Contacts of the helix formed by residues 107 - 122 (chain E) in PDB entry 3ZXR
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 107 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E PHE* 5.8 0.3 - - - +
26E CYS 4.6 2.8 + - - +
61E PHE* 4.7 2.5 - - - -
93E PHE 5.0 0.5 - - - +
94E PHE* 3.4 15.0 - - - +
95E VAL* 2.7 50.0 + - + +
104E TYR* 3.3 19.0 + - + +
106E ARG* 1.3 75.9 - - - +
108E PRO* 1.4 75.1 - - - +
109E ARG* 2.9 16.2 + - - +
110E ASN* 3.0 27.6 + - + +
111E ILE* 3.1 14.8 + - - +
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Residues in contact with PRO 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E CYS* 3.4 20.6 - - + +
27E ASP 3.3 25.4 - - - +
28E LEU* 4.2 9.0 - - + -
61E PHE* 4.5 1.8 - - + -
106E ARG 3.3 10.3 - - - +
107E ASP* 1.4 89.0 - - - +
109E ARG* 1.3 59.6 + - - +
111E ILE* 3.2 12.2 + - + +
112E ALA 3.3 6.6 + - - -
375E ASN* 3.4 28.7 - - - +
377E TYR* 3.2 25.3 - - + +
378E LEU* 4.1 13.5 - - + -
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Residues in contact with ARG 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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25E PHE* 5.2 0.2 - - - +
26E CYS* 4.5 13.7 - - + +
32E MET* 5.1 2.0 - - - -
74E ASP* 2.8 29.7 + - - +
77E THR* 3.7 4.6 - - - +
92E ASN* 4.0 14.8 - - - +
93E PHE 3.3 29.4 + - - +
94E PHE* 3.4 43.4 - - + -
107E ASP* 2.9 12.3 + - - +
108E PRO* 1.3 73.4 - - - +
110E ASN* 1.3 64.0 - - - +
112E ALA* 3.5 4.2 + - - +
113E ARG* 3.1 20.6 + - - +
236E LEU* 4.0 8.7 - - + +
240E ASP* 2.9 35.7 + - - -
377E TYR* 3.6 35.5 - - + -
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Residues in contact with ASN 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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103E PRO* 3.4 25.0 + - + +
104E TYR 3.0 25.1 + - - +
105E SER* 4.6 1.2 - - - +
107E ASP* 3.0 23.8 + - + +
109E ARG* 1.3 77.0 - - - +
111E ILE* 1.3 59.3 + - - +
113E ARG* 3.1 34.9 + - - +
114E LYS* 2.8 56.8 + - - +
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Residues in contact with ILE 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E LEU* 6.3 0.4 - - + -
105E SER 3.4 17.7 - - - +
106E ARG 5.4 0.4 - - - -
107E ASP 3.1 14.3 + - - +
108E PRO* 3.2 7.4 + - + +
110E ASN* 1.3 77.0 - - - +
112E ALA* 1.3 58.1 + - - +
114E LYS* 3.3 17.3 + - - +
115E ALA* 2.8 27.9 + - - +
377E TYR 5.2 0.2 - - - +
378E LEU* 3.7 17.5 - - + -
381E SER* 3.8 8.7 - - - +
442E VAL* 3.6 23.2 - - + +
443E PHE* 3.9 31.4 - - + -
447E LEU* 3.4 28.5 - - + -
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Residues in contact with ALA 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E PRO 3.3 8.4 + - - +
109E ARG 3.7 3.4 - - - +
110E ASN 3.2 0.2 - - - -
111E ILE* 1.3 75.3 - - - +
113E ARG* 1.3 66.5 + - - +
115E ALA* 3.2 2.3 + - - +
116E GLU* 3.0 29.4 + - - +
235E LEU* 3.6 21.0 - - + +
236E LEU* 3.7 26.2 - - + -
377E TYR* 4.2 13.0 - - + +
381E SER* 3.4 12.7 + - - +
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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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94E PHE* 3.2 65.9 - - + +
95E VAL 5.3 0.6 + - - -
96E HIS* 3.9 10.3 + - - -
103E PRO* 3.8 20.1 - - - +
107E ASP* 5.0 0.2 + - - -
109E ARG 3.1 10.1 + - - +
110E ASN* 3.1 32.1 + - - +
112E ALA* 1.3 74.6 - - - +
114E LYS* 1.3 62.1 + - - +
116E GLU* 3.2 16.3 + - - +
117E ASN* 3.2 27.5 + - - +
236E LEU* 4.6 13.6 - - + +
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Residues in contact with LYS 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E SER* 4.6 6.3 + - - +
110E ASN* 2.8 45.8 + - - +
111E ILE* 3.7 20.7 - - - +
113E ARG* 1.3 72.4 - - - +
115E ALA* 1.3 57.9 + - - +
117E ASN* 3.2 9.8 + - - +
118E TYR* 2.8 31.2 + - - +
440E GLY 5.6 1.8 - - - +
441E GLY 3.0 20.0 + - - +
442E VAL* 2.8 35.5 + - + +
444E THR* 4.0 14.3 - - - +
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Residues in contact with ALA 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E ILE 2.8 21.2 + - - +
112E ALA 3.2 5.4 + - - +
114E LYS* 1.3 73.0 - - - +
116E GLU* 1.3 64.4 + - - +
118E TYR* 3.3 2.6 + - - +
119E LEU* 3.1 23.0 + - - +
235E LEU* 4.3 12.6 - - + -
381E SER* 3.6 25.4 - - - +
384E LEU* 3.9 11.8 - - + +
385E MET* 5.1 2.9 - - - +
442E VAL* 3.9 17.0 - - + +
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Residues in contact with GLU 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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112E ALA 3.0 15.4 + - - +
113E ARG* 3.2 8.9 + - - +
115E ALA* 1.3 76.0 - - - +
117E ASN* 1.3 63.5 + - - +
119E LEU* 3.5 11.8 + - + +
120E ILE* 3.3 29.8 + - + +
126E ASP 5.1 0.7 - - - +
128E ALA* 6.3 1.8 - - + +
234E SER* 3.6 14.8 + - - -
235E LEU* 3.3 26.8 + - + -
236E LEU* 3.1 43.8 + - - +
384E LEU* 5.2 2.0 - - + -
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Residues in contact with ASN 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E ARG* 3.2 25.6 + - - +
114E LYS* 3.7 9.8 - - - +
116E GLU* 1.3 76.6 - - - +
118E TYR* 1.3 65.3 + - - +
120E ILE* 3.2 17.7 + - - +
121E SER* 3.0 23.7 + - - -
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Residues in contact with TYR 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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114E LYS 2.8 20.9 + - - +
115E ALA 3.7 2.9 - - - +
117E ASN* 1.3 73.2 - - - +
119E LEU* 1.3 64.6 + - - +
121E SER* 2.7 30.4 + - - -
122E THR* 3.0 28.7 + - + +
385E MET* 3.7 28.3 - - + -
388E LEU* 4.0 19.7 - - + -
392E LYS* 3.3 21.3 + - - +
439E GLU* 3.6 25.1 + - + +
440E GLY* 3.8 32.8 - - - +
442E VAL* 3.5 14.8 - - + -
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Residues in contact with LEU 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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115E ALA 3.1 13.1 + - - +
116E GLU* 3.5 12.8 - - + +
117E ASN 3.3 0.2 - - - -
118E TYR* 1.3 75.7 - - - +
120E ILE* 1.3 61.8 + - - +
122E THR* 2.6 26.2 + - - +
123E GLY 3.7 0.2 + - - -
125E ALA* 3.2 36.4 - - + +
126E ASP 4.0 2.9 - - - +
127E THR* 3.6 15.9 - - - +
128E ALA* 3.5 41.1 - - + +
281E LEU* 4.3 4.5 - - + -
384E LEU* 4.2 9.4 - - + -
388E LEU* 3.7 35.4 - - + -
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Residues in contact with ILE 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 GLU* 3.3 16.6 + - + +
117E ASN* 3.2 21.6 + - - +
119E LEU* 1.3 76.4 - - - +
121E SER* 1.3 64.1 + - - +
123E GLY* 3.1 15.8 + - - -
125E ALA 3.7 7.0 - - - +
126E ASP* 3.7 33.4 - - + +
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Residues in contact with SER 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E ASN 3.0 12.2 + - - -
118E TYR* 2.7 32.6 + - - -
120E ILE* 1.3 79.7 - - - +
122E THR* 1.3 58.7 + - - +
123E GLY 3.3 0.2 - - - -
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Residues in contact with THR 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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118E TYR* 3.0 38.8 + - + +
119E LEU* 2.6 21.9 + - - +
121E SER* 1.3 77.6 - - - +
123E GLY* 1.3 56.7 + - - +
124E ILE* 3.1 34.7 + - + +
388E LEU* 4.6 3.1 - - + -
392E LYS* 3.3 32.1 + - - +
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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