Contacts of the helix formed by residues 138 - 151 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A ARG 4.1 11.2 - - - +
106A LEU* 4.0 35.7 - - + -
108A LEU* 4.9 11.4 - - + +
109A LEU* 4.4 10.1 - - + -
137A ASN* 1.3 92.7 - - + +
139A VAL* 1.3 55.9 + - + -
140A ASP* 2.9 7.7 + - - +
141A ILE* 2.9 11.4 + - + +
142A LEU* 2.4 59.5 + - + +
192A HIS 4.7 9.9 - - - +
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Residues in contact with VAL 139 (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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134A VAL* 4.1 9.1 - - - +
135A VAL 2.9 29.6 - - - +
137A ASN* 2.6 29.3 - - - +
138A PRO* 1.3 77.4 - - - +
140A ASP* 1.3 69.4 + - - +
142A LEU* 4.3 2.7 - - - -
143A THR* 2.5 43.9 + - - +
160A SER* 2.8 31.0 - - - +
161A GLY 4.4 6.3 - - - +
192A HIS* 3.8 27.1 - - + -
273A THR* 4.7 1.8 - - + -
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Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PRO* 2.9 4.4 + - - +
139A VAL* 1.3 95.0 - - - +
141A ILE* 1.3 56.9 + - + +
143A THR* 2.7 19.6 + - - -
144A TYR* 2.9 11.4 + - - +
190A GLY 4.6 1.2 - - - +
191A GLU* 4.2 10.6 - - - +
192A HIS* 3.5 27.6 + - - +
273A THR* 2.8 35.3 - - - +
287A PHE* 3.5 25.3 - - - +
288A LEU* 4.1 4.3 - - - -
289A SER* 4.4 1.4 + - - -
322A LEU* 3.6 21.5 - - + +
326A GLN* 5.6 0.2 - - - -
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Residues in contact with ILE 141 (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 LEU* 3.8 26.2 - - + -
109A LEU* 3.9 32.8 - - + -
138A PRO* 2.9 11.4 + - + +
140A ASP* 1.3 72.1 - - + +
142A LEU* 1.3 56.8 + - - +
144A TYR* 3.3 12.4 - - + +
145A VAL* 2.9 35.2 + - + +
322A LEU* 3.3 29.6 - - + +
325A MET* 3.9 25.8 - - + -
326A GLN* 4.3 23.6 - - + +
328A ASN* 5.0 6.5 - - - +
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Residues in contact with LEU 142 (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 LEU* 3.9 20.4 - - + -
112A ASN* 4.3 15.0 - - + +
113A VAL* 4.2 21.1 - - - +
116A MET* 4.3 11.2 - - + -
134A VAL* 4.3 5.8 - - + -
136A THR* 2.9 32.3 - - - +
137A ASN* 3.3 7.2 - - + +
138A PRO* 2.4 48.4 + - + +
139A VAL 3.9 1.3 - - - +
141A ILE* 1.3 70.2 - - - +
143A THR* 1.3 56.4 + - - +
144A TYR 3.0 0.7 - - - -
145A VAL* 2.8 13.2 + - + +
146A VAL* 2.5 41.3 + - - +
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Residues in contact with THR 143 (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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134A VAL* 4.0 4.8 - - - +
139A VAL 2.5 30.4 + - - -
140A ASP* 2.7 5.1 + - - -
142A LEU* 1.3 69.6 - - - +
144A TYR* 1.3 51.3 + - - +
146A VAL* 2.8 11.5 - - - +
147A TRP* 2.5 39.0 + - - +
157A VAL* 3.8 19.0 - - + +
158A ILE 3.9 3.9 + - - -
159A GLY* 3.5 14.2 + - - -
273A THR* 3.2 25.8 + - - +
287A PHE* 3.3 33.7 - - + -
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Residues in contact with TYR 144 (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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140A ASP 2.9 9.7 + - - +
141A ILE* 3.3 17.0 - - + +
143A THR* 1.3 75.5 - - - +
145A VAL* 1.3 77.0 - - + +
147A TRP* 3.1 7.5 + + - +
148A LYS* 2.9 62.6 + - + +
285A GLU* 3.4 24.9 - - + +
287A PHE* 3.7 21.5 - + + -
323A TRP* 4.8 6.4 - + - -
326A GLN* 3.1 59.8 + - + +
328A ASN* 4.8 10.2 - - + +
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Residues in contact with VAL 145 (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 LEU* 5.7 0.7 - - + -
113A VAL* 3.8 37.9 - - + +
116A MET* 3.9 24.9 - - + -
117A LYS* 5.2 0.9 - - - +
141A ILE* 2.9 31.8 + - + +
142A LEU* 2.8 17.8 + - + +
144A TYR* 1.3 79.7 - - + +
146A VAL* 1.3 53.4 + - - +
148A LYS* 2.9 5.9 - - - +
149A ILE* 2.6 46.0 + - + +
328A ASN* 4.7 9.9 - - + +
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Residues in contact with VAL 146 (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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93A ILE* 4.4 0.9 - - + -
116A MET* 4.2 22.4 - - + -
120A VAL* 3.2 39.0 - - + -
132A ILE* 5.5 2.9 - - + -
134A VAL* 3.5 23.3 - - + -
142A LEU 2.5 21.4 + - - +
143A THR* 2.8 31.6 - - - +
145A VAL* 1.3 72.4 - - - +
147A TRP* 1.3 56.5 + - - +
149A ILE* 3.3 7.2 - - - -
150A SER* 2.6 40.6 + - - -
157A VAL* 3.9 10.5 - - + -
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Residues in contact with TRP 147 (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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143A THR 2.5 27.4 + - - +
144A TYR* 3.3 6.7 - + - +
146A VAL* 1.3 72.6 - - - +
148A LYS* 1.3 97.7 - - + +
150A SER* 3.2 3.1 + - - -
151A GLY* 2.9 33.0 + - - -
152A PHE 3.4 26.2 + - - -
153A PRO* 4.7 0.6 - - - +
154A VAL* 3.6 25.1 - - + +
157A VAL* 3.7 14.4 - - + -
275A LEU* 4.2 13.5 - - + -
285A GLU* 2.9 26.7 - - + -
287A PHE* 3.3 39.0 - + + -
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Residues in contact with LYS 148 (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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144A TYR* 2.9 46.5 + - + +
145A VAL* 2.9 11.7 - - - +
147A TRP* 1.3 117.8 - - + +
149A ILE* 1.3 63.3 + - + +
150A SER 3.3 1.2 + - - -
151A GLY* 3.8 7.8 + - - -
285A GLU* 3.8 14.1 + - - +
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Residues in contact with ILE 149 (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 LYS* 4.4 29.8 - - + +
120A VAL* 3.6 12.6 - - + -
121A PRO* 3.2 38.7 - - + +
145A VAL* 2.6 32.3 + - + +
146A VAL* 3.3 18.2 - - - +
148A LYS* 1.3 74.5 - - + +
150A SER* 1.3 59.9 + - - +
329A LEU* 6.2 3.8 - - + -
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Residues in contact with SER 150 (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 PRO* 4.0 12.6 - - - -
124A ILE* 3.6 35.2 - - - +
132A ILE* 4.9 3.8 - - - -
146A VAL* 2.6 22.2 + - - -
147A TRP 3.2 4.2 + - - -
148A LYS 4.1 0.4 - - - -
149A ILE* 1.3 76.3 - - - +
151A GLY* 1.3 69.7 + - - +
152A PHE* 3.3 18.8 + - - -
157A VAL* 3.9 14.0 - - - +
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Residues in contact with GLY 151 (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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147A TRP* 2.9 14.7 + - - -
148A LYS 3.8 6.7 + - - -
150A SER* 1.3 83.9 + - - +
152A PHE* 1.3 60.6 + - - +
153A PRO* 4.5 0.9 - - - +
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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