Contacts of the helix formed by residues 81 - 94 (chain B) in PDB entry 1ZVM
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 ASP 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B HIS 3.6 4.8 + - - +
80B VAL* 1.3 73.1 - - - +
82B CYS* 1.3 55.7 + - - +
83B GLN* 3.8 14.0 + - - +
84B SER* 2.4 68.7 + - - +
85B VAL* 3.1 6.9 + - - +
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Residues in contact with CYS 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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64B LEU* 3.8 18.9 - - + +
67B CYS* 2.0 70.1 - - + +
68B VAL* 3.6 11.7 - - + -
71B THR* 3.9 14.1 - - - -
80B VAL 3.3 4.9 + - - -
81B ASP* 1.3 71.9 + - - +
83B GLN* 1.3 63.1 + - - +
85B VAL* 3.0 4.7 + - - +
86B TRP* 3.0 19.4 + - - +
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Residues in contact with GLN 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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64B LEU* 3.9 27.8 - - + +
81B ASP* 3.1 14.5 + - - +
82B CYS* 1.3 78.2 - - - +
84B SER* 1.3 61.0 + - - +
86B TRP* 3.4 13.0 + - - +
87B ASP* 3.1 49.0 + - - +
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Residues in contact with SER 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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81B ASP* 2.4 40.4 + - - +
83B GLN* 1.3 76.3 - - - +
85B VAL* 1.3 61.1 + - - +
87B ASP* 3.5 10.0 + - - +
88B ALA* 3.1 18.4 + - - +
112B LEU* 3.2 25.6 - - - +
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Residues in contact with VAL 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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63B VAL* 5.1 4.7 - - + -
67B CYS* 4.1 9.9 - - + -
80B VAL* 3.4 32.8 - - + -
81B ASP 3.7 4.3 - - - +
82B CYS* 3.0 11.8 + - - +
84B SER* 1.3 76.0 - - - +
86B TRP* 1.3 66.7 + - - +
88B ALA* 3.3 3.0 + - - +
89B PHE* 3.0 22.8 + - + +
109B LEU* 3.9 13.3 - - + +
112B LEU* 4.0 22.4 - - + +
113B GLY* 6.0 0.9 - - - -
149B LEU* 5.3 3.4 - - + -
150B LEU* 5.5 0.7 - - + -
153B LEU* 3.7 30.7 - - + -
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Residues in contact with TRP 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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59B PHE* 3.6 33.4 - + - -
60B PRO* 3.6 42.5 - - + +
63B VAL* 3.9 29.4 - - + +
64B LEU* 4.7 12.6 - - + -
82B CYS 3.0 11.5 + - - +
83B GLN* 3.7 20.0 - - - +
84B SER 3.4 0.4 - - - -
85B VAL* 1.3 79.3 - - - +
87B ASP* 1.3 66.8 + - - +
89B PHE* 3.2 6.2 + - + +
90B LYS* 2.7 79.1 + - + +
93B PHE* 5.0 0.9 - + - -
168B ILE* 4.3 11.9 - - + -
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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
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83B GLN* 3.1 39.7 + - - +
84B SER* 3.7 9.1 - - - +
85B VAL 3.3 0.2 - - - -
86B TRP* 1.3 86.3 - - - +
88B ALA* 1.3 56.3 + - - +
90B LYS* 3.9 17.8 + - - +
91B GLY* 2.9 27.2 + - - -
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Residues in contact with ALA 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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84B SER 3.1 17.6 + - - +
85B VAL 3.7 4.3 - - - +
86B TRP 3.3 0.2 - - - -
87B ASP* 1.3 73.6 - - - +
89B PHE* 1.3 65.7 + - - +
91B GLY* 3.5 2.2 + - - -
92B ALA* 3.2 20.4 + - - +
105B ASP 4.6 3.1 - - - +
108B PRO* 4.1 13.8 - - + +
109B LEU* 3.8 29.2 + - - +
112B LEU* 3.8 15.0 - - + -
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Residues in contact with PHE 89 (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 PHE* 4.0 14.4 - + - -
63B VAL* 3.9 33.7 - - + -
85B VAL 3.0 16.8 + - - +
86B TRP* 3.4 11.0 - + + +
88B ALA* 1.3 74.2 - - - +
90B LYS* 1.3 66.7 + - - +
92B ALA* 2.9 20.4 + - - +
93B PHE* 3.3 10.2 - + - -
106B TYR* 4.1 11.2 - + - -
109B LEU* 3.7 31.4 - - + +
153B LEU* 4.6 16.8 - - + -
154B ALA* 4.4 10.1 - - + -
159B TRP* 3.7 45.5 - + - -
188B PHE* 4.4 6.5 - + - -
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Residues in contact with LYS 90 (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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86B TRP* 2.7 59.8 + - + +
87B ASP* 3.9 18.3 + - - +
89B PHE* 1.3 71.9 - - - +
91B GLY* 1.3 62.5 + - - +
92B ALA 3.0 0.9 + - - -
93B PHE* 3.0 15.8 + - + -
94B ILE* 2.9 65.1 + - + +
168B ILE* 5.5 2.2 - - + -
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Residues in contact with GLY 91 (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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87B ASP 2.9 19.4 + - - -
88B ALA* 3.9 3.4 - - - -
89B PHE 3.2 0.4 - - - -
90B LYS* 1.3 77.1 - - - +
92B ALA* 1.3 61.0 + - - +
93B PHE 3.2 1.0 + - - -
94B ILE* 3.9 16.2 + - - +
96B LYS* 3.4 17.5 + - - -
105B ASP 5.0 0.7 - - - -
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Residues in contact with ALA 92 (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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88B ALA 3.2 7.6 + - - +
89B PHE 2.9 15.6 + - - +
91B GLY* 1.3 77.9 - - - +
93B PHE* 1.3 58.5 + - - +
96B LYS* 3.5 10.7 - - - +
101B ILE* 4.1 5.5 - - - +
105B ASP* 3.2 47.1 - - + +
106B TYR* 3.4 32.8 - - + -
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Residues in contact with PHE 93 (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 PHE* 4.0 18.8 - + - -
86B TRP* 5.0 0.7 - + - -
89B PHE* 3.3 29.4 - + - -
90B LYS* 3.0 19.2 + - + -
92B ALA* 1.3 80.6 - - - +
94B ILE* 1.3 80.7 + - + +
96B LYS* 3.3 24.9 + - - +
101B ILE* 4.5 4.8 - - + +
106B TYR* 4.6 4.9 - - + +
159B TRP* 3.7 27.8 - + + -
160B CYS* 3.6 42.8 - - - -
161B GLY* 3.6 5.3 + - - -
168B ILE* 4.5 13.0 - - + -
184B PRO* 3.9 22.4 - - + +
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Residues in contact with ILE 94 (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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90B LYS* 2.9 63.6 + - + +
91B GLY* 3.9 11.3 - - - +
93B PHE* 1.3 89.8 - - + +
95B SER* 1.3 72.1 + - - +
96B LYS* 2.9 16.1 + - - +
161B GLY* 4.9 3.8 - - - -
166B SER* 4.0 22.2 - - - +
167B LYS 5.2 2.5 - - - +
168B ILE* 4.6 11.9 - - + -
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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
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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