Contacts of the helix formed by residues 104 - 115 (chain E) in PDB entry 1W4R
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 104 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B GLU* 5.8 2.5 - - - +
80E LEU* 3.9 11.9 - - + +
81E LEU* 3.0 29.4 + - - +
82E ARG* 3.0 52.3 + - + +
102E PHE* 3.9 5.0 - - - +
103E PRO* 1.3 74.9 - - + +
105E ILE* 1.3 64.4 + - - +
106E VAL 3.1 3.2 + - - -
107E GLU* 3.3 8.9 + - + +
108E PHE* 3.0 25.2 + - + +
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Residues in contact with ILE 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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81E LEU* 3.6 19.3 - - + -
96E ILE* 3.9 11.4 - - + -
99E GLY* 3.6 33.4 - - - +
100E GLN* 5.6 0.9 - - - -
102E PHE* 3.2 18.6 + - + +
103E PRO 3.4 1.0 - - - +
104E ASP* 1.3 77.7 + - - +
106E VAL* 1.3 77.6 + - + +
108E PHE* 4.0 0.2 - - - +
109E CYS* 3.1 50.2 + - - -
121E VAL* 4.1 7.0 - - + -
135E ALA* 4.6 5.8 - - + +
136E ILE* 3.8 31.6 - - + +
139E LEU* 4.0 7.9 - - + -
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Residues in contact with VAL 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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82B ARG* 4.6 2.7 - - - +
103E PRO 5.0 1.5 + - - +
104E ASP 3.2 0.6 - - - -
105E ILE* 1.3 85.6 - - + +
107E GLU* 1.3 81.1 + - + +
109E CYS* 4.0 1.6 - - - +
110E GLU* 3.2 23.2 + - - +
135E ALA* 3.5 34.1 - - + +
138E ASN* 3.7 19.1 - - + +
139E LEU* 3.9 13.9 - - + +
142E LEU* 3.7 23.8 - - + -
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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
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80B LEU* 4.2 8.3 - - - +
82B ARG* 2.9 39.1 + - - -
103B PRO* 3.8 24.6 - - + +
104B ASP* 3.2 20.9 - - - +
107B GLU* 3.8 24.9 - - - +
104E ASP* 3.3 9.6 + - + +
106E VAL* 1.3 84.9 - - + +
108E PHE* 1.3 66.0 + - - +
110E GLU* 4.2 0.6 - - - +
111E ALA* 3.0 26.9 + - - +
1193E DTU 4.3 2.1 + - - -
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Residues in contact with PHE 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU* 4.7 3.9 + - - -
53E ILE* 4.3 9.2 - - + -
81E LEU* 3.4 57.0 - - + -
82E ARG* 4.5 3.4 - - + -
84E VAL* 4.9 0.4 - - + -
85E ALA* 4.1 19.7 - - + -
88E ALA* 3.9 23.6 - - + -
94E ILE* 4.4 10.5 - - + -
96E ILE* 4.1 21.3 - - + -
104E ASP* 3.0 21.2 + - + +
107E GLU* 1.3 78.0 - - - +
109E CYS* 1.3 61.1 + - - +
111E ALA* 3.4 4.3 + - - +
112E MET* 3.0 54.4 + - + +
119E VAL* 5.4 0.9 - - + -
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Residues in contact with CYS 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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21E ILE* 3.8 12.6 - - + +
96E ILE* 3.7 20.0 - - - -
105E ILE* 3.1 38.2 + - - +
108E PHE* 1.3 76.0 - - - +
110E GLU* 1.3 61.9 + - - +
112E MET* 3.4 1.7 + - - +
113E ALA* 2.9 31.4 + - - +
119E VAL* 3.7 29.9 - - + +
121E VAL* 3.7 10.1 - - - -
139E LEU* 3.8 17.0 - - + -
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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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82B ARG* 3.3 26.9 - - - +
21E ILE* 3.8 4.5 - - - +
106E VAL 3.2 18.0 + - - +
107E GLU 4.2 2.0 - - - +
109E CYS* 1.3 75.4 - - - +
111E ALA* 1.3 57.3 - - - +
113E ALA* 3.5 1.1 + - - +
114E ASN* 2.9 53.2 + - - -
142E LEU* 3.7 19.1 - - + +
1193E DTU 3.4 16.2 - - - +
130H ARG* 2.8 36.7 + - - -
186H ARG* 2.9 24.1 + - - -
190H PHE* 3.6 1.9 - - - -
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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
----------------------------------------------------------
107B GLU* 3.7 23.8 - - + -
107E GLU 3.0 20.5 + - - +
108E PHE* 3.7 4.7 - - - +
110E GLU* 1.3 76.5 - - - +
112E MET* 1.3 69.2 + - + +
114E ASN* 3.2 4.0 + - - +
115E ALA* 2.8 28.9 + - - +
1193E DTU 3.6 23.3 + - - +
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Residues in contact with MET 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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85E ALA* 5.1 5.8 - - + +
88E ALA* 4.3 13.0 - - - -
89E LEU* 3.7 34.8 - - + -
94E ILE* 3.9 14.8 - - + -
108E PHE* 3.0 48.2 + - + +
111E ALA* 1.3 87.6 - - + +
113E ALA* 1.3 62.3 + - - +
115E ALA* 3.0 11.9 + - + -
116E GLY 3.3 0.3 + - - -
117E LYS* 3.0 36.5 + - + +
119E VAL* 3.8 18.6 - - + -
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Residues in contact with ALA 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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19E GLY* 3.3 15.6 + - - -
20E GLN 3.7 14.8 - - - +
21E ILE* 3.7 15.3 - - + -
109E CYS 2.9 18.4 + - - +
110E GLU 4.0 0.2 - - - +
112E MET* 1.3 75.3 - - - +
114E ASN* 1.3 59.0 + - - +
116E GLY* 3.1 14.6 + - - -
117E LYS 3.4 11.2 - - - -
119E VAL* 4.0 1.4 - - - +
186H ARG* 3.5 31.5 - - - +
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Residues in contact with ASN 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* 2.9 41.7 + - - +
111E ALA 3.6 0.9 - - - +
113E ALA* 1.3 75.8 - - - +
115E ALA* 1.3 57.0 + - - +
116E GLY 3.2 3.4 + - - -
1193E DTU 3.2 53.3 - - + -
186H ARG* 2.9 28.7 + - - +
190H PHE* 3.6 16.5 - - - -
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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
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89E LEU* 5.1 6.3 - - + -
111E ALA 2.8 15.2 + - - +
112E MET* 3.0 17.8 + - + +
114E ASN* 1.3 77.3 - - - +
116E GLY* 1.3 56.1 + - - +
117E LYS* 3.5 19.5 + - - +
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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