Contacts of the helix formed by residues 104 - 125 (chain B) in PDB entry 4DHI
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B ILE* 3.2 15.6 + - + +
101B MET* 3.3 10.2 + - - +
102B LEU 3.6 0.2 - - - -
103B LYS* 1.3 81.4 - - + +
105B ARG* 1.3 62.7 + - - +
106B ALA* 3.1 21.7 + - - +
107B ARG* 3.2 24.2 + - + +
108B LEU 3.0 17.0 + - - -
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Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B MET 4.7 2.0 - - - +
102B LEU 5.4 6.5 + - - -
103B LYS 4.2 0.2 - - - -
104B ASP* 1.3 73.1 + - - +
106B ALA* 1.3 57.7 + - - +
108B LEU* 3.5 11.9 - - + +
109B GLU* 2.8 39.3 + - - +
146B ILE* 3.0 24.9 + - - +
147B HIS* 2.9 42.1 + - + +
148B SER 5.4 0.2 - - - -
149B GLY* 3.6 17.4 - - - -
151B HIS 5.6 1.2 + - - -
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASP* 3.1 10.4 + - - +
105B ARG* 1.3 77.4 - - - +
107B ARG* 1.3 61.6 + - - +
109B GLU* 3.5 13.3 + - - +
110B LYS* 3.3 39.6 + - - +
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 4.6 4.2 - - - +
100B ILE* 4.0 15.7 - - + +
101B MET* 3.7 29.6 - - + +
104B ASP* 3.2 32.0 + - + +
106B ALA* 1.3 74.4 - - - +
108B LEU* 1.3 61.3 + - - +
110B LYS* 3.2 15.5 + - - +
111B PHE* 2.9 33.1 + - - +
225B ALA 4.9 2.6 + - - -
226B GLY 3.6 19.8 + - - -
227B THR* 4.5 2.8 - - - +
258B GLU* 2.8 43.4 + - - -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B MET* 3.7 40.1 - - + +
104B ASP 3.0 12.8 + - - +
105B ARG* 3.5 16.2 - - + +
107B ARG* 1.3 77.4 - - - +
109B GLU* 1.3 56.5 + - - +
111B PHE* 3.2 1.4 + - + -
112B ILE* 2.9 55.1 + - + +
143B LEU* 4.1 22.2 - - + +
146B ILE* 3.8 17.7 - - + -
147B HIS* 3.6 37.5 - - + +
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ARG* 2.8 27.8 + - - +
106B ALA* 3.7 11.5 - - - +
108B LEU* 1.3 72.5 - - - +
110B LYS* 1.3 58.1 + - + +
112B ILE* 3.4 8.0 + - - +
113B ALA* 3.0 27.9 + - - +
147B HIS* 2.7 41.5 + - + +
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ALA* 3.3 28.3 + - - +
107B ARG* 3.2 17.9 + - - +
109B GLU* 1.3 78.2 - - + +
111B PHE* 1.3 58.2 + - - +
113B ALA* 3.3 7.4 + - - +
114B SER* 2.9 29.1 + - - -
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Residues in contact with PHE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 4.3 17.3 - - + -
98B ILE* 6.6 0.2 - - + -
101B MET* 3.6 28.0 - - + -
107B ARG* 2.9 22.6 + - - +
108B LEU* 3.2 4.7 + - + +
110B LYS* 1.3 73.6 - - - +
112B ILE* 1.3 60.6 + - - +
114B SER* 3.0 11.6 + - - -
115B SER* 2.8 50.2 + - - -
139B PHE* 3.7 22.7 - + - -
143B LEU* 3.6 15.0 - - + -
172B PHE* 5.2 2.5 - + - -
173B PHE* 4.2 24.0 - + - -
176B ILE* 5.7 1.1 - - + -
225B ALA* 3.6 28.3 - - + -
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Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LEU* 2.9 32.6 + - + +
109B GLU* 3.7 5.8 - - - +
111B PHE* 1.3 75.9 - - - +
113B ALA* 1.3 59.2 + - - +
115B SER* 3.2 6.7 + - - -
116B ARG* 2.9 30.1 + - + +
140B ILE* 4.3 13.9 - - + +
143B LEU* 3.6 48.0 - - + +
144B GLU* 3.5 31.2 - - - +
147B HIS* 4.0 15.5 - - + -
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLU 3.0 17.5 + - - +
110B LYS* 3.6 7.9 - - - +
111B PHE 3.3 0.2 - - - -
112B ILE* 1.3 78.9 - - - +
114B SER* 1.3 57.5 + - - +
116B ARG* 3.3 8.9 + - - +
117B ASP* 3.0 25.8 + - - +
120B ARG* 4.7 1.9 + - - -
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LYS 2.9 15.6 + - - -
111B PHE* 3.0 25.3 + - - -
113B ALA* 1.3 76.7 - - - +
115B SER* 1.3 56.5 + - - +
117B ASP* 3.2 8.3 + - - +
118B TRP* 2.9 39.9 + - - -
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PHE* 2.8 44.7 + - - -
112B ILE* 3.6 6.1 - - - -
114B SER* 1.3 75.1 + - - +
116B ARG* 1.3 64.7 + - - +
118B TRP* 3.3 6.7 + - - +
119B THR* 3.0 23.0 + - - -
139B PHE* 3.8 8.1 - - - -
140B ILE* 3.8 18.4 - - - +
143B LEU* 4.7 0.7 - - - -
172B PHE* 3.7 25.8 - - - -
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Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ILE* 2.9 19.2 + - + +
113B ALA* 3.5 8.7 - - - +
114B SER 3.3 0.2 - - - -
115B SER* 1.3 75.0 - - - +
117B ASP* 1.3 62.3 + - - +
119B THR* 3.2 25.0 + - - +
120B ARG* 3.3 47.3 + - - +
137B ASP* 6.2 0.2 - - - -
140B ILE* 3.7 22.5 - - + +
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Residues in contact with ASP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ALA 3.0 13.6 + - - +
114B SER* 3.2 11.6 + - - +
116B ARG* 1.3 75.3 - - - +
118B TRP* 1.3 64.0 + - - +
120B ARG* 2.9 35.5 + - - +
121B THR* 3.0 32.3 + - - -
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Residues in contact with TRP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B SER* 2.9 30.9 + - - -
115B SER* 3.3 11.4 + - - +
117B ASP* 1.3 75.3 - - - +
119B THR* 1.3 57.7 + - - +
121B THR* 3.0 25.4 + - + -
122B LEU* 2.8 37.2 + - + +
172B PHE* 4.4 4.0 - + + -
176B ILE* 3.5 38.5 - - + +
179B ALA* 3.5 31.6 - - + -
180B PHE* 3.9 29.4 - + + -
183B GLN* 4.1 12.3 - - - -
224B ALA* 3.2 39.9 + - + -
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Residues in contact with THR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B SER 3.0 15.2 + - - -
116B ARG* 3.2 22.4 + - - +
117B ASP 3.2 0.4 - - - -
118B TRP* 1.3 77.3 - - - +
120B ARG* 1.3 63.3 + - - +
122B LEU* 3.5 9.4 + - + +
123B VAL* 3.5 16.3 + - + +
133B THR* 4.3 24.6 + - + +
136B CYS* 3.1 41.3 - - + +
137B ASP* 4.8 4.5 - - - +
140B ILE* 3.7 8.6 - - + +
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ALA 4.7 1.4 + - - -
116B ARG* 3.6 51.2 - - - +
117B ASP* 2.9 50.3 + - - +
118B TRP 3.2 0.2 - - - -
119B THR* 1.3 76.6 - - - +
121B THR* 1.3 63.8 + - - +
123B VAL* 3.3 9.2 + - - +
124B GLU* 3.2 30.7 + - + +
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ASP* 3.0 23.0 + - - -
118B TRP* 3.0 29.8 + - + -
120B ARG* 1.3 74.6 - - - +
122B LEU* 1.3 64.8 + - - +
124B GLU* 3.2 18.6 + - + +
125B LEU* 2.9 40.6 + - + +
183B GLN* 3.6 28.3 + - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B TRP* 2.8 20.9 + - + +
119B THR* 3.7 5.2 - - - +
121B THR* 1.3 76.5 - - - +
123B VAL* 1.3 62.2 + - + +
125B LEU 3.2 6.6 + - - -
127B PHE* 3.0 55.3 + - + -
132B CYS* 4.5 10.5 - - + -
136B CYS* 3.4 33.0 - - - -
175B LEU* 3.9 30.3 - - + +
176B ILE* 5.0 5.4 - - + +
179B ALA* 3.5 30.5 - - + -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B THR* 3.5 13.4 + - + +
120B ARG* 3.3 9.9 + - - +
122B LEU* 1.3 75.4 - - + +
124B GLU* 1.3 65.2 + - + +
126B GLY* 3.1 14.2 + - - -
127B PHE 4.7 7.2 - - - +
129B ASP* 3.8 40.8 - - + +
133B THR* 4.4 8.7 - - - +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ARG* 3.2 17.7 + - - +
121B THR* 3.5 28.1 + - + +
123B VAL* 1.3 78.1 - - + +
125B LEU* 1.3 61.3 + - + +
126B GLY* 3.2 2.8 + - - -
183B GLN* 5.5 1.9 + - - -
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B THR* 2.9 37.9 + - + +
122B LEU 3.2 3.8 + - - +
124B GLU* 1.3 77.0 - - + +
126B GLY* 1.3 59.8 + - - +
127B PHE* 3.5 14.8 + - + -
179B ALA* 3.5 38.6 - - + +
182B LYS* 4.5 16.0 + - + +
183B GLN* 4.1 29.4 - - + +
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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
------------------------------------------------------------
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