Contacts of the helix formed by residues 108 - 125 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D LYS* 3.3 8.3 + - + +
105D LEU 3.5 0.3 - - - +
106D ALA 3.5 0.2 - - - -
107D LEU* 1.3 78.3 - - - +
109D GLU* 1.3 77.2 + - - +
110D ASP* 3.5 15.3 + - - +
111D LEU* 3.3 37.6 + - + +
112D ARG* 2.8 35.8 + - - +
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Residues in contact with GLU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LEU 3.6 9.3 + - - +
108D ASP* 1.3 82.6 + - - +
110D ASP* 1.3 66.7 + - - +
112D ARG* 3.7 7.6 - - - +
113D LEU* 2.9 37.8 + - + +
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Residues in contact with ASP 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ASP* 3.3 10.0 + - - +
109D GLU* 1.3 85.5 - - - +
111D LEU* 1.3 62.3 + - + +
113D LEU* 3.2 11.5 + - - +
114D LYS* 2.9 43.7 + - - +
131D ARG* 5.7 5.7 + - - +
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Residues in contact with LEU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LYS* 4.0 24.2 - - + +
105D LEU* 3.8 22.2 - - + +
108D ASP* 3.3 36.0 + - + +
110D ASP* 1.3 76.0 - - + +
112D ARG* 1.3 66.0 + - - +
114D LYS* 3.1 16.1 + - + +
115D VAL* 3.0 27.6 + - - +
275D GLY* 3.2 26.0 - - - +
277D ILE* 3.6 28.3 - - + -
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Residues in contact with ARG 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C PRO* 3.4 41.7 - - - +
285C ASP* 3.8 23.0 + - - +
286C ALA* 3.8 21.8 - - - +
105D LEU 3.2 12.8 + - - +
106D ALA* 4.0 15.7 - - - +
108D ASP 2.8 22.4 + - - +
109D GLU* 3.7 7.6 - - - +
111D LEU* 1.3 72.4 - - - +
113D LEU* 1.3 69.7 + - - +
115D VAL* 3.2 2.8 + - - +
116D VAL* 2.9 41.8 + - + +
134D VAL* 5.5 3.4 - - - +
206D PHE* 3.1 47.0 + - + +
207D VAL* 5.1 0.8 - - - +
209D THR* 5.4 1.2 - - - +
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Residues in contact with LEU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C ASP* 4.4 7.2 - - - +
109D GLU* 2.9 23.9 + - + +
110D ASP* 3.2 11.2 + - - +
112D ARG* 1.3 96.5 - - - +
114D LYS* 1.3 58.4 + - + +
116D VAL* 3.4 5.0 + - + +
117D ARG* 2.9 46.0 + - - +
131D ARG* 3.4 36.1 - - - +
134D VAL* 4.1 16.8 - - + -
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Residues in contact with LYS 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ASP* 2.9 29.3 + - + +
111D LEU* 3.4 15.0 - - - +
113D LEU* 1.3 75.1 - - - +
115D VAL* 1.3 58.2 + - - +
117D ARG* 3.4 7.5 + - - +
118D LYS* 2.9 28.6 + - - +
131D ARG* 5.9 5.1 - - - +
274D ALA* 3.5 20.0 - - - +
275D GLY* 3.6 22.7 - - - +
276D GLU* 3.5 25.3 + - - +
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Residues in contact with VAL 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D LEU* 4.3 13.2 - - + -
111D LEU 3.0 19.1 + - - +
112D ARG 3.5 7.2 - - - +
114D LYS* 1.3 76.6 - - - +
116D VAL* 1.3 57.1 + - - +
118D LYS* 3.2 5.3 + - - +
119D MET* 2.9 29.5 + - + +
206D PHE* 3.6 44.4 - - + -
271D VAL* 3.8 37.7 - - + +
272D LEU* 4.4 2.9 - - + +
274D ALA* 4.7 0.9 - - - -
275D GLY 4.3 12.8 - - - +
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Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ARG* 2.9 38.9 + - + +
113D LEU* 3.8 7.6 - - + +
115D VAL* 1.3 73.5 - - - +
117D ARG* 1.3 59.3 + - + +
119D MET* 3.2 9.1 + - - +
120D PHE* 2.9 54.8 + - + -
134D VAL* 3.8 25.1 - - + -
137D LEU* 5.4 0.7 - - + -
206D PHE* 3.9 32.5 - - + +
207D VAL* 4.1 7.0 - - + -
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Residues in contact with ARG 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LEU* 2.9 23.6 + - - +
114D LYS* 3.7 6.1 - - - +
116D VAL* 1.3 77.0 - - + +
118D LYS* 1.3 56.9 + - - +
120D PHE* 3.4 6.9 + - - +
121D GLU* 2.9 29.6 + - - +
128D ALA* 5.0 5.2 - - + +
129D PRO 4.9 4.9 + - - -
130D ALA 4.1 7.7 + - - -
131D ARG* 3.1 58.7 - - - +
132D ARG 2.8 34.2 + - - +
133D SER* 4.2 2.0 - - - +
134D VAL* 3.9 25.1 - - - +
137D LEU* 4.6 15.8 - - + +
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Residues in contact with LYS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LYS 2.9 8.5 + - - +
115D VAL* 3.5 7.0 - - - +
117D ARG* 1.3 74.1 - - - +
119D MET* 1.3 65.0 + - - +
121D GLU* 3.2 31.2 + - - +
122D LEU* 2.9 46.2 + - + +
270D ASP* 3.6 31.6 + - - -
271D VAL* 4.4 10.5 - - - +
274D ALA* 3.4 34.3 - - + -
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Residues in contact with MET 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D VAL* 2.9 19.6 + - - +
116D VAL* 3.4 8.1 - - - +
118D LYS* 1.3 74.1 - - - +
120D PHE* 1.3 59.0 + - - +
122D LEU* 3.2 7.5 + - - +
123D ARG* 3.0 42.3 + - - +
206D PHE* 4.3 14.8 - - - -
207D VAL* 3.6 26.9 - - + -
215D PHE* 5.4 0.2 - - - -
218D ASP* 3.5 51.8 - - + +
219D ILE* 5.4 1.8 - - - -
222D ILE* 4.3 13.0 - - + +
271D VAL* 3.7 30.1 - - + -
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Residues in contact with PHE 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D VAL* 2.9 46.8 + - + +
117D ARG 3.9 4.0 - - - +
119D MET* 1.3 77.4 - - + +
121D GLU* 1.3 57.9 + - - +
123D ARG* 3.1 20.0 + - - +
124D PHE* 2.9 59.9 + + + -
128D ALA* 4.5 3.1 - - + -
134D VAL* 4.4 7.4 - - + -
137D LEU* 3.8 31.9 - - + -
138D ARG* 4.1 25.1 - - + -
141D GLU* 3.7 28.0 - - + -
207D VAL* 4.1 21.3 - - + -
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Residues in contact with GLU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ARG 2.9 18.0 + - - +
118D LYS* 3.2 34.1 + - - +
120D PHE* 1.3 76.8 - - - +
122D LEU* 1.3 55.2 + - + +
124D PHE* 4.6 1.6 - - - -
125D GLY 2.7 35.8 + - - +
126D GLU* 3.0 44.7 + - + +
127D PRO* 3.7 14.5 - - + +
128D ALA* 4.2 15.7 - - - +
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Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LYS* 2.9 44.3 + - + +
119D MET 3.5 6.5 - - - +
121D GLU* 1.3 78.4 - - + +
123D ARG* 1.3 60.7 + - - +
125D GLY* 3.7 10.6 + - - +
222D ILE* 4.0 25.4 - - + +
267D LEU* 4.0 22.7 - - + -
270D ASP* 4.4 9.6 - - - +
271D VAL* 3.7 30.7 - - + -
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Residues in contact with ARG 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D MET* 3.0 43.3 + - - +
120D PHE* 3.1 27.2 + - - +
122D LEU* 1.3 79.8 - - - +
124D PHE* 1.3 60.1 + - + +
125D GLY 3.8 0.2 + - - -
141D GLU* 3.1 40.6 + - - +
144D ARG* 3.0 42.2 + - - +
207D VAL* 4.6 15.1 - - - +
208D HIS* 4.8 4.8 - - - -
218D ASP 4.1 3.2 + - - -
221D ASP* 3.3 42.6 + - - +
222D ILE* 4.0 25.1 - - + -
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Residues in contact with PHE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D PHE* 2.9 36.9 + + - +
121D GLU* 4.0 3.6 - - - +
123D ARG* 1.3 79.5 - - + +
125D GLY* 1.3 58.1 + - - +
126D GLU 3.5 13.4 + - - +
127D PRO 5.3 0.2 - - - +
128D ALA* 3.6 33.9 - - + -
129D PRO* 5.0 1.8 - - + -
137D LEU* 4.1 16.6 - - + -
140D ILE* 3.8 38.8 - - + -
141D GLU* 3.4 24.7 - - + -
144D ARG* 4.2 11.4 - - - +
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Residues in contact with GLY 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D GLU* 2.7 12.1 + - - +
122D LEU* 3.7 9.5 + - - +
123D ARG 3.4 3.0 + - - -
124D PHE* 1.3 77.2 - - - +
126D GLU* 1.3 68.4 + - - +
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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
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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