Contacts of the helix formed by residues 104 - 125 (chain A) in PDB entry 4DHZ
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ILE* 2.9 13.1 + - + +
101A MET 3.3 10.7 - - - +
102A LEU 5.2 0.2 - - - -
103A LYS* 1.3 79.3 - - + +
105A ARG* 1.3 63.8 + - - +
106A ALA* 3.0 23.0 + - - +
107A ARG* 3.3 30.4 + - + +
108A LEU 3.3 15.1 + - - -
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Residues in contact with ARG 105 (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 MET 4.6 2.0 - - - -
103A LYS 4.1 1.2 + - - -
104A ASP* 1.3 71.2 + - - +
106A ALA* 1.3 66.1 + - - +
108A LEU* 3.1 15.0 + - + +
109A GLU* 3.0 33.8 + - - +
146A ILE 4.9 1.4 + - - -
147A HIS* 2.9 66.4 + - + +
148A SER* 5.1 1.4 + - - +
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Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASP* 3.0 11.7 + - - +
105A ARG* 1.3 77.2 - - - +
107A ARG* 1.3 52.4 + - - +
109A GLU* 3.0 11.3 + - - +
110A LYS* 2.7 44.2 + - + +
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Residues in contact with ARG 107 (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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97A LEU* 5.0 7.3 - - - +
100A ILE* 3.9 24.9 - - + +
101A MET* 4.4 9.0 - - + -
104A ASP* 3.3 31.3 + - + +
106A ALA* 1.3 78.1 - - - +
108A LEU* 1.3 56.8 + - - +
110A LYS* 3.2 22.8 + - - +
111A PHE* 2.9 33.4 + - + +
225A ALA 5.2 1.4 + - - -
226A GLY 3.1 23.8 + - - -
227A THR* 4.0 6.5 - - - +
258A GLU* 2.6 44.8 + - - -
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Residues in contact with LEU 108 (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 MET* 3.6 40.9 - - + +
104A ASP 3.3 2.4 + - - -
105A ARG* 3.1 17.8 + - + +
107A ARG* 1.3 77.8 - - - +
109A GLU* 1.3 56.9 + - - +
111A PHE* 3.3 3.5 + - - +
112A ILE* 3.0 37.0 + - + +
143A LEU* 3.9 39.7 - - + +
146A ILE* 4.2 14.4 - - + +
147A HIS* 3.7 41.7 - - + +
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Residues in contact with GLU 109 (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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105A ARG* 3.0 26.5 + - - +
106A ALA* 3.0 12.2 + - - +
108A LEU* 1.3 72.5 - - - +
110A LYS* 1.3 64.2 + - - +
112A ILE* 3.4 11.3 + - + +
113A ALA* 3.3 20.8 + - - +
147A HIS* 3.0 39.2 + - + +
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Residues in contact with LYS 110 (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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106A ALA* 2.7 25.0 + - + +
107A ARG* 3.5 26.1 - - - +
109A GLU* 1.3 73.1 - - - +
111A PHE* 1.3 62.5 + - - +
113A ALA* 3.4 7.0 + - - +
114A SER* 3.2 23.0 + - - -
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Residues in contact with PHE 111 (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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97A LEU* 4.4 22.9 - - + -
101A MET* 3.8 24.0 - - + -
107A ARG* 2.9 18.0 + - + +
108A LEU 3.3 5.1 + - - +
110A LYS* 1.3 76.6 - - - +
112A ILE* 1.3 63.1 + - - +
114A SER* 3.3 14.4 + - - -
115A SER* 2.8 35.2 + - - -
118A TRP* 6.1 4.5 - + - -
139A PHE* 3.7 27.1 - + - -
143A LEU* 3.7 21.1 - - + -
172A PHE* 4.9 4.9 - + - -
173A PHE* 4.4 11.2 - + - -
176A ILE* 5.5 4.0 - - + -
224A ALA 5.7 0.2 - - - -
225A ALA* 3.6 31.2 - - + -
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Residues in contact with ILE 112 (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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108A LEU* 3.0 19.7 + - + +
109A GLU* 3.8 13.0 - - + +
110A LYS 3.3 0.4 - - - -
111A PHE* 1.3 74.8 - - - +
113A ALA* 1.3 62.2 + - - +
115A SER* 3.3 7.5 + - - -
116A ARG* 3.1 51.9 + - - +
140A ILE* 4.2 14.4 - - + -
143A LEU* 3.8 44.0 - - + +
144A GLU* 4.2 14.1 - - + +
147A HIS* 4.3 15.7 - - + -
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Residues in contact with ALA 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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109A GLU 3.3 10.7 + - - +
110A LYS* 3.6 10.3 - - + +
111A PHE 3.2 0.6 - - - -
112A ILE* 1.3 80.0 - - - +
114A SER* 1.3 60.1 + - - +
115A SER 3.4 0.7 + - - -
116A ARG* 3.5 19.5 + - - +
117A ASP* 3.5 18.2 + - - +
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Residues in contact with SER 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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110A LYS* 3.2 13.3 + - - -
111A PHE* 3.3 23.6 + - - -
112A ILE 3.4 0.2 - - - -
113A ALA* 1.3 78.4 - - - +
115A SER* 1.3 61.9 + - - +
117A ASP* 3.5 15.9 - - - +
118A TRP* 3.1 33.0 + - - -
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Residues in contact with SER 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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111A PHE* 2.8 28.1 + - - -
112A ILE* 3.4 8.3 - - - -
113A ALA 3.2 0.4 - - - -
114A SER* 1.3 75.7 + - - +
116A ARG* 1.3 64.6 + - - +
117A ASP 3.1 2.0 - - - -
118A TRP* 3.0 22.9 + - - +
119A THR* 3.2 13.2 + - - -
139A PHE* 3.9 20.3 - - - -
140A ILE* 3.5 17.8 - - - +
143A LEU* 4.3 1.6 - - - +
172A PHE* 4.1 15.6 - - - -
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Residues in contact with ARG 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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112A ILE* 3.1 34.3 - - - +
113A ALA* 3.5 11.6 + - - +
115A SER* 1.3 76.4 - - - +
117A ASP* 1.3 61.5 + - - +
119A THR* 3.4 22.0 - - - -
120A ARG* 3.5 26.3 + - - +
140A ILE* 3.8 19.7 - - + +
144A GLU* 2.8 31.0 + - - +
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Residues in contact with ASP 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 ALA 3.5 16.3 + - - +
114A SER* 3.5 16.1 - - - +
116A ARG* 1.3 75.5 - - - +
118A TRP* 1.3 66.2 + - - +
120A ARG* 3.0 36.4 + - - +
121A THR* 2.8 28.0 + - - +
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Residues in contact with TRP 118 (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 PHE* 6.1 4.0 - + - -
114A SER* 3.1 29.7 + - - -
115A SER* 3.0 13.1 + - - +
117A ASP* 1.3 78.4 - - - +
119A THR* 1.3 63.1 + - - +
121A THR* 3.1 19.2 + - + -
122A LEU* 2.8 30.9 + - + +
172A PHE* 4.2 11.7 - + + -
176A ILE* 3.7 33.1 - - + +
179A ALA* 3.8 29.6 - - + -
180A PHE* 4.3 9.2 - + + -
183A GLN* 3.8 26.2 - - - -
224A ALA* 3.6 45.8 + - + -
225A ALA* 5.7 0.2 - - - +
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Residues in contact with THR 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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115A SER 3.2 11.3 + - - -
116A ARG* 3.4 13.2 + - - -
117A ASP 3.2 0.6 + - - -
118A TRP* 1.3 80.8 - - - +
120A ARG* 1.3 61.1 + - + +
122A LEU* 3.0 18.3 + - - +
123A VAL* 3.3 12.4 - - + +
133A THR* 3.7 34.4 + - + +
136A CYS* 3.3 35.3 - - + +
137A ASP* 4.8 5.2 + - - +
140A ILE* 4.7 3.1 - - - +
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Residues in contact with ARG 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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116A ARG* 3.5 24.9 + - - +
117A ASP* 3.0 37.0 + - - +
119A THR* 1.3 79.8 - - + +
121A THR* 1.3 63.2 + - - +
123A VAL* 3.4 12.0 - - + +
124A GLU* 3.2 28.8 + - - +
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Residues in contact with THR 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 ASP* 2.8 26.3 + - - +
118A TRP* 3.4 28.6 - - + -
120A ARG* 1.3 72.1 - - - +
122A LEU* 1.3 57.7 + - - +
124A GLU* 3.5 9.5 + - + +
125A LEU* 3.0 43.0 + - + +
183A GLN* 3.5 24.2 - - - +
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Residues in contact with LEU 122 (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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118A TRP* 2.8 18.5 + - + +
119A THR* 3.0 7.2 + - - +
121A THR* 1.3 75.6 - - - +
123A VAL* 1.3 65.7 - - - +
125A LEU* 3.0 10.1 + - - -
127A PHE* 3.2 57.7 + - + -
132A CYS* 4.4 17.7 - - + -
136A CYS* 3.6 31.2 - - - -
172A PHE* 5.2 2.2 - - + -
175A LEU* 4.3 20.9 - - + +
176A ILE* 5.4 1.8 - - + -
179A ALA* 3.6 28.7 - - + -
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Residues in contact with VAL 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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119A THR* 3.3 17.5 + - + +
120A ARG* 3.4 18.8 - - + +
122A LEU* 1.3 73.9 - - - +
124A GLU* 1.3 61.0 + - - +
126A GLY* 3.1 14.4 + - - -
127A PHE* 4.6 10.6 - - - +
129A ASP* 4.4 29.6 - - + +
133A THR* 5.3 5.2 - - - +
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Residues in contact with GLU 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 ARG* 3.2 24.5 + - - +
121A THR* 3.6 9.1 - - - +
122A LEU 3.2 0.2 - - - -
123A VAL* 1.3 78.1 - - - +
125A LEU* 1.3 59.7 + - + +
126A GLY 3.3 1.0 + - - -
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Residues in contact with LEU 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 THR* 3.0 34.7 + - + +
122A LEU 3.0 7.3 + - - +
124A GLU* 1.3 78.4 - - + +
126A GLY* 1.3 61.4 + - - +
127A PHE* 3.5 15.2 + - + -
179A ALA* 3.8 35.7 - - + +
182A LYS* 4.4 15.7 + - + +
183A GLN* 4.3 26.0 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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