Contacts of the helix formed by residues 78 - 88 (chain A) in PDB entry 1ZDR
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 SER 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A VAL* 6.4 0.4 - - - -
76A LEU 3.7 0.4 - - - -
77A HIS* 1.3 80.7 - - - +
79A LEU* 1.3 66.1 - - - +
80A GLU* 3.4 11.2 + - - +
81A GLU* 3.0 29.3 + - - +
82A VAL* 2.9 27.3 + - - +
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Residues in contact with LEU 79 (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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78A SER* 1.3 73.7 - - - +
80A GLU* 1.3 62.4 + - - +
82A VAL* 4.0 6.4 - - + +
83A LYS* 3.1 26.8 + - - +
104A ALA* 6.3 2.9 - - + -
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Residues in contact with GLU 80 (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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78A SER* 3.0 9.9 + - - +
79A LEU* 1.3 80.3 - - - +
81A GLU* 1.3 63.5 + - + +
83A LYS* 3.1 30.7 + - - +
84A GLN* 3.0 62.3 + - - +
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Residues in contact with GLU 81 (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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75A VAL 3.9 2.1 - - - +
76A LEU* 3.6 17.1 - - + +
77A HIS* 2.9 47.2 + - - +
78A SER* 3.0 27.4 + - - +
80A GLU* 1.3 79.0 - - + +
82A VAL* 1.3 61.9 + - - +
84A GLN* 4.0 10.9 - - - +
85A TRP* 3.0 24.9 + - - +
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Residues in contact with VAL 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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62A VAL* 3.9 26.0 - - + -
76A LEU* 3.6 35.6 - - + +
78A SER 2.9 18.9 + - - +
79A LEU* 4.0 7.6 - - + +
81A GLU* 1.3 77.1 - - - +
83A LYS* 1.3 57.7 + - - +
85A TRP* 3.3 1.8 + - + +
86A ILE* 2.9 41.8 + - + +
101A LEU* 6.5 0.7 - - + -
105A THR* 5.8 7.0 - - + -
108A ILE* 5.5 5.2 - - + -
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Residues in contact with LYS 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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79A LEU 3.1 16.9 + - - +
80A GLU* 3.1 36.5 + - - +
82A VAL* 1.3 74.3 - - - +
84A GLN* 1.3 70.4 + - + +
86A ILE* 3.3 8.1 + - - +
87A ALA* 2.8 32.5 + - - +
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Residues in contact with GLN 84 (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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80A GLU* 3.0 42.4 + - - +
81A GLU* 4.0 10.0 - - - +
83A LYS* 1.3 82.5 - - + +
85A TRP* 1.3 63.4 + - - +
87A ALA* 3.3 14.0 + - - +
88A SER* 3.4 12.6 + - - -
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Residues in contact with TRP 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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39A ALA* 3.7 26.5 - - + -
41A VAL* 3.7 26.9 - - + -
58A ASP* 6.1 0.9 - - + -
60A VAL* 3.8 18.2 - - + -
74A LEU* 3.4 25.4 - - + +
76A LEU* 3.9 27.1 - - + -
81A GLU 3.0 17.6 + - - +
82A VAL* 3.7 3.1 - - + +
83A LYS 3.2 0.2 - - - -
84A GLN* 1.3 78.7 - - - +
86A ILE* 1.3 83.4 + - + +
88A SER* 3.0 9.9 + - - -
89A ARG* 2.9 66.7 + - - +
93A VAL* 3.8 11.2 - - + -
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Residues in contact with ILE 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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2A ILE* 3.8 45.3 - - + +
41A VAL* 5.9 0.9 - - + -
82A VAL* 2.9 37.0 + - + +
83A LYS* 3.5 8.3 - - - +
85A TRP* 1.3 99.2 - - + +
87A ALA* 1.3 66.8 + - - +
89A ARG* 3.0 22.2 + - - +
93A VAL* 4.9 0.7 - - + -
95A ILE* 6.1 0.7 - - + -
108A ILE* 4.2 21.8 - - + -
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Residues in contact with ALA 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 LYS* 2.8 18.6 + - - +
84A GLN* 3.5 10.3 - - - +
85A TRP 3.2 0.2 - - - -
86A ILE* 1.3 80.4 - - - +
88A SER* 1.3 57.9 + - - +
89A ARG 3.6 3.1 + - - +
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Residues in contact with SER 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 GLN 3.4 7.3 + - - -
85A TRP* 3.0 12.4 + - - -
86A ILE 3.1 0.6 - - - -
87A ALA* 1.3 77.2 - - - +
89A ARG* 1.3 92.4 + - - +
90A ALA* 3.6 4.5 + - - +
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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