Contacts of the helix formed by residues 101 - 110 (chain E) in PDB entry 3ZP0
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 101 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99E PHE 3.5 0.8 + - - -
100E ASN* 1.3 92.1 + - - +
102E TYR* 1.3 62.7 + - - +
103E GLU* 3.3 4.7 - - - -
104E GLU* 3.4 16.6 + - + +
105E LEU 3.2 16.8 + - - -
234E TRP* 3.3 24.1 + - + +
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Residues in contact with TYR 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E SER* 3.7 6.6 + - - -
61E VAL* 3.4 21.7 + - + +
62E ALA* 2.8 46.4 + - + +
65E LEU* 6.1 0.2 - - + -
85E GLU* 4.1 3.3 + - - -
92E ASP* 4.1 4.9 + - - -
99E PHE* 3.4 45.4 + + + +
100E ASN 3.2 1.4 - - - -
101E ASP* 1.3 76.5 - - - +
103E GLU* 1.3 76.3 + - - +
105E LEU* 3.1 8.4 + - + +
106E LYS* 2.9 53.9 + - + +
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Residues in contact with GLU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E ASP* 3.3 1.8 - - - -
102E TYR* 1.3 96.4 + - - +
104E GLU* 1.3 63.4 + - + +
106E LYS* 3.4 12.6 + - + +
107E HIS* 2.9 27.9 + - - +
69F GLU* 3.3 46.2 + - + +
70F PHE* 3.7 6.3 - - - +
71F ASN* 3.6 40.3 + - - +
74F GLU* 4.4 4.5 - - - +
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Residues in contact with GLU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E ASP* 3.4 25.1 + - + +
102E TYR 3.3 0.6 - - - -
103E GLU* 1.3 79.4 - - + +
105E LEU* 1.3 60.1 + - - +
107E HIS* 3.5 17.1 - - - +
108E LEU* 3.3 23.9 + - - +
234E TRP* 4.3 9.7 - - + -
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Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E VAL* 5.5 1.3 - - + -
65E LEU* 3.9 22.0 - - + -
99E PHE* 3.6 35.0 - - + -
101E ASP 3.2 12.3 + - - +
102E TYR* 3.1 14.1 + - + +
103E GLU 3.1 0.6 - - - -
104E GLU* 1.3 73.8 - - - +
106E LYS* 1.3 60.0 + - - +
107E HIS 3.1 1.1 - - - -
108E LEU* 2.9 31.3 + - + +
109E LEU* 2.9 16.9 + - + +
115E PHE* 6.0 1.6 - - + -
177E LEU* 4.0 28.0 - - + -
179E LEU* 4.7 3.8 - - + -
234E TRP* 3.8 27.1 - - + -
236E ILE* 5.1 0.4 - - + -
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Residues in contact with LYS 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E VAL* 4.2 17.0 - - + -
85E GLU* 3.8 19.9 + - - -
102E TYR* 2.9 58.7 + - + +
103E GLU* 3.7 15.1 + - + +
105E LEU* 1.3 74.7 - - - +
107E HIS* 1.3 61.9 + - - +
109E LEU* 3.2 17.0 + - - +
110E SER* 3.3 10.6 + - - -
268E ILE* 3.4 24.6 - - + +
270E LYS* 4.6 2.8 - - - +
69F GLU* 2.7 47.6 + - + +
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Residues in contact with HIS 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E GLU 2.9 18.0 + - - +
104E GLU* 3.5 22.0 - - - +
105E LEU 3.1 0.2 - - - -
106E LYS* 1.3 76.1 - - - +
108E LEU* 1.3 70.8 + - + +
110E SER* 2.8 29.0 + - - -
111E ARG* 3.8 34.4 + - - -
66F VAL* 6.3 3.4 - - + -
67F GLY 5.4 2.8 + - - -
68F ARG* 5.1 18.8 - - + +
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Residues in contact with LEU 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E GLU 3.3 7.0 + - - +
105E LEU* 2.9 19.4 + - + +
107E HIS* 1.3 86.7 - - + +
109E LEU* 1.3 61.3 + - - +
111E ARG* 3.2 20.8 + - + +
112E ILE* 3.5 25.3 - - + +
234E TRP* 4.0 19.7 - - + -
236E ILE* 3.7 33.4 - - + -
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Residues in contact with LEU 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E VAL* 3.5 38.6 - - + -
64E TRP* 3.8 15.5 - - + -
65E LEU* 4.6 6.5 - - + -
80E TRP* 3.9 21.1 - - + -
83E ILE* 4.1 10.7 - - + +
105E LEU* 2.9 13.3 + - + +
106E LYS* 3.3 13.0 - - - +
108E LEU* 1.3 73.2 - - - +
110E SER* 1.3 54.4 + - - +
111E ARG 3.0 10.6 + - - -
112E ILE* 3.2 29.0 + - + +
115E PHE* 3.6 33.7 - - + -
266E SER* 3.7 3.8 + - - -
268E ILE* 4.1 8.1 - - + -
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Residues in contact with SER 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LYS 3.3 8.0 + - - -
107E HIS* 2.8 24.1 + - - -
108E LEU 3.2 0.6 - - - -
109E LEU* 1.3 77.3 - - - +
111E ARG* 1.3 67.6 + - - +
112E ILE 3.6 0.7 - - - -
265E ASP* 4.2 1.2 + - - -
266E SER* 2.5 44.6 + - - +
267E THR* 4.6 10.8 - - - +
268E ILE* 4.8 8.0 - - - +
66F VAL* 6.0 1.7 - - - +
67F GLY 5.7 4.6 + - - -
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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