 + - - +
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Residues in contact with MET 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.9 38.4 - - + +
43B LEU* 3.9 29.8 - - + -
46B GLU* 3.9 32.5 - - + +
53B ARG* 4.5 3.8 - - - +
57B LEU* 4.1 4.3 - - + -
71B THR* 3.3 27.1 + - + +
72B VAL* 3.3 9.7 + - + +
73B LEU 3.3 0.2 - - - -
74B ASP* 1.3 79.9 - - + +
76B LEU* 1.3 63.7 + - - +
78B ASP* 3.6 6.6 - - - +
79B ALA* 3.1 23.7 + - - +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.1 31.2 - - + +
39B THR* 4.2 15.3 - - + -
42B LEU* 4.1 9.4 - - + +
72B VAL 2.9 17.3 + - - +
73B LEU* 3.9 7.0 - - + +
75B MET* 1.3 75.3 - - - +
77B ARG* 1.3 66.0 + - - +
79B ALA* 3.3 4.5 + - - +
80B MET* 3.2 23.4 + - + +
92B ILE* 3.9 15.3 - - + -
95B TYR* 3.6 42.8 - - + -
105B PHE* 3.9 24.9 - - + -
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 6.3 0.2 - - - +
78A ASP* 3.6 60.4 + - - +
81A VAL* 4.5 6.7 - - - +
82A ALA* 5.9 0.2 - - - +
1B MET* 4.7 6.7 - - - +
2B GLU* 5.5 5.7 - - - +
5B LEU* 3.7 24.0 - - + +
73B LEU* 2.9 23.3 + - + +
74B ASP* 4.3 2.7 - - - +
76B LEU* 1.3 70.1 - - - +
78B ASP* 1.3 62.9 + - - +
80B MET* 3.2 4.6 + - + +
81B VAL* 2.9 46.2 + - + +
108B ARG* 3.2 30.1 + - - +
109B ILE* 3.7 33.0 - - + +
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Residues in contact with ASP 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A SER* 6.4 0.2 - - - -
1A MET* 3.5 38.8 - - + +
2A GLU* 4.1 9.0 + - - +
77A ARG* 2.9 42.0 + - - -
81A VAL* 3.3 17.8 - - - +
74B ASP 3.0 23.5 + - - +
75B MET* 3.6 7.3 - - - +
77B ARG* 1.3 78.9 + - - +
79B ALA* 1.3 58.2 + - - +
81B VAL* 3.4 0.9 + - - +
82B ALA* 3.0 24.8 + - - +
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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
----------------------------------------------------------
37B LEU* 3.8 28.0 - - + +
42B LEU* 4.7 15.0 - - + -
75B MET 3.1 15.0 + - - +
76B LEU 3.6 5.2 - - - +
77B ARG 3.3 0.2 - - - -
78B ASP* 1.3 80.1 - - - +
80B MET* 1.3 61.4 + - - +
82B ALA* 3.6 6.0 + - - +
83B LYS* 3.3 28.8 + - + +
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Residues in contact with MET 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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5B LEU* 4.3 12.3 - - + -
8B THR* 4.8 0.9 - - + -
10B ILE* 4.1 13.5 - - + -
37B LEU* 3.6 16.6 - - + -
76B LEU* 3.2 15.2 + - - +
77B ARG* 3.2 8.9 + - + +
79B ALA* 1.3 75.2 - - - +
81B VAL* 1.3 66.7 + - - +
83B LYS 3.1 1.2 + - - -
84B VAL* 2.9 28.7 + - - +
90B PHE* 3.6 39.8 - - + -
92B ILE* 4.1 9.4 - - + -
105B PHE* 3.9 31.2 - - + -
109B ILE* 3.9 29.2 - - + -
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Residues in contact with VAL 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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1A MET* 4.5 6.7 - - + -
81A VAL* 3.9 33.2 - - + +
82A ALA* 4.6 1.6 - - - +
1B MET* 3.9 34.6 - - + +
5B LEU* 4.2 11.0 - - + -
77B ARG* 2.9 45.0 + - - +
78B ASP 3.7 4.3 - - - +
80B MET* 1.3 75.8 - - - +
82B ALA* 1.3 63.3 + - - +
83B LYS 3.1 1.2 + - - -
84B VAL* 3.6 18.5 + - - +
85B ASN* 5.0 2.6 + - - -
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Residues in contact with ALA 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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0A SER* 6.4 0.9 - - - -
1A MET* 3.9 23.5 - - + +
78B ASP 3.0 16.9 + - - +
79B ALA* 3.9 9.6 - - - +
80B MET 3.2 0.6 - - - -
81B VAL* 1.3 78.9 - - - +
83B LYS* 1.3 65.5 - - + +
85B ASN* 5.5 1.4 + - - +
86B THR* 5.0 1.6 + - - -
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Residues in contact with LYS 83 (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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35B THR* 4.0 17.7 - - + +
36B HIS 5.7 0.6 + - - -
37B LEU* 4.9 7.9 - - - +
79B ALA 3.3 18.4 - - - +
80B MET 3.1 3.0 + - - +
81B VAL 3.1 0.4 - - - -
82B ALA* 1.3 87.5 - - + +
84B VAL* 1.3 60.5 + - - +
85B ASN* 3.2 3.1 - - - -
86B THR* 3.1 10.2 + - - +
87B SER* 2.9 27.0 + - - -
90B PHE* 4.1 12.1 - - + -
701B SO4 3.4 35.3 + - - +
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Residues in contact with VAL 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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1B MET* 3.5 36.6 - - + -
4B LYS* 4.0 30.1 - - + +
5B LEU* 4.1 16.2 - - + -
8B THR* 4.4 17.1 + - - -
80B MET 2.9 13.6 + - - +
81B VAL* 3.6 10.5 + - - +
83B LYS* 1.3 77.1 - - - +
85B ASN* 1.3 69.9 + - - +
86B THR 3.3 0.5 + - - -
87B SER* 3.8 10.4 + - - +
90B PHE* 4.1 9.9 - - + -
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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