Contacts of the helix formed by residues 138 - 151 (chain D) in PDB entry 2LDX
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 PRO 138 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D ARG 4.1 11.2 - - - +
106D LEU* 4.0 36.1 - - + -
108D LEU* 4.9 10.5 - - + +
109D LEU* 4.4 10.8 - - + -
137D ASN* 1.3 92.1 - - + +
139D VAL* 1.3 55.1 + - - -
140D ASP* 2.9 7.3 + - - +
141D ILE* 2.9 12.2 + - + +
142D LEU* 2.4 58.7 + - + +
192D HIS 4.7 9.0 - - - +
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Residues in contact with VAL 139 (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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134D VAL* 4.1 9.0 - - - +
135D VAL 2.9 29.6 - - - +
137D ASN* 2.6 28.6 - - - +
138D PRO* 1.3 78.0 - - - +
140D ASP* 1.3 68.3 + - - +
142D LEU* 4.3 2.5 - - - -
143D THR* 2.5 44.3 + - - +
160D SER* 2.8 29.2 - - - +
161D GLY 4.4 6.5 - - - +
192D HIS* 3.8 28.5 - - + -
273D THR* 4.7 1.8 - - + -
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Residues in contact with ASP 140 (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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138D PRO* 2.9 4.2 + - - +
139D VAL* 1.3 94.0 - - - +
141D ILE* 1.3 57.1 + - + +
143D THR* 2.7 19.5 + - - -
144D TYR* 2.9 11.8 + - - +
190D GLY 4.6 0.9 - - - +
191D GLU* 4.2 10.3 - - - +
192D HIS* 3.5 27.3 + - - +
273D THR* 2.8 34.4 - - - +
287D PHE* 3.5 24.0 - - - +
288D LEU* 4.1 4.1 - - - -
289D SER* 4.4 1.7 + - - -
322D LEU* 3.6 22.5 - - + +
326D GLN* 5.6 0.2 - - - -
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Residues in contact with ILE 141 (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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106D LEU* 3.8 26.2 - - + -
109D LEU* 3.9 32.8 - - + -
138D PRO* 2.9 12.0 + - + +
140D ASP* 1.3 72.2 - - + +
142D LEU* 1.3 56.2 + - - +
144D TYR* 3.3 11.8 - - + +
145D VAL* 2.9 34.6 + - + +
322D LEU* 3.3 29.6 - - + +
325D MET* 3.9 26.5 - - + -
326D GLN* 4.3 22.2 - - + +
328D ASN* 5.0 6.7 - - - +
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Residues in contact with LEU 142 (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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109D LEU* 3.9 20.9 - - + -
112D ASN* 4.3 15.0 - - + +
113D VAL* 4.2 21.5 - - - +
116D MET* 4.3 10.8 - - + -
134D VAL* 4.3 5.4 - - + -
136D THR* 2.9 31.6 - - - +
137D ASN* 3.3 7.0 - - + +
138D PRO* 2.4 49.5 + - + +
139D VAL 3.9 1.3 - - - +
141D ILE* 1.3 70.2 - - - +
143D THR* 1.3 57.4 + - - +
144D TYR 3.0 0.9 - - - -
145D VAL* 2.8 12.5 + - + +
146D VAL* 2.5 41.7 + - - +
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Residues in contact with THR 143 (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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134D VAL* 4.0 5.4 - - - +
139D VAL 2.5 30.9 + - - -
140D ASP* 2.7 4.7 + - - -
142D LEU* 1.3 68.9 - - - +
144D TYR* 1.3 52.4 + - - +
146D VAL* 2.8 11.2 - - - +
147D TRP* 2.5 38.5 + - - +
157D VAL* 3.8 19.2 - - + +
158D ILE 3.9 3.4 + - - -
159D GLY* 3.5 14.6 + - - -
273D THR* 3.2 25.7 + - - +
287D PHE* 3.3 32.5 - - + -
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Residues in contact with TYR 144 (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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140D ASP 2.9 9.7 + - - +
141D ILE* 3.3 17.7 - - + +
143D THR* 1.3 74.7 - - - +
145D VAL* 1.3 76.9 + - + +
147D TRP* 3.1 6.8 + + - +
148D LYS* 2.9 61.6 + - + +
285D GLU* 3.4 25.1 - - + +
287D PHE* 3.7 21.8 - + + -
323D TRP* 4.8 6.8 - + - -
326D GLN* 3.1 59.3 + - + +
328D ASN* 4.8 10.3 - - + +
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Residues in contact with VAL 145 (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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109D LEU* 5.7 0.4 - - + -
113D VAL* 3.8 37.2 - - + +
116D MET* 3.9 25.1 - - + -
117D LYS 5.2 0.7 - - - +
141D ILE* 2.9 31.4 + - + +
142D LEU* 2.8 19.0 + - + +
144D TYR* 1.3 80.4 - - + +
146D VAL* 1.3 53.6 + - - +
148D LYS* 2.9 6.4 - - - +
149D ILE* 2.6 45.5 + - + +
328D ASN* 4.7 10.1 - - + +
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Residues in contact with VAL 146 (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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93D ILE* 4.4 0.7 - - + -
116D MET* 4.2 23.1 - - + -
120D VAL* 3.2 37.9 - - + -
132D ILE* 5.5 3.6 - - + -
134D VAL* 3.5 22.9 - - + -
142D LEU 2.5 21.1 + - - +
143D THR* 2.8 32.8 - - - +
145D VAL* 1.3 73.0 - - - +
147D TRP* 1.3 56.3 + - - +
149D ILE* 3.3 7.4 - - - -
150D SER* 2.6 40.5 + - - -
157D VAL* 3.9 9.9 - - + -
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Residues in contact with TRP 147 (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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143D THR 2.5 27.0 + - - +
144D TYR* 3.1 7.2 + + - +
146D VAL* 1.3 72.4 - - - +
148D LYS* 1.3 98.2 + - + +
150D SER* 3.2 3.1 + - - -
151D GLY* 2.9 33.0 + - - -
152D PHE 3.4 25.4 + - - -
153D PRO* 4.7 0.8 - - - +
154D VAL* 3.6 26.2 - - + +
157D VAL* 3.7 15.5 - - + -
275D LEU* 4.2 13.0 - - + -
285D GLU* 2.9 26.5 - - + -
287D PHE* 3.3 39.5 - + + -
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Residues in contact with LYS 148 (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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144D TYR* 2.9 45.7 + - + +
145D VAL* 2.9 11.9 - - - +
147D TRP* 1.3 118.5 - - + +
149D ILE* 1.3 64.0 + - + +
150D SER 3.3 1.0 + - - -
151D GLY* 3.8 8.2 + - - -
285D GLU* 3.8 14.1 + - - +
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Residues in contact with ILE 149 (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 LYS* 4.4 30.7 - - + +
120D VAL* 3.6 11.9 - - + -
121D PRO* 3.2 40.0 - - + +
145D VAL* 2.6 31.8 + - + +
146D VAL* 3.3 18.8 - - - +
148D LYS* 1.3 75.4 - - + +
150D SER* 1.3 60.8 + - - +
329D LEU* 6.2 4.0 - - + -
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Residues in contact with SER 150 (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 PRO* 4.0 12.6 - - - -
124D ILE* 3.6 34.5 - - - +
132D ILE* 4.9 4.0 - - - -
146D VAL* 2.6 23.2 + - - -
147D TRP 3.2 4.2 + - - -
148D LYS 4.1 0.7 - - - -
149D ILE* 1.3 77.1 - - - +
151D GLY* 1.3 68.7 + - - +
152D PHE* 3.3 19.9 + - - -
157D VAL* 3.9 13.4 - - - +
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Residues in contact with GLY 151 (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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147D TRP* 2.9 15.5 + - - -
148D LYS 3.8 6.7 + - - -
150D SER* 1.3 85.8 + - - +
152D PHE* 1.3 60.6 + - - -
153D PRO* 4.5 1.2 - - - +
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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