Contacts of the helix formed by residues 138 - 151 (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 PRO 138 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C ARG 4.1 11.9 - - - +
106C LEU* 4.0 34.8 - - + -
108C LEU* 4.9 11.2 - - + +
109C LEU* 4.4 10.3 - - + -
137C ASN* 1.3 90.8 - - + +
139C VAL* 1.3 56.1 + - - -
140C ASP* 2.9 6.8 + - - +
141C ILE* 2.9 11.6 + - + +
142C LEU* 2.4 58.3 + - + +
192C HIS 4.7 9.6 - - - +
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Residues in contact with VAL 139 (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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134C VAL* 4.1 9.6 - - - +
135C VAL 2.9 28.9 - - - +
137C ASN* 2.6 28.6 - - - +
138C PRO* 1.3 78.0 - - - +
140C ASP* 1.3 68.4 - - - +
142C LEU* 4.3 2.7 - - - -
143C THR* 2.5 43.9 + - - +
160C SER* 2.8 30.5 - - - +
161C GLY 4.4 5.8 - - - +
192C HIS* 3.8 27.6 - - + -
273C THR* 4.7 2.0 - - + -
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Residues in contact with ASP 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C PRO* 2.9 3.8 + - - +
139C VAL* 1.3 94.3 - - - +
141C ILE* 1.3 57.5 + - + +
143C THR* 2.7 19.8 + - - +
144C TYR* 2.9 11.2 + - - +
162C CYS* 5.4 0.2 - - - -
190C GLY 4.6 1.2 - - - +
191C GLU* 4.2 9.8 - - - +
192C HIS* 3.5 27.9 + - - +
273C THR* 2.8 34.3 - - - +
287C PHE* 3.5 25.8 - - - +
288C LEU* 4.1 4.4 - - - -
289C SER* 4.4 1.4 + - - -
322C LEU* 3.6 22.2 - - + +
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Residues in contact with ILE 141 (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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106C LEU* 3.8 25.8 - - + -
109C LEU* 3.9 33.0 - - + -
138C PRO* 2.9 12.0 + - + +
140C ASP* 1.3 73.7 - - + +
142C LEU* 1.3 56.9 + - - +
144C TYR* 3.3 12.4 - - + +
145C VAL* 2.9 34.8 + - + +
322C LEU* 3.3 29.3 - - + +
325C MET* 3.9 26.9 - - + -
326C GLN* 4.3 22.4 - - + +
328C ASN* 5.0 5.8 - - - +
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Residues in contact with LEU 142 (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* 3.9 20.9 - - + -
112C ASN* 4.3 15.7 - - + +
113C VAL* 4.2 21.5 - - - +
116C MET* 4.3 11.0 - - + -
134C VAL* 4.3 6.5 - - + -
136C THR* 2.9 31.6 - - - +
137C ASN* 3.3 6.5 - - + +
138C PRO* 2.4 49.5 + - + +
139C VAL 3.9 1.1 - - - +
141C ILE* 1.3 68.2 - - - +
143C THR* 1.3 57.3 + - - +
144C TYR 3.0 0.9 - - - -
145C VAL* 2.8 12.6 + - + +
146C VAL* 2.5 41.0 + - - +
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Residues in contact with THR 143 (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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134C VAL* 4.0 5.7 - - - +
139C VAL 2.5 31.1 + - - -
140C ASP* 2.7 4.7 + - - -
142C LEU* 1.3 69.0 - - - +
144C TYR* 1.3 52.6 + - - +
146C VAL* 2.8 12.0 - - - +
147C TRP* 2.5 38.1 + - - +
157C VAL* 3.8 19.0 - - + +
158C ILE 3.9 3.8 + - - -
159C GLY* 3.5 13.9 + - - -
273C THR* 3.2 26.4 + - - +
287C PHE* 3.3 33.0 - - + -
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Residues in contact with TYR 144 (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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140C ASP 2.9 9.9 + - - +
141C ILE* 3.3 17.3 - - + +
143C THR* 1.3 75.5 - - - +
145C VAL* 1.3 76.3 + - + +
147C TRP* 3.1 7.0 + - - +
148C LYS* 2.9 62.4 + - + +
285C GLU* 3.4 24.6 - - + +
287C PHE* 3.7 21.5 - + + -
323C TRP* 4.8 6.8 - + - -
326C GLN* 3.1 59.1 + - + +
328C ASN* 4.8 10.5 - - + +
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Residues in contact with VAL 145 (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* 5.7 1.1 - - + -
113C VAL* 3.8 37.2 - - + +
116C MET* 3.9 25.1 - - + -
117C LYS 5.2 0.7 - - - +
141C ILE* 2.9 31.8 + - + +
142C LEU* 2.8 18.1 + - + +
144C TYR* 1.3 80.3 - - + +
146C VAL* 1.3 54.2 + - - +
148C LYS* 2.9 6.3 - - - +
149C ILE* 2.6 45.2 + - + +
328C ASN* 4.7 9.6 - - + +
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Residues in contact with VAL 146 (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* 4.4 0.7 - - + -
116C MET* 4.2 22.7 - - + -
120C VAL* 3.2 38.8 - - + -
132C ILE* 5.4 2.9 - - + -
134C VAL* 3.5 23.3 - - + -
142C LEU 2.5 21.1 + - - +
143C THR* 2.8 32.5 - - - +
145C VAL* 1.3 71.5 - - - +
147C TRP* 1.3 56.4 + - - +
149C ILE* 3.3 7.6 - - - -
150C SER* 2.6 40.1 + - - -
157C VAL* 3.9 10.3 - - + -
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Residues in contact with TRP 147 (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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143C THR 2.5 27.7 + - - +
144C TYR* 3.3 6.7 - + - +
146C VAL* 1.3 72.2 - - - +
148C LYS* 1.3 97.5 + - + +
150C SER* 3.2 3.3 + - - -
151C GLY* 2.9 33.2 + - - -
152C PHE 3.4 25.4 + - - -
153C PRO* 4.7 0.8 - - - +
154C VAL* 3.6 26.4 - - + +
157C VAL* 3.7 14.8 - - + -
275C LEU* 4.2 13.5 - - + -
285C GLU* 2.9 26.7 - - + -
287C PHE* 3.3 37.9 - + + -
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Residues in contact with LYS 148 (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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144C TYR* 2.9 46.1 + - + +
145C VAL* 2.9 12.3 - - - +
147C TRP* 1.3 120.3 - - + +
149C ILE* 1.3 63.4 + - + +
150C SER 3.2 1.1 + - - -
151C GLY* 3.8 8.4 + - - -
285C GLU* 3.8 13.9 + - - +
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Residues in contact with ILE 149 (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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117C LYS* 4.4 31.0 - - + +
120C VAL* 3.6 11.9 - - + -
121C PRO* 3.2 40.6 - - + +
145C VAL* 2.6 32.4 + - + +
146C VAL* 3.3 18.6 - - - +
148C LYS* 1.3 74.5 - - + +
150C SER* 1.3 59.3 + - - +
329C LEU* 6.2 4.0 - - + -
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Residues in contact with SER 150 (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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121C PRO* 4.0 13.0 - - - -
124C ILE* 3.6 34.2 - - - +
132C ILE* 4.9 3.6 - - - -
146C VAL* 2.6 22.8 + - - -
147C TRP 3.2 4.3 + - - -
148C LYS 4.1 0.4 - - - -
149C ILE* 1.3 77.1 - - - +
151C GLY* 1.3 70.2 + - - +
152C PHE* 3.3 19.5 + - - -
157C VAL* 3.9 13.9 - - - +
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Residues in contact with GLY 151 (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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147C TRP* 2.9 15.3 + - - -
148C LYS 3.8 6.2 + - - -
150C SER* 1.3 85.2 + - - +
152C PHE* 1.3 60.3 + - - +
153C 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