Contacts of the helix formed by residues 112 - 129 (chain A) in PDB entry 4WTM
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 SER 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A GLU* 3.0 30.9 + - - +
110A SER* 3.4 8.5 - - - -
111A LEU* 1.3 80.3 - - - +
113A GLY* 1.3 59.7 + - - +
114A ARG* 3.9 6.6 + - - +
115A ALA* 3.5 20.4 + - - +
116A VAL* 3.0 25.6 + - - +
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU 3.8 1.9 + - - -
112A SER* 1.3 72.4 - - - +
114A ARG* 1.3 65.9 + - - +
116A VAL* 3.9 5.2 - - - +
117A ASN* 2.9 27.9 + - - +
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TYR 4.0 7.6 + - - +
102A GLY* 3.0 38.6 + - - -
103A PHE* 4.4 12.8 - - + -
107A GLU* 6.1 1.3 - - - -
112A SER* 3.5 5.8 - - - +
113A GLY* 1.3 75.1 - - - +
115A ALA* 1.3 57.1 + - - +
117A ASN* 3.5 4.9 - - - +
118A HIS* 3.0 29.2 + - + +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A CYS* 6.3 0.2 - - - -
103A PHE* 3.7 38.5 - - + -
107A GLU* 4.3 15.7 - - + +
108A VAL* 4.3 6.3 - - + +
112A SER* 3.3 18.4 + - - +
113A GLY 3.2 0.4 - - - -
114A ARG* 1.3 77.5 - - - +
116A VAL* 1.3 66.6 + - + +
118A HIS* 3.1 5.0 + - - +
119A ILE* 3.0 29.4 + - + +
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 3.8 29.4 - - + +
86A GLN* 5.5 5.4 - - + -
89A CYS* 4.9 2.9 - - - -
111A LEU* 4.0 31.4 - - + +
112A SER 3.0 20.8 + - - +
113A GLY* 3.9 5.6 - - - +
115A ALA* 1.3 75.7 - - + +
117A ASN* 1.3 57.4 - - - +
119A ILE* 3.5 5.3 + - - +
120A LYS* 3.0 48.5 + - - +
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Residues in contact with ASN 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLY 2.9 19.9 + - - +
114A ARG* 3.5 6.7 - - - +
116A VAL* 1.3 77.0 - - - +
118A HIS* 1.3 66.0 + - - +
120A LYS* 3.4 22.5 + - - +
121A SER* 3.3 19.1 + - - -
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Residues in contact with HIS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR* 3.2 54.4 - + + +
103A PHE* 3.8 27.3 - + + -
114A ARG* 3.0 14.6 + - + +
115A ALA 3.5 7.0 - - - +
117A ASN* 1.3 75.6 - - - +
119A ILE* 1.3 69.6 + - + +
121A SER* 2.7 26.9 + - - -
122A VAL* 2.9 33.6 + - + +
164A ASP* 4.3 7.9 + - - -
166A GLY* 4.3 3.7 - - - -
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 3.7 23.6 - - + -
89A CYS* 4.0 23.8 - - - -
103A PHE* 4.6 3.6 - - + -
108A VAL* 4.3 13.9 - - + -
115A ALA 3.0 23.6 + - - +
116A VAL* 3.9 4.7 - - - +
118A HIS* 1.3 82.7 - - + +
120A LYS* 1.3 61.9 + - - +
122A VAL* 3.6 4.2 - - - +
123A TRP* 3.0 23.7 + - - +
166A GLY* 4.0 19.1 - - - +
169A VAL* 4.0 27.4 - - + -
170A CYS* 4.0 17.5 - - - -
173A MET* 4.6 1.6 - - - -
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Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 3.8 16.2 - - + -
116A VAL* 3.0 33.8 + - - +
117A ASN* 3.4 25.9 - - - +
119A ILE* 1.3 78.0 - - - +
121A SER* 1.3 57.6 + - - +
123A TRP* 3.6 6.3 - - - +
124A LYS* 3.0 26.5 + - - +
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Residues in contact with SER 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASN 3.3 6.2 + - - -
118A HIS* 2.7 28.0 + - - -
120A LYS* 1.3 76.8 - - - +
122A VAL* 1.3 65.7 + - - +
124A LYS* 3.0 9.1 + - - +
125A ASP* 2.8 26.4 + - - +
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Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A HIS* 2.9 49.6 + - + +
119A ILE* 3.6 8.3 - - - +
121A SER* 1.3 75.6 + - - +
123A TRP* 1.3 63.5 + - - +
125A ASP* 3.3 8.3 + - - +
126A LEU* 3.1 26.3 + - + +
166A GLY 4.1 8.1 - - - +
167A VAL* 4.0 27.4 - - + +
170A CYS* 3.6 19.3 - - + -
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Residues in contact with TRP 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LEU* 3.9 30.5 - - + -
85A LEU* 5.7 0.9 - - + -
119A ILE 3.0 17.4 + - - +
120A LYS* 3.6 6.5 - - - +
122A VAL* 1.3 75.3 - - - +
124A LYS* 1.3 68.0 + - - +
126A LEU* 3.0 21.4 + - + +
127A LEU* 3.1 27.9 + - + +
170A CYS* 3.6 47.5 - - + -
173A MET* 3.8 29.9 - - + +
174A ALA* 4.0 6.7 - - + -
248A GLU* 3.1 33.9 + - + -
252A ALA* 3.5 30.1 - - + -
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Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LYS 3.0 13.0 + - - +
121A SER* 3.0 12.2 + - - +
123A TRP* 1.3 78.8 - - - +
125A ASP* 1.3 57.0 + - - +
127A LEU* 3.1 10.3 + - - +
128A GLU* 3.0 43.5 + - - +
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Residues in contact with ASP 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A SER 2.8 12.2 + - - +
122A VAL* 3.5 11.5 - - - +
124A LYS* 1.3 76.4 - - - +
126A LEU* 1.3 60.0 + - - +
128A GLU* 4.4 7.7 - - - +
129A ASP* 2.9 34.3 + - - +
259A ARG* 2.8 40.0 + - - -
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A VAL* 3.1 18.6 + - + +
123A TRP* 3.0 25.8 + - + +
125A ASP* 1.3 75.9 + - - +
127A LEU* 1.3 64.1 + - + +
128A GLU 3.4 0.3 + - - -
129A ASP 3.5 4.9 + - - +
130A PRO* 4.8 0.5 - - - +
134A ILE* 4.1 20.9 - - + -
167A VAL* 5.9 2.2 - - + -
170A CYS* 3.8 28.9 - - + -
251A THR* 4.5 2.3 - - - +
252A ALA* 4.8 9.2 - - + -
255A SER* 3.0 40.6 + - - +
256A LEU* 3.9 37.2 - - + +
259A ARG* 3.9 7.0 - - - +
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A TRP* 3.1 40.5 + - + +
124A LYS* 3.1 11.6 + - - +
126A LEU* 1.3 77.9 - - - +
128A GLU* 1.3 61.8 + - + +
130A PRO* 5.7 0.7 - - - +
248A GLU* 3.7 42.2 - - + +
251A THR* 3.9 31.5 - - + +
252A ALA* 4.1 12.8 - - + +
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Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LYS* 3.0 27.7 + - - +
125A ASP* 4.2 5.9 - - - +
127A LEU* 1.3 84.8 - - + +
129A ASP* 1.3 59.7 + - + +
130A PRO* 3.7 7.9 - - - +
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Residues in contact with ASP 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASP* 2.9 24.0 + - - +
126A LEU 3.5 2.0 - - - +
128A GLU* 1.3 77.6 - - + +
130A PRO* 1.3 62.7 - - - +
131A GLN* 2.8 19.2 + - - +
132A THR* 2.2 38.2 + - - -
255A SER* 3.0 8.8 + - - -
259A ARG* 2.9 29.5 + - - +
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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