Contacts of the helix formed by residues 108 - 125 (chain A) in PDB entry 5DQZ
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 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A LYS* 3.3 8.1 + - + +
105A LEU 3.5 0.3 - - - +
107A LEU* 1.3 78.3 - - + +
109A GLU* 1.3 82.3 + - - +
110A ASP* 3.6 11.7 + - - +
111A LEU* 3.3 42.3 + - + +
112A ARG* 2.8 35.8 + - - +
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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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107A LEU 3.6 9.4 + - - +
108A ASP* 1.3 82.4 - - - +
110A ASP* 1.3 67.9 + - - +
112A ARG* 3.6 10.5 + - - +
113A LEU* 2.9 27.5 + - - +
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Residues in contact with ASP 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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108A ASP* 3.3 8.8 + - - +
109A GLU* 1.3 86.1 - - - +
111A LEU* 1.3 62.2 + - + +
113A LEU* 3.2 15.5 + - + +
114A LYS* 2.9 42.1 + - - +
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Residues in contact with LEU 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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104A LYS* 3.9 23.1 - - + +
105A LEU* 3.8 22.2 - - + +
108A ASP* 3.3 36.5 + - + +
110A ASP* 1.3 76.4 - - + +
112A ARG* 1.3 65.6 - - - +
114A LYS* 3.1 14.7 + - + +
115A VAL* 3.0 27.1 + - - +
275A GLY* 3.3 26.5 - - - +
277A ILE* 3.7 28.5 - - + -
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Residues in contact with ARG 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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105A LEU 3.1 13.9 + - - +
106A ALA* 4.0 15.5 - - - +
108A ASP 2.8 17.7 + - - +
109A GLU* 3.6 8.4 + - - +
111A LEU* 1.3 75.7 - - - +
113A LEU* 1.3 62.5 + - - +
115A VAL* 3.1 2.4 + - - +
116A VAL* 2.9 45.0 + - + +
134A VAL* 5.3 6.9 - - - +
205A GLY 5.3 1.0 + - - -
206A PHE* 2.7 48.5 + - + +
207A VAL* 4.6 1.2 + - - +
209A THR* 5.3 1.2 - - - +
283B PRO* 3.6 36.3 - - - +
285B ASP* 4.1 21.2 + - - +
286B ALA* 3.7 28.9 - - - +
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Residues in contact with LEU 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 2.9 18.9 + - - +
110A ASP* 3.4 17.9 - - + +
111A LEU 3.2 0.4 - - - -
112A ARG* 1.3 81.3 - - - +
114A LYS* 1.3 57.1 + - + +
116A VAL* 3.4 4.6 + - + +
117A ARG* 2.9 53.7 + - + +
134A VAL* 3.6 31.6 - - + -
285B ASP* 5.4 2.7 - - - +
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Residues in contact with LYS 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 ASP* 2.9 27.8 + - - +
111A LEU* 3.1 12.3 + - - +
113A LEU* 1.3 75.0 - - + +
115A VAL* 1.3 58.1 + - - +
117A ARG* 3.3 9.8 + - - +
118A LYS* 2.9 29.1 + - - +
274A ALA* 3.6 19.4 - - - +
275A GLY* 3.9 17.5 - - - +
276A GLU* 3.5 26.6 + - - +
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Residues in contact with VAL 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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105A LEU* 4.4 14.1 - - + -
111A LEU 3.0 19.2 + - - +
112A ARG 3.1 7.2 + - - +
114A LYS* 1.3 76.9 - - - +
116A VAL* 1.3 57.7 + - - +
118A LYS* 3.2 4.9 + - - +
119A MET* 2.9 30.0 + - + +
206A PHE* 3.7 43.7 - - + -
271A VAL* 3.9 38.3 - - + +
272A LEU* 4.4 3.4 - - + +
274A ALA* 4.7 0.9 - - - -
275A GLY 4.3 12.8 - - - +
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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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112A ARG* 2.9 35.4 + - + +
113A LEU* 3.7 6.5 - - - +
115A VAL* 1.3 75.6 - - - +
117A ARG* 1.3 60.1 + - + +
119A MET* 3.2 9.6 + - - +
120A PHE* 2.9 55.6 + - + -
134A VAL* 4.0 23.1 - - + -
137A LEU* 5.5 0.9 - - + -
206A PHE* 3.8 34.8 - - + +
207A VAL* 4.0 7.6 - - + -
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Residues in contact with ARG 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 LEU* 2.9 49.8 + - + +
114A LYS* 3.6 9.2 - - - +
116A VAL* 1.3 77.6 - - + +
118A LYS* 1.3 57.6 + - - +
120A PHE* 3.4 7.1 + - - +
121A GLU* 2.9 29.6 + - - +
128A ALA* 4.6 12.9 + - + +
129A PRO 3.3 10.0 + - - -
130A ALA 2.3 34.2 + - - -
131A ARG* 3.4 22.7 - - - +
132A ARG 3.5 16.0 + - - +
134A VAL* 5.9 0.9 - - + -
137A LEU* 4.8 14.6 - - + +
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Residues in contact with LYS 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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114A LYS 2.9 8.4 + - - +
115A VAL* 3.5 7.4 - - - +
117A ARG* 1.3 74.3 - - - +
119A MET* 1.3 66.0 + - - +
121A GLU* 3.2 26.3 + - - +
122A LEU* 2.9 53.0 + - + +
270A ASP* 3.8 28.7 + - - -
271A VAL* 4.5 10.1 - - - +
274A ALA* 3.5 32.3 - - + -
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Residues in contact with MET 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 VAL* 2.9 20.0 + - - +
116A VAL* 3.4 7.6 - - - +
118A LYS* 1.3 75.4 - - - +
120A PHE* 1.3 58.3 + - - +
122A LEU* 3.4 5.3 + - - +
123A ARG* 3.0 54.3 + - - +
206A PHE* 4.4 13.9 - - - -
207A VAL* 3.6 18.4 - - + -
215A PHE* 5.3 1.3 - - - -
218A ASP* 3.5 50.7 - - + +
219A ILE* 5.4 0.9 - - - -
222A ILE* 4.3 13.0 - - + +
271A VAL* 3.7 28.9 - - + -
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Residues in contact with PHE 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 VAL* 2.9 47.0 + - + +
117A ARG 3.8 4.3 - - - +
118A LYS 3.2 0.2 - - - -
119A MET* 1.3 77.1 - - - +
121A GLU* 1.3 58.0 + - - +
123A ARG* 3.3 20.4 + - - +
124A PHE* 2.9 58.6 + + + -
128A ALA* 4.7 2.9 - - + -
134A VAL* 4.5 7.0 - - + -
137A LEU* 3.8 41.5 - - + -
138A ARG* 4.1 14.1 - - + -
141A GLU* 3.7 21.1 - - + -
207A VAL* 4.1 12.8 - - + -
35G T 3.6 17.9 - - - -
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Residues in contact with GLU 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 ARG 2.9 18.1 + - - +
118A LYS* 3.2 27.7 + - - +
120A PHE* 1.3 74.6 - - - +
122A LEU* 1.3 57.3 + - + +
124A PHE* 4.4 2.0 - - - +
125A GLY* 2.6 34.7 + - - -
126A GLU* 3.4 23.2 + - - +
127A PRO* 3.5 34.0 - - + +
128A ALA* 3.9 17.0 + - + +
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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 LYS* 2.9 49.9 + - + +
119A MET* 3.8 3.1 - - - +
121A GLU* 1.3 77.0 - - + +
123A ARG* 1.3 62.2 + - - +
125A GLY* 3.5 11.7 + - - -
222A ILE* 4.3 20.4 - - + +
267A LEU* 4.1 21.1 - - + +
270A ASP* 4.5 10.8 - - - +
271A VAL* 3.7 29.4 - - + -
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Residues in contact with ARG 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 MET* 3.0 54.4 + - - +
120A PHE* 3.5 25.1 - - - +
122A LEU* 1.3 80.2 - - - +
124A PHE* 1.3 61.6 + - + +
141A GLU* 2.9 35.5 + - + +
144A ARG* 3.1 48.6 + - - +
207A VAL* 3.9 10.5 - - - +
208A HIS* 5.2 0.6 - - - -
218A ASP* 4.2 8.1 + - - +
221A ASP* 3.7 38.9 - - - +
222A ILE* 4.5 16.3 - - + +
35G T 4.2 11.1 - - - +
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Residues in contact with PHE 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 PHE* 2.9 38.5 + + + +
121A GLU* 4.0 2.5 - - - +
123A ARG* 1.3 81.0 - - + +
125A GLY* 1.3 59.1 + - - +
126A GLU 3.6 10.7 + - - +
128A ALA* 4.5 14.4 - - + -
129A PRO* 5.1 4.7 - - + -
137A LEU* 4.1 29.4 - - + -
140A ILE* 4.3 14.4 - - + -
141A GLU* 3.5 45.5 - - + -
144A ARG* 4.3 14.6 - - + +
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Residues in contact with GLY 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 GLU* 2.6 20.6 + - - -
122A LEU* 3.9 11.2 - - - -
123A ARG 3.4 1.8 - - - -
124A PHE* 1.3 74.8 - - - +
126A GLU* 1.3 67.7 + - - +
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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