Contacts of the helix formed by residues 105 - 127 (chain E) in PDB entry 3ZPL
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 105 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57E ARG* 5.0 1.3 + - - -
86E GLY 2.7 29.8 + - - +
87E TRP 3.1 7.3 + - - -
88E VAL 3.8 22.2 - - - +
89E ARG* 4.1 22.2 - - + +
103E ILE 3.5 0.2 + - - -
104E LEU* 1.3 78.2 - - - +
106E ASP* 1.3 65.7 + - - +
107E GLU* 3.6 3.8 + - - -
108E GLY 3.0 15.1 + - - -
109E TYR* 3.1 18.9 + - - +
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Residues in contact with ASP 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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57E ARG* 4.3 12.7 + - - +
105E THR* 1.3 73.8 - - - +
107E GLU* 1.3 66.1 + - - +
109E TYR* 3.0 12.3 + - - +
110E GLU* 2.9 20.4 + - - +
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Residues in contact with GLU 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E GLY 4.3 9.0 - - - +
87E TRP* 4.2 12.8 - - + +
105E THR* 3.3 8.3 + - - +
106E ASP* 1.3 80.7 - - - +
108E GLY* 1.3 60.6 + - - +
110E GLU* 3.1 16.3 + - - +
111E VAL* 3.1 27.1 + - + +
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Residues in contact with GLY 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E LEU* 5.0 0.7 - - - -
87E TRP* 3.7 22.6 - - - -
104E LEU* 3.6 22.2 - - - -
105E THR* 3.0 15.0 + - - -
107E GLU* 1.3 74.0 - - - +
109E TYR* 1.3 63.7 + - - +
111E VAL* 3.1 12.6 + - - +
112E LEU* 3.1 18.0 - - - +
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Residues in contact with TYR 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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52E ALA* 4.4 17.9 - - + -
57E ARG* 3.0 48.7 + - - +
104E LEU* 3.7 19.5 - - + +
105E THR 3.1 9.4 + - - +
106E ASP* 3.0 10.4 + - - +
108E GLY* 1.3 76.2 - - - +
110E GLU* 1.3 57.4 + - - +
112E LEU* 3.3 10.7 + - + +
113E ARG* 3.1 31.5 + - + +
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Residues in contact with GLU 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 ASP 2.9 11.6 + - - +
107E GLU* 3.1 23.9 + - - +
109E TYR* 1.3 78.3 - - - +
111E VAL* 1.3 59.5 + - + +
113E ARG* 3.6 6.8 + - - +
114E ARG* 3.0 41.3 + - - +
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Residues in contact with VAL 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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38E ALA* 4.5 11.0 - - - +
40E MET* 4.3 24.7 - - + -
48E LEU* 5.3 0.7 - - + -
87E TRP* 3.4 38.1 - - + +
107E GLU* 3.1 12.3 + - + +
108E GLY* 3.1 8.9 + - - +
110E GLU* 1.3 75.8 - - + +
112E LEU* 1.3 55.2 + - + +
114E ARG* 4.3 8.7 - - - +
115E THR* 2.7 51.0 + - + +
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Residues in contact with LEU 112 (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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45E TYR* 4.8 11.0 - - + +
48E LEU* 3.6 44.2 - - + +
49E VAL* 3.9 17.3 - - + -
52E ALA* 3.6 30.7 - - + -
104E LEU* 4.7 3.6 - - + -
108E GLY 3.1 24.8 + - - +
109E TYR* 3.3 11.4 + - + +
111E VAL* 1.3 77.2 - - + +
113E ARG* 1.3 61.8 + - - +
115E THR* 3.9 3.8 - - - -
116E ALA* 2.8 38.7 + - + +
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Residues in contact with ARG 113 (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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109E TYR* 3.1 22.6 + - + +
110E GLU* 3.9 8.3 - - - +
112E LEU* 1.3 79.8 - - - +
114E ARG* 1.3 63.6 + - + +
116E ALA* 5.3 1.1 - - - -
117E PRO* 3.7 16.5 - - - +
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Residues in contact with ARG 114 (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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110E GLU* 3.0 32.6 + - + +
111E VAL* 3.8 10.8 - - - +
113E ARG* 1.3 80.8 - - + +
115E THR* 1.3 66.5 + - + +
117E PRO* 4.2 7.4 - - - +
118E GLY 5.3 0.5 + - - -
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Residues in contact with THR 115 (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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33E GLN* 4.9 1.5 + - - -
34E LEU* 5.2 2.9 - - - -
37E ASP* 3.5 19.0 - - + +
38E ALA* 3.4 30.8 - - + +
45E TYR* 3.3 23.0 - - - -
111E VAL* 2.7 28.2 + - + +
112E LEU 3.7 0.3 + - - -
114E ARG* 1.3 83.3 - - + +
116E ALA* 1.3 70.1 + - - +
117E PRO* 3.3 2.9 - - - -
118E GLY* 2.8 16.9 + - - -
119E HIS* 3.1 9.8 + - - +
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Residues in contact with ALA 116 (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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45E TYR* 3.0 20.2 - - - +
112E LEU* 2.8 23.1 + - + +
113E ARG* 5.0 1.1 - - - +
115E THR* 1.3 72.9 + - - +
117E PRO* 1.3 62.0 - - + +
119E HIS* 2.9 2.5 + - - +
120E VAL* 2.6 45.8 + - + +
7F TRP* 4.8 10.3 - - + -
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Residues in contact with PRO 117 (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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113E ARG 3.7 18.6 - - - +
114E ARG 4.2 7.0 - - - +
115E THR 3.6 0.9 - - - -
116E ALA* 1.3 94.5 - - + +
118E GLY* 1.3 63.7 + - - +
120E VAL* 3.4 4.1 + - + +
121E ASP* 3.0 24.3 + - - +
7F TRP* 4.1 30.1 - - + -
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Residues in contact with GLY 118 (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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33E GLN* 3.7 10.9 + - - -
37E ASP* 5.4 4.0 - - - -
114E ARG 5.3 0.4 + - - -
115E THR* 2.8 14.5 + - - +
117E PRO* 1.3 74.2 - - - +
119E HIS* 1.3 60.5 + - - -
121E ASP* 3.2 8.5 + - - +
122E ALA* 3.0 22.3 + - - +
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Residues in contact with HIS 119 (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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30E LEU* 4.2 9.3 - - + +
33E GLN* 3.2 26.4 + - - +
34E LEU* 3.4 31.1 - - + +
42E HIS* 3.7 23.2 + + - -
45E TYR* 3.7 33.1 - + - +
115E THR 3.1 6.6 + - - +
116E ALA 2.9 7.4 + - - +
118E GLY* 1.3 75.0 - - - +
120E VAL* 1.3 69.0 + - + +
122E ALA* 3.5 1.4 + - - +
123E VAL* 3.0 47.1 + - + +
16F TRP* 4.8 6.1 + - - -
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Residues in contact with VAL 120 (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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116E ALA* 2.6 31.7 + - + +
117E PRO* 3.8 7.4 - - + +
119E HIS* 1.3 76.6 - - + +
121E ASP* 1.3 54.7 + - - +
123E VAL* 3.1 7.7 + - - +
124E ARG* 2.8 40.9 + - + +
7F TRP* 4.3 29.2 - - + +
8F LEU* 3.5 33.6 - - + +
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Residues in contact with ASP 121 (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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117E PRO 3.0 14.0 + - - +
118E GLY* 3.4 10.5 - - - +
120E VAL* 1.3 76.7 - - - +
122E ALA* 1.3 54.8 + - - +
124E ARG* 2.9 10.9 + - - +
125E GLN* 2.7 37.0 + - - +
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Residues in contact with ALA 122 (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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29E HIS* 4.3 15.7 + - + +
30E LEU* 4.1 12.7 - - + +
33E GLN* 3.9 28.0 - - + +
118E GLY 3.0 9.7 + - - +
119E HIS 3.7 8.1 - - - +
121E ASP* 1.3 78.1 - - - +
123E VAL* 1.3 57.8 + - - +
125E GLN* 4.1 4.7 - - - +
126E ALA* 3.1 31.2 + - - +
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Residues in contact with VAL 123 (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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30E LEU* 4.0 10.1 - - + -
119E HIS* 3.0 46.7 + - + +
120E VAL* 3.6 6.3 - - - +
122E ALA* 1.3 72.8 - - - +
124E ARG* 1.3 66.2 + - - +
126E ALA* 4.8 2.0 - - - -
127E VAL* 3.3 22.2 + - - +
128E PHE* 3.8 16.4 + - + -
8F LEU* 4.9 7.9 - - + -
16F TRP* 3.8 48.0 - - + +
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Residues in contact with ARG 124 (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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120E VAL* 2.8 24.5 + - + +
121E ASP* 2.9 12.3 + - - +
123E VAL* 1.3 71.4 - - - +
125E GLN* 1.3 64.7 + - - +
127E VAL 3.1 0.2 + - - -
128E PHE* 3.0 46.3 + - + +
129E ASP* 3.0 33.2 + - - +
7F TRP 2.5 35.3 + - - +
8F LEU* 3.6 13.9 - - + +
9F THR* 4.2 3.2 - - - +
12F GLU* 2.6 38.1 + - - -
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Residues in contact with GLN 125 (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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29E HIS* 6.0 1.8 - - - +
121E ASP 2.7 19.3 + - - +
122E ALA* 4.2 5.4 - - - +
124E ARG* 1.3 73.7 - - - +
126E ALA* 1.3 60.3 + - - +
129E ASP* 4.0 13.4 - - - +
130E ARG* 3.1 31.2 + - - +
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Residues in contact with ALA 126 (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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26E LEU* 3.9 27.6 - - + -
29E HIS* 4.3 13.9 - - + +
122E ALA 3.1 19.2 + - - +
123E VAL* 4.4 0.7 - - - +
125E GLN* 1.3 80.0 - - - +
127E VAL* 1.3 60.9 + - + +
130E ARG* 3.6 22.9 + - - +
146F VAL* 4.1 18.7 - - - +
150F LEU* 4.4 10.5 - - + -
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Residues in contact with VAL 127 (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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26E LEU* 4.0 28.5 - - + -
123E VAL 3.3 12.6 + - - +
124E ARG 3.1 4.2 + - - -
126E ALA* 1.3 87.6 - - + +
128E PHE* 1.3 83.2 + - + +
129E ASP 3.4 1.8 - - - -
130E ARG* 2.9 26.3 + - - +
131E LEU* 3.5 29.9 - - + +
139E LEU* 4.6 11.0 - - + -
16F TRP* 4.2 15.3 - - + -
146F VAL* 4.5 13.0 - - + -
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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