Contacts of the helix formed by residues 138 - 151 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B ARG 4.1 11.2 - - - +
106B LEU* 4.0 35.4 - - + -
108B LEU* 4.9 11.4 - - + +
109B LEU* 4.4 11.4 - - + -
137B ASN* 1.3 92.0 - - + +
139B VAL* 1.3 55.2 + - + -
140B ASP* 2.9 7.6 + - - +
141B ILE* 2.9 11.7 + - + +
142B LEU* 2.4 59.3 + - + +
192B HIS 4.7 9.4 - - - +
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Residues in contact with VAL 139 (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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134B VAL* 4.1 8.7 - - - +
135B VAL 2.9 28.7 - - - +
137B ASN* 2.6 29.3 - - - +
138B PRO* 1.3 78.2 - - - +
140B ASP* 1.3 67.3 + - - +
142B LEU* 4.3 2.7 - - - -
143B THR* 2.5 44.4 + - - +
159B GLY 5.3 0.2 - - - -
160B SER* 2.8 30.3 - - - +
161B GLY 4.4 6.5 - - - +
192B HIS* 3.8 27.4 - - + -
273B THR* 4.7 1.3 - - - -
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Residues in contact with ASP 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PRO* 2.9 4.4 + - - +
139B VAL* 1.3 94.0 + - - +
141B ILE* 1.3 57.5 + - + +
143B THR* 2.7 19.3 + - - +
144B TYR* 2.9 11.6 + - - +
161B GLY* 4.6 0.2 - - - -
162B CYS* 5.4 0.2 - - - -
190B GLY 4.6 1.2 - - - +
191B GLU* 4.2 10.1 - - - +
192B HIS* 3.5 27.8 + - - +
273B THR* 2.8 34.3 - - - +
287B PHE* 3.5 24.9 - - - +
288B LEU* 4.1 4.7 - - - -
289B SER 4.4 1.0 + - - -
322B LEU* 3.6 21.6 - - + +
326B GLN* 5.5 0.2 - - - -
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Residues in contact with ILE 141 (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 LEU* 3.8 26.5 - - + -
109B LEU* 3.9 31.4 - - + -
138B PRO* 2.9 12.1 + - + +
140B ASP* 1.3 73.2 - - + +
142B LEU* 1.3 55.5 + - - +
144B TYR* 3.3 11.4 - - + +
145B VAL* 2.9 34.3 + - + +
322B LEU* 3.3 30.5 - - + +
325B MET* 3.9 25.6 - - + -
326B GLN* 4.3 23.3 - - + +
328B ASN* 5.0 6.3 - - - +
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Residues in contact with LEU 142 (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 LEU* 3.9 20.9 - - + -
112B ASN* 4.3 15.7 - - + +
113B VAL* 4.2 20.9 - - - +
116B MET* 4.3 11.4 - - + -
134B VAL* 4.3 6.3 - - + -
136B THR* 2.9 31.2 - - - +
137B ASN* 3.3 6.3 - - + +
138B PRO* 2.4 49.6 + - + +
139B VAL 3.9 1.1 - - - +
141B ILE* 1.3 69.4 - - - +
143B THR* 1.3 56.2 + - - +
144B TYR 3.0 0.7 - - - -
145B VAL* 2.8 12.4 + - + +
146B VAL* 2.5 41.2 + - - +
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Residues in contact with THR 143 (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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134B VAL* 4.0 5.9 - - - +
139B VAL 2.5 30.3 + - - -
140B ASP* 2.7 5.6 + - - -
142B LEU* 1.3 68.7 - - - +
144B TYR* 1.3 52.5 + - - +
146B VAL* 2.8 11.9 - - - +
147B TRP* 2.5 37.4 + - - +
157B VAL* 3.8 19.7 - - + +
158B ILE 3.9 3.5 + - - -
159B GLY* 3.5 13.9 + - - -
273B THR* 3.2 25.8 + - - +
287B PHE* 3.3 32.3 - - + -
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Residues in contact with TYR 144 (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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140B ASP 2.9 9.7 + - - +
141B ILE* 3.3 17.0 - - + +
143B THR* 1.3 74.2 - - - +
145B VAL* 1.3 77.5 + - + +
147B TRP* 3.1 7.0 + + - +
148B LYS* 2.9 62.2 + - + +
285B GLU* 3.4 24.7 - - + +
287B PHE* 3.7 22.0 - + + -
323B TRP* 4.8 6.8 - + - -
326B GLN* 3.1 59.6 + - + +
328B ASN* 4.8 10.5 - - + +
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Residues in contact with VAL 145 (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 LEU* 5.7 0.7 - - + -
113B VAL* 3.8 37.2 - - + +
116B MET* 3.9 24.7 - - + -
117B LYS 5.2 0.7 - - - +
141B ILE* 2.9 32.3 + - + +
142B LEU* 2.8 18.1 + - + +
144B TYR* 1.3 80.3 - - + +
146B VAL* 1.3 54.2 + - - +
148B LYS* 2.9 5.7 - - - +
149B ILE* 2.6 46.0 + - + +
328B ASN* 4.6 9.6 - - + +
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Residues in contact with VAL 146 (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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93B ILE* 4.4 0.7 - - + -
116B MET* 4.2 22.7 - - + -
120B VAL* 3.2 39.0 - - + -
132B ILE* 5.4 2.9 - - + -
134B VAL* 3.5 23.3 - - + -
142B LEU 2.5 21.1 + - - +
143B THR* 2.8 32.5 - - - +
145B VAL* 1.3 71.6 - - - +
147B TRP* 1.3 56.6 + - - +
149B ILE* 3.3 7.2 - - - -
150B SER* 2.6 40.4 + - - -
157B VAL* 3.9 9.9 - - + -
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Residues in contact with TRP 147 (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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143B THR 2.5 27.5 + - - +
144B TYR* 3.3 6.3 - + - +
146B VAL* 1.3 72.0 - - - +
148B LYS* 1.3 98.6 - - + +
150B SER* 3.2 2.6 + - - -
151B GLY* 2.9 32.2 + - - -
152B PHE 3.4 26.4 + - - -
153B PRO* 4.7 0.6 - - - +
154B VAL* 3.6 25.8 - - + +
157B VAL* 3.7 15.7 - - + -
275B LEU* 4.2 13.5 - - + -
285B GLU* 2.9 26.9 - - + -
287B PHE* 3.3 38.6 - + + -
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Residues in contact with LYS 148 (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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144B TYR* 2.9 44.8 + - + +
145B VAL* 2.9 11.9 - - - +
147B TRP* 1.3 118.1 - - + +
149B ILE* 1.3 64.5 + - + +
150B SER 3.3 1.4 + - - -
151B GLY* 3.8 7.8 + - - -
285B GLU* 3.8 14.3 + - - +
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Residues in contact with ILE 149 (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 LYS* 4.4 30.5 - - + +
120B VAL* 3.6 12.3 - - + -
121B PRO* 3.2 38.2 - - + +
145B VAL* 2.6 31.6 + - + +
146B VAL* 3.3 18.6 - - - +
148B LYS* 1.3 74.7 - - + +
150B SER* 1.3 59.3 + - - +
329B LEU* 6.2 3.8 - - + -
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Residues in contact with SER 150 (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 PRO* 4.0 12.8 - - - -
124B ILE* 3.6 34.4 - - - +
132B ILE* 4.9 4.3 - - - -
146B VAL 2.6 22.9 + - - -
147B TRP 3.2 4.2 + - - -
148B LYS 4.1 0.4 - - - -
149B ILE* 1.3 77.5 - - - +
151B GLY* 1.3 70.7 + - - +
152B PHE* 3.3 19.3 + - - -
157B VAL* 3.9 13.9 - - - +
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Residues in contact with GLY 151 (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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147B TRP* 2.9 14.7 + - - -
148B LYS 3.8 6.9 + - - -
150B SER* 1.3 85.4 + - - +
152B PHE* 1.3 60.2 + - - +
153B PRO* 4.5 1.6 - - - +
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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