Contacts of the helix formed by residues 109 - 120 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106C LEU* 3.0 28.0 - - + +
107C ASP 2.5 10.7 + - - +
108C LEU* 1.3 72.0 - - - +
110C GLN* 1.3 79.1 + - + +
111C ARG* 2.9 5.8 - - - +
112C ASN* 3.0 0.7 + - - -
113C VAL* 3.0 27.6 + - + +
138C PRO* 4.4 9.9 - - + -
141C ILE* 3.9 35.0 - - + -
142C LEU* 3.9 22.9 - - + -
145C VAL* 5.7 1.3 - - + -
325C MET* 4.3 22.7 - - + +
328C ASN* 4.9 10.5 - - - +
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Residues in contact with GLN 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ASP 4.2 3.2 + - - -
109C LEU* 1.3 90.6 - - + +
111C ARG* 1.3 60.5 + - - +
113C VAL* 2.9 26.7 - - + +
114C ALA* 3.5 11.1 + - - +
325C MET 5.8 0.2 - - - +
327C LYS* 5.4 6.3 + - - +
328C ASN* 5.1 11.9 + - - +
329C LEU 5.2 9.5 + - - +
330C GLU* 6.0 2.7 - - - +
331C LEU 4.8 10.9 + - - -
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Residues in contact with ARG 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C GLY 5.2 0.9 - - - +
97C ALA* 3.7 31.4 - - + +
103C GLN* 2.5 41.3 + - - +
107C ASP* 3.8 18.4 + - - +
108C LEU* 3.3 33.7 - - - +
109C LEU 4.0 0.9 - - - +
110C GLN* 1.3 77.9 - - - +
112C ASN* 1.3 62.7 + - - +
114C ALA* 3.6 7.5 - - - +
115C ILE* 3.6 12.6 + - - +
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Residues in contact with ASN 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ALA 5.0 0.2 - - - -
96C GLY* 3.1 34.4 - - - +
97C ALA* 3.5 30.6 + - - +
108C LEU* 2.8 26.2 + - - +
109C LEU 3.0 3.9 + - - +
111C ARG* 1.3 81.1 - - - +
113C VAL* 1.3 56.9 + - - +
114C ALA 2.8 4.5 - - - -
115C ILE* 2.4 35.1 + - + +
116C MET* 2.7 11.9 + - - -
136C THR* 5.2 5.2 - - - -
137C ASN* 5.4 3.4 - - - +
142C LEU* 4.3 22.5 - - + +
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Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C LEU* 3.0 18.1 + - + +
110C GLN* 2.9 36.6 - - + +
112C ASN* 1.3 69.1 - - - +
114C ALA* 1.3 51.1 + - - +
116C MET* 3.0 12.4 + - - +
117C LYS* 2.8 35.6 + - + +
142C LEU* 4.2 5.0 - - + +
145C VAL* 3.8 32.3 - - + +
328C ASN* 4.6 13.5 - - + +
329C LEU* 5.3 13.5 - - - +
330C GLU* 5.9 2.5 - - - +
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C GLN 3.8 8.3 - - - +
111C ARG* 3.6 13.5 - - - +
112C ASN 2.6 3.6 + - - -
113C VAL* 1.3 77.0 - - - +
115C ILE* 1.3 69.1 + - - +
116C MET 2.8 3.0 + - - -
117C LYS* 3.2 12.9 + - - +
118C ALA* 3.5 10.6 + - - +
330C GLU* 5.8 10.1 - - + +
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Residues in contact with ILE 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ALA* 3.5 20.6 - - + +
96C GLY* 3.0 39.5 - - - +
111C ARG 3.6 4.2 + - - +
112C ASN* 2.4 51.0 + - + +
114C ALA* 1.3 72.0 - - - +
116C MET* 1.3 68.7 + - + +
118C ALA* 3.5 1.0 - - - +
119C ILE* 2.9 51.8 + - + +
136C THR* 5.4 0.2 - - + -
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Residues in contact with MET 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ILE* 3.9 22.9 - - + -
95C ALA 4.6 0.7 - - - +
112C ASN 2.7 18.5 + - - +
113C VAL* 3.2 8.5 - - - +
114C ALA 2.8 0.6 + - - -
115C ILE* 1.3 81.0 - - + +
117C LYS* 1.3 54.4 + - - +
118C ALA 2.4 20.8 + - - -
119C ILE* 2.7 17.6 + - - +
120C VAL* 3.0 31.3 - - + +
134C VAL* 4.6 3.6 - - + -
136C THR* 3.3 39.3 - - + +
142C LEU* 4.3 15.3 - - + -
145C VAL* 3.9 22.0 - - + -
146C VAL* 4.2 14.6 - - + -
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Residues in contact with LYS 117 (chain C).
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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113C VAL* 2.8 19.1 + - + +
114C ALA* 3.8 7.6 - - - +
116C MET* 1.3 70.1 - - - +
118C ALA* 1.3 63.5 + - - +
120C VAL* 4.0 0.9 - - - +
121C PRO* 4.2 13.3 - - - +
145C VAL* 5.2 1.0 - - - +
149C ILE* 4.4 28.3 - - + +
330C GLU* 4.5 19.6 + - + +
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Residues in contact with ALA 118 (chain C).
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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82C TYR* 5.2 3.9 - - - -
114C ALA 3.5 6.2 + - - +
115C ILE* 3.5 9.0 - - - +
116C MET 2.4 12.5 + - - -
117C LYS* 1.3 74.2 - - - +
119C ILE* 1.3 77.5 + - + +
120C VAL 3.5 0.2 - - - -
121C PRO 3.4 14.0 - - - +
122C GLY* 5.3 0.9 - - - -
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Residues in contact with ILE 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C VAL* 3.6 30.7 - - + -
82C TYR* 3.6 25.2 - - - +
93C ILE* 4.0 18.8 - - + -
95C ALA* 4.8 9.9 - - + +
115C ILE* 2.9 45.8 - - + +
116C MET* 2.7 7.7 + - - +
118C ALA* 1.3 88.1 - - + +
120C VAL* 1.3 70.1 + - + +
122C GLY* 5.0 0.2 - - - -
123C VAL* 2.8 17.5 + - + +
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Residues in contact with VAL 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ILE* 3.3 23.6 - - + -
116C MET* 3.0 42.8 - - + +
118C ALA 4.3 0.2 - - - -
119C ILE* 1.3 86.0 - - + +
121C PRO* 1.3 91.5 - - + -
123C VAL* 2.8 24.8 + - + +
132C ILE* 4.9 7.0 - - + -
146C VAL* 3.2 29.8 - - + -
149C ILE* 3.6 11.2 - - + -
150C 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