Contacts of the helix formed by residues 102 - 111 (chain E) in PDB entry 1NTZ
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 THR 102 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83E GLU* 3.5 39.9 - - + +
84E GLY* 3.8 14.8 - - - +
101E ARG* 1.3 76.9 - - - +
103E LYS* 1.3 68.3 + - - +
104E LYS* 4.1 8.1 + - - +
105E GLU* 3.2 32.6 + - - +
106E ILE* 3.3 13.4 + - - +
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Residues in contact with LYS 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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83E GLU* 4.8 2.6 + - - -
102E THR* 1.3 73.8 - - - +
104E LYS* 1.3 61.5 + - - +
106E ILE* 3.3 14.5 + - + +
107E ASP* 3.3 43.6 + - - +
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Residues in contact with LYS 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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102E THR* 3.2 9.2 + - - +
103E LYS* 1.3 78.5 - - - +
105E GLU* 1.3 59.9 + - + +
107E ASP* 3.6 8.3 + - - +
108E GLN* 3.2 39.4 + - - +
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Residues in contact with GLU 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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84E GLY* 4.8 6.9 - - - -
99E ARG* 2.5 34.9 + - - -
100E HIS 4.6 1.2 - - - +
101E ARG* 3.7 18.3 - - + +
102E THR* 3.2 32.4 + - - +
104E LYS* 1.3 77.6 - - + +
106E ILE* 1.3 64.8 + - - +
108E GLN* 3.5 10.6 + - - +
109E GLU* 3.3 29.5 + - - +
149E ASN* 4.7 0.7 - - - +
154E GLY 3.7 8.5 - - - +
167E ALA* 4.4 13.7 - - + -
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Residues in contact with ILE 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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101E ARG* 4.5 13.9 - - + +
102E THR 3.3 17.0 - - - +
103E LYS* 3.3 14.6 + - - +
105E GLU* 1.3 76.7 - - - +
107E ASP* 1.3 67.6 + - - +
109E GLU* 3.5 3.5 + - - +
110E ALA* 3.3 23.6 + - + +
123E ASP* 4.3 8.6 - - - +
124E LEU* 5.8 2.9 - - + -
130E PRO* 3.4 51.6 - - + +
131E GLU* 3.9 15.5 - - + +
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Residues in contact with ASP 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 LYS* 3.3 39.7 + - - +
104E LYS* 3.8 10.3 - - - +
106E ILE* 1.3 81.7 - - - +
108E GLN* 1.3 63.8 + - - +
110E ALA* 3.5 6.7 + - - +
111E ALA* 3.2 24.1 + - - +
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Residues in contact with GLN 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 LYS* 3.2 28.7 + - - +
105E GLU* 3.8 12.2 - - - +
106E ILE 3.3 0.2 - - - -
107E ASP* 1.3 81.7 - - - +
109E GLU* 1.3 69.1 + - - +
111E ALA* 3.5 12.3 + - - +
112E VAL* 3.4 18.5 + - + +
153E PHE* 4.2 19.8 + - - +
154E GLY* 5.6 1.6 - - - -
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Residues in contact with GLU 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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101E ARG* 4.0 10.8 - - - +
105E GLU 3.3 16.8 + - - +
106E ILE 4.0 2.0 - - - +
108E GLN* 1.3 85.1 + - - +
110E ALA* 1.3 63.6 + - - +
111E ALA 3.2 0.7 - - - -
112E VAL* 3.5 11.7 + - - +
114E VAL* 6.1 0.3 - - - +
122E HIS* 5.3 1.6 + - - -
123E ASP* 3.7 28.2 + - + +
153E PHE 4.5 3.8 - - - +
166E ASP* 3.0 23.0 - - - +
167E ALA* 3.0 41.6 + - + +
168E SER* 3.9 2.2 - - - +
170E ARG* 3.0 40.9 + - - +
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Residues in contact with ALA 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 ILE* 3.3 19.5 + - + +
107E ASP* 3.9 7.0 - - - +
108E GLN 3.4 0.4 - - - -
109E GLU* 1.3 77.2 - - - +
111E ALA* 1.3 59.0 + - - +
112E VAL 3.3 4.1 + - - +
122E HIS* 4.1 30.0 + - + -
123E ASP* 4.6 3.5 - - - +
124E LEU* 5.9 2.9 - - + -
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Residues in contact with ALA 111 (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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107E ASP 3.2 17.5 + - - +
108E GLN* 3.5 8.7 + - - +
109E GLU 3.2 0.6 - - - -
110E ALA* 1.3 77.8 - - - +
112E VAL* 1.3 61.1 + - - +
113E GLU* 3.5 2.9 + - - +
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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