Contacts of the helix formed by residues 81 - 94 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A HIS 3.5 4.3 + - - +
80A VAL* 1.3 71.3 - - - +
82A CYS* 1.3 65.7 + - - +
83A GLN* 3.6 12.7 + - - +
84A SER* 2.7 40.4 + - - +
85A VAL* 3.1 13.2 + - - +
112A LEU* 6.5 0.2 - - + -
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Residues in contact with CYS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 3.7 20.4 - - + +
67A CYS* 2.0 67.2 - - + +
68A VAL* 3.5 14.4 - - + -
71A THR* 4.1 11.2 - - - -
80A VAL* 3.4 5.2 + - - -
81A ASP* 1.3 72.4 + - - +
83A GLN* 1.3 66.4 + - - +
85A VAL* 3.1 3.5 + - - +
86A TRP* 3.0 18.9 + - - +
68D VAL* 5.9 1.6 - - + -
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Residues in contact with GLN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 3.9 24.7 - - + +
81A ASP* 3.3 10.3 + - - +
82A CYS* 1.3 77.2 - - - +
84A SER* 1.3 57.6 + - - +
86A TRP* 3.4 15.4 + - - +
87A ASP* 2.9 54.2 + - - +
90A LYS* 5.4 0.2 + - - -
68D VAL* 6.0 2.4 - - + +
69D LYS* 4.0 19.2 + - - +
72D GLU* 3.3 37.8 + - - +
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Residues in contact with SER 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASP* 2.7 36.5 + - - +
83A GLN* 1.3 77.1 - - - +
85A VAL* 1.3 64.6 + - - +
87A ASP* 3.3 11.0 + - - +
88A ALA* 2.9 18.7 + - - +
112A LEU* 3.3 26.8 - - - +
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A VAL* 5.2 3.8 - - + -
67A CYS* 4.2 9.4 - - + -
80A VAL* 3.6 31.4 - - + -
81A ASP 3.1 6.6 + - - +
82A CYS* 3.1 9.4 + - - +
84A SER* 1.3 75.7 - - - +
86A TRP* 1.3 65.8 + - - +
88A ALA* 3.0 4.9 + - - +
89A PHE* 2.8 21.6 + - + +
109A LEU* 3.5 20.5 - - + +
112A LEU* 3.8 25.3 - - + +
113A GLY* 5.3 0.4 - - - +
149A LEU* 5.1 4.5 - - + -
150A LEU* 5.3 1.8 - - + -
153A LEU* 3.7 25.1 - - + -
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Residues in contact with TRP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 3.5 32.8 - + - -
60A PRO* 3.5 47.0 - - + +
63A VAL* 3.8 26.9 - - + -
64A LEU* 4.7 13.2 - - + -
82A CYS 3.0 11.6 + - - +
83A GLN* 3.5 21.8 - - - +
85A VAL* 1.3 77.7 - - - +
87A ASP* 1.3 73.6 + - - +
89A PHE* 3.0 9.9 + - + +
90A LYS* 2.8 71.2 + - + +
93A PHE* 5.1 1.3 - + - -
168A ILE* 4.4 9.6 - - + -
69D LYS* 6.4 0.2 - - - -
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLN* 2.9 45.3 + - - +
84A SER* 3.6 11.1 + - - +
85A VAL 3.3 0.2 - - - -
86A TRP* 1.3 76.3 - - - +
88A ALA* 1.3 57.6 + - - +
90A LYS* 3.5 28.9 + - - +
91A GLY* 2.9 26.7 + - - -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A SER 2.9 14.2 + - - +
85A VAL 3.4 7.4 - - - +
87A ASP* 1.3 74.1 - - - +
89A PHE* 1.3 66.1 + - - +
91A GLY* 3.5 2.1 + - - -
92A ALA* 3.2 19.9 + - - +
105A ASP 4.8 1.7 - - - +
108A PRO* 4.0 13.6 - - + +
109A LEU* 3.8 28.0 + - - +
112A LEU* 3.8 17.5 - - + -
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Residues in contact with PHE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 3.9 13.2 - + - -
63A VAL* 3.9 30.1 - - + -
85A VAL 2.8 11.6 + - - +
86A TRP* 3.3 16.4 - + + +
88A ALA* 1.3 74.4 - - - +
90A LYS* 1.3 66.1 + - - +
92A ALA* 2.9 21.3 + - - +
93A PHE* 3.4 11.2 - + - -
106A TYR* 4.1 10.5 - + - -
109A LEU* 3.7 30.5 - - + +
153A LEU* 4.7 12.6 - - + -
154A ALA* 4.4 14.1 - - + -
159A TRP* 3.6 48.7 - + - -
188A PHE* 4.5 7.2 - + - -
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLN* 5.4 0.4 + - - -
86A TRP* 2.8 54.5 + - + +
87A ASP* 3.5 30.6 + - - +
89A PHE* 1.3 72.3 - - - +
91A GLY* 1.3 62.9 + - - +
92A ALA 2.9 1.2 + - - -
93A PHE* 3.1 14.1 + - - -
94A ILE* 3.0 63.0 + - + +
168A ILE* 5.8 2.5 - - + -
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Residues in contact with GLY 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ASP 2.9 19.1 + - - -
88A ALA* 3.8 3.1 - - - -
89A PHE 3.2 0.2 - - - -
90A LYS* 1.3 77.6 - - - +
92A ALA* 1.3 59.8 + - - +
93A PHE 3.5 0.5 + - - -
94A ILE* 4.3 14.4 + - - +
96A LYS* 3.3 17.2 + - - -
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ALA 3.2 9.6 + - - +
89A PHE 2.9 15.9 + - - +
91A GLY* 1.3 78.3 - - - +
93A PHE* 1.3 57.5 + - - +
96A LYS* 3.2 19.4 + - - +
101A ILE* 4.2 3.6 - - - +
105A ASP* 3.1 40.6 - - - +
106A TYR* 3.7 30.3 - - + -
109A LEU* 5.7 0.2 - - + -
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Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 4.1 17.7 - + - -
86A TRP* 5.1 1.1 - + - -
89A PHE* 3.4 26.5 - + - -
90A LYS* 3.1 14.0 + - - -
92A ALA* 1.3 79.3 - - - +
94A ILE* 1.3 82.6 + - + +
95A SER 3.6 0.2 + - - -
96A LYS* 3.3 23.5 + - - +
101A ILE* 4.1 8.8 - - + +
106A TYR* 4.6 4.5 - - - +
159A TRP* 3.5 29.8 - + + -
160A CYS* 3.5 28.3 - - - -
161A GLY* 3.4 21.4 + - - -
168A ILE* 4.7 12.6 - - + -
184A PRO* 4.0 22.4 - - + +
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Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LYS* 3.0 55.8 + - + +
91A GLY* 4.3 9.0 - - - +
93A PHE* 1.3 91.0 - - + +
95A SER* 1.3 73.2 + - - +
96A LYS* 3.0 20.3 + - - +
161A GLY* 4.7 4.0 - - - -
166A SER* 4.5 22.7 - - - +
167A LYS 5.0 3.8 - - - +
168A ILE* 4.6 12.3 - - + -
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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