Contacts of the helix formed by residues 76 - 84 (chain A) in PDB entry 3ZYQ
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 GLY 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A VAL 4.4 0.6 + - - -
73A LYS 5.3 0.2 + - - -
74A ASN 3.7 2.2 - - - -
75A CYS* 1.3 76.7 - - - +
77A GLN* 1.3 65.9 - - - -
78A THR 3.2 2.7 - - - -
79A VAL* 3.0 13.7 + - - -
80A HIS* 3.0 34.4 + - - -
153A ALA 5.4 4.1 + - - -
155A GLU* 3.4 24.0 - - - +
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Residues in contact with GLN 77 (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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76A GLY* 1.3 70.1 - - - -
78A THR* 1.3 56.5 + - - +
80A HIS* 3.8 12.6 - - + +
81A ASP* 2.8 40.1 + - - +
122A GLU* 6.0 3.4 - - - +
124A LYS* 5.0 8.5 - - - +
125A TYR* 3.9 16.6 - - + +
155A GLU* 2.9 27.3 + - - +
202A LYS* 3.9 27.8 - - + +
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Residues in contact with THR 78 (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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35A ILE* 4.2 13.5 - - + +
36A ARG* 6.1 0.7 - - - -
42A ALA* 3.3 30.6 + - + +
75A CYS 3.5 18.8 - - - +
77A GLN* 1.3 78.3 - - - +
79A VAL* 1.3 66.2 + - + +
81A ASP* 4.0 9.9 - - - +
82A GLU* 3.6 13.2 - - - +
155A GLU* 5.2 1.2 + - - -
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Residues in contact with VAL 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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35A ILE* 3.7 25.4 - - + -
42A ALA* 3.9 10.5 - - + -
46A VAL* 4.1 14.4 - - + -
71A VAL* 3.7 29.6 - - + +
72A VAL* 3.8 23.6 - - + -
75A CYS* 3.6 23.1 - - + -
76A GLY 3.0 8.1 + - - +
78A THR* 1.3 76.2 - - + +
80A HIS* 1.3 65.9 + - - +
81A ASP 3.2 1.8 - - - -
82A GLU* 2.8 17.4 + - - +
83A VAL* 3.3 9.9 + - + +
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Residues in contact with HIS 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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72A VAL* 2.8 46.6 + - + -
76A GLY* 3.0 33.0 + - - -
77A GLN* 3.2 10.3 + - + +
79A VAL* 1.3 76.3 - - + +
81A ASP* 1.3 58.5 + - - +
83A VAL* 3.1 6.9 + - - -
84A ALA* 2.9 34.1 + - - +
119A PHE* 3.6 18.8 - + + -
125A TYR* 3.5 24.3 - - + +
152A PHE* 3.6 22.9 - + + -
153A ALA 6.0 0.7 - - - -
155A GLU* 5.2 1.3 - - - -
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Residues in contact with ASP 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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77A GLN* 2.8 21.0 + - - +
78A THR* 4.0 9.4 - - - +
79A VAL 3.2 0.2 - - - -
80A HIS* 1.3 76.6 - - - +
82A GLU* 1.3 62.7 + - - +
84A ALA 4.4 1.2 + - - +
85A ASN* 3.0 21.5 + - - +
124A LYS* 3.4 15.6 + - - +
125A TYR* 2.5 36.0 + - - -
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Residues in contact with GLU 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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42A ALA* 4.0 5.3 - - - +
43A LYS* 2.8 67.4 + - - +
46A VAL* 3.9 19.2 - - + +
47A ASN* 4.8 5.4 - - - +
50A LYS* 3.2 15.6 + - - -
78A THR 3.6 17.8 - - - +
79A VAL 2.8 9.6 + - - +
81A ASP* 1.3 78.8 - - - +
83A VAL* 1.3 58.5 + - - +
85A ASN* 3.1 12.9 + - - +
88A THR* 3.1 15.4 + - - -
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Residues in contact with VAL 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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46A VAL* 4.0 18.2 - - + -
68A MET* 4.6 12.6 - - + -
71A VAL* 6.1 0.2 - - + -
72A VAL* 3.9 31.2 - - + -
79A VAL* 3.3 12.8 + - + +
80A HIS* 3.1 12.9 + - - +
82A GLU* 1.3 85.0 - - - +
84A ALA* 1.3 65.1 + - + +
85A ASN 3.0 11.1 + - - -
88A THR* 3.3 25.7 - - + +
89A MET* 3.5 11.1 - - - +
115A TRP* 4.2 23.8 - - + -
119A PHE* 4.5 7.4 - - + -
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Residues in contact with ALA 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 HIS 2.9 11.5 + - - +
81A ASP 4.7 1.7 - - - +
82A GLU 3.9 0.2 - - - -
83A VAL* 1.3 74.0 - - - +
85A ASN* 1.3 59.4 + - - +
119A PHE* 3.6 13.9 - - + -
124A LYS 4.0 6.4 - - - +
125A TYR* 3.3 44.0 - - + -
127A VAL* 3.7 11.1 - - - +
128A VAL* 3.6 25.1 - - + -
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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