Contacts of the helix formed by residues 109 - 120 (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 LEU 109 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D LEU* 3.0 27.4 - - + +
107D ASP 2.5 11.9 + - - +
108D LEU* 1.3 70.1 - - - +
110D GLN* 1.3 80.2 + - + +
111D ARG* 2.9 5.8 - - - +
112D ASN* 3.0 0.7 + - - -
113D VAL* 3.0 26.7 + - + +
138D PRO* 4.4 9.6 - - + -
141D ILE* 3.9 34.5 - - + -
142D LEU* 3.9 22.7 - - + -
145D VAL* 5.7 0.9 - - + -
325D MET* 4.3 24.0 - - + +
328D ASN* 4.9 10.3 - - - +
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Residues in contact with GLN 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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107D ASP 4.2 3.0 + - - -
109D LEU* 1.3 90.7 - - + +
111D ARG* 1.3 59.5 + - - +
113D VAL* 2.9 27.1 - - + +
114D ALA* 3.5 11.3 + - - +
327D LYS* 5.4 6.9 + - - +
328D ASN* 5.1 12.1 + - - +
329D LEU 5.2 9.1 + - - +
330D GLU* 6.1 2.9 - - - +
331D LEU 4.8 11.5 + - - -
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Residues in contact with ARG 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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96D GLY 5.2 0.7 - - - +
97D ALA* 3.7 31.9 - - + +
103D GLN* 2.5 40.0 + - - +
107D ASP* 3.8 19.2 + - - +
108D LEU* 3.3 34.5 - - - +
109D LEU 4.0 0.4 - - - +
110D GLN* 1.3 78.8 - - - +
112D ASN* 1.3 62.8 + - - +
114D ALA* 3.6 7.7 - - - +
115D ILE* 3.6 12.8 + - - +
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Residues in contact with ASN 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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95D ALA 5.0 0.2 - - - -
96D GLY* 3.1 34.1 - - - +
97D ALA* 3.5 29.8 + - - +
108D LEU* 2.8 25.9 + - - +
109D LEU 3.0 4.9 + - - +
111D ARG* 1.3 81.6 - - - +
113D VAL* 1.3 55.4 + - - +
114D ALA 2.8 4.3 - - - -
115D ILE* 2.4 35.9 + - + +
116D MET* 2.7 12.3 + - - -
136D THR* 5.2 5.2 - - - -
137D ASN* 5.4 3.2 - - - +
142D LEU* 4.3 22.6 - - + +
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Residues in contact with VAL 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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109D LEU* 3.0 17.7 + - + +
110D GLN* 2.9 36.6 - - + +
112D ASN* 1.3 69.9 - - - +
114D ALA* 1.3 51.1 - - - +
116D MET* 3.0 12.5 + - - +
117D LYS* 2.8 35.9 + - + +
142D LEU* 4.2 5.1 - - + +
145D VAL* 3.8 32.5 - - + +
328D ASN* 4.6 13.2 - - + +
329D LEU* 5.3 13.5 - - - +
330D GLU* 5.9 2.2 - - - +
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Residues in contact with ALA 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 GLN 3.8 8.5 - - - +
111D ARG* 3.6 13.2 - - - +
112D ASN 2.6 3.2 + - - -
113D VAL* 1.3 77.3 - - - +
115D ILE* 1.3 68.3 + - - +
116D MET 2.8 2.4 + - - -
117D LYS* 3.2 13.3 + - - +
118D ALA* 3.5 10.2 + - - +
330D GLU* 5.8 10.3 - - + +
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Residues in contact with ILE 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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95D ALA* 3.5 20.6 - - + +
96D GLY* 3.0 39.7 - - - +
111D ARG 3.6 4.2 + - - +
112D ASN* 2.4 52.2 + - + +
114D ALA* 1.3 73.4 - - - +
116D MET* 1.3 69.3 + - + +
118D ALA* 3.5 1.0 - - - +
119D ILE* 2.9 51.4 + - + +
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Residues in contact with MET 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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93D ILE* 3.9 23.3 - - + -
95D ALA 4.6 0.7 - - - +
112D ASN 2.7 18.1 + - - +
113D VAL* 3.2 9.6 - - - +
114D ALA 2.8 1.0 + - - -
115D ILE* 1.3 80.6 - - + +
117D LYS* 1.3 55.7 + - - +
118D ALA 2.4 21.3 + - - -
119D ILE* 2.7 17.8 + - - +
120D VAL* 3.0 30.1 - - + +
134D VAL* 4.6 4.0 - - + -
136D THR* 3.3 38.4 - - + +
142D LEU* 4.3 15.7 - - + -
145D VAL* 3.9 20.9 - - + -
146D VAL* 4.2 14.6 - - + -
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Residues in contact with LYS 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 VAL* 2.8 18.9 + - + +
114D ALA* 3.8 7.9 - - - +
116D MET* 1.3 69.5 - - - +
118D ALA* 1.3 62.3 + - - +
120D VAL* 4.0 1.1 - - - +
121D PRO* 4.2 13.5 - - - +
145D VAL* 5.2 1.0 - - - +
149D ILE* 4.4 28.9 - - + +
330D GLU* 4.5 18.7 + - + +
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Residues in contact with ALA 118 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82D TYR* 5.2 3.7 - - - -
114D ALA 3.5 6.7 + - - +
115D ILE* 3.5 9.9 - - - +
116D MET 2.4 12.5 + - - -
117D LYS* 1.3 74.3 - - - +
119D ILE* 1.3 76.0 + - + +
121D PRO 3.4 14.9 - - - +
122D GLY* 5.3 0.7 - - - -
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Residues in contact with ILE 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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25D VAL* 3.6 31.2 - - + -
82D TYR* 3.6 24.8 - - - +
93D ILE* 4.0 18.4 - - + -
95D ALA* 4.8 10.1 - - + -
115D ILE* 2.9 45.1 - - + +
116D MET* 2.7 8.1 + - - +
118D ALA* 1.3 87.0 - - + +
120D VAL* 1.3 71.1 + - + +
122D GLY* 5.0 0.3 - - - -
123D VAL* 2.8 17.4 + - + +
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Residues in contact with VAL 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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93D ILE* 3.3 23.6 - - + -
116D MET* 3.0 43.3 - - + +
119D ILE* 1.3 85.2 - - + +
121D PRO* 1.3 92.4 - - + -
123D VAL* 2.8 25.2 + - + +
132D ILE* 4.9 7.4 - - + -
146D VAL* 3.2 30.3 - - + -
149D ILE* 3.6 11.4 - - + -
150D SER* 5.5 0.2 - - - -
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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