Contacts of the helix formed by residues 129 - 144 (chain C) in PDB entry 1IBL
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 ALA 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C PHE* 1.3 76.2 - - + +
130C VAL* 1.3 58.5 + - - +
131C ARG 3.4 1.6 - - - -
132C ARG* 2.8 43.1 + - + +
133C ALA* 2.5 36.6 + - - +
47D ARG* 6.1 3.1 - - - +
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Residues in contact with VAL 130 (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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124C ILE* 4.3 26.7 - - + -
128C PHE 3.3 9.5 + - - +
129C ALA* 1.3 72.7 - - - +
131C ARG* 1.3 67.4 + - - +
132C ARG 2.9 0.2 + - - -
133C ALA* 3.1 6.1 + - - +
134C ILE* 2.8 45.0 + - + +
153C VAL* 4.2 11.9 - - + -
157C ILE* 4.0 37.2 - - + -
158C GLY* 4.5 9.4 - - - +
166C GLU* 4.1 12.3 - - + -
196C LEU* 5.4 1.1 - - + -
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Residues in contact with ARG 131 (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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129C ALA 3.4 0.4 - - - -
130C VAL* 1.3 79.5 - - - +
132C ARG* 1.3 56.9 + - - +
134C ILE* 3.8 8.9 - - + +
135C LYS* 3.0 40.9 + - - +
157C ILE* 5.7 0.2 - - - +
164C ARG* 3.5 27.1 - - - +
166C GLU* 3.6 31.2 + - + -
28E PHE* 5.2 13.7 - - - -
50E GLU* 4.4 26.6 - - - +
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Residues in contact with ARG 132 (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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128C PHE* 6.4 0.4 - - - -
129C ALA* 2.8 31.6 + - + +
131C ARG* 1.3 75.9 - - - +
133C ALA* 1.3 67.4 + - - +
134C ILE 2.9 1.8 - - - -
135C LYS* 2.6 15.9 + - + +
136C GLN* 2.6 50.6 + - + +
47D ARG* 5.0 13.3 - - - +
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Residues in contact with ALA 133 (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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120C VAL* 4.2 13.7 - - + -
123C GLN* 3.6 35.1 + - + +
124C ILE* 5.6 1.6 - - + -
128C PHE* 4.8 3.4 - - + -
129C ALA 2.5 22.6 + - - +
130C VAL* 3.5 6.3 - - - +
132C ARG* 1.3 70.9 - - - +
134C ILE* 1.3 51.9 + - - +
136C GLN* 3.3 16.9 - - - +
137C ALA* 2.6 38.5 + - - +
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Residues in contact with ILE 134 (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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120C VAL* 4.4 9.9 - - + -
130C VAL* 2.8 39.9 - - + +
131C ARG* 3.8 4.0 - - + +
132C ARG 2.8 2.8 + - - -
133C ALA* 1.3 70.5 - - - +
135C LYS* 1.3 67.9 + - - +
136C GLN 3.0 1.1 + - - -
137C ALA* 4.2 5.2 - - - -
138C VAL* 2.7 29.4 + - + +
151C VAL* 3.8 19.1 - - + -
153C VAL* 3.6 20.4 - - + +
166C GLU* 3.5 25.6 - - + -
167C TRP 3.1 28.7 - - - +
168C ALA* 3.2 12.6 - - + -
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Residues in contact with LYS 135 (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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131C ARG* 3.0 32.0 + - + +
132C ARG* 2.6 17.4 + - + +
134C ILE* 1.3 77.0 - - - +
136C GLN* 1.3 61.9 + - + +
138C VAL* 3.6 6.0 - - - +
139C GLN* 3.1 27.9 + - - +
168C ALA* 4.5 8.7 - - + +
170C GLN* 5.5 0.7 + - - -
50E GLU* 2.6 54.2 + - - +
52E PRO* 4.8 18.5 - - + +
53E LEU* 4.6 9.9 - - - +
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Residues in contact with GLN 136 (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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123C GLN* 4.1 8.5 + - - +
128C PHE* 4.8 8.9 - - - -
129C ALA* 5.8 0.2 - - - +
132C ARG* 2.6 49.8 + - + +
133C ALA* 3.3 20.2 - - - +
134C ILE 3.0 0.4 + - - -
135C LYS* 1.3 69.2 - - + +
137C ALA* 1.3 59.0 + - - +
138C VAL 3.0 1.1 - - - -
139C GLN* 2.6 30.7 + - - +
140C ARG* 2.7 34.7 + - + +
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Residues in contact with ALA 137 (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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116C VAL* 4.3 10.5 - - + -
120C VAL* 3.4 28.5 - - + -
133C ALA 2.6 21.3 + - - +
134C ILE* 3.7 4.9 - - - +
136C GLN* 1.3 73.2 - - - +
138C VAL* 1.3 64.5 + - - +
140C ARG* 3.3 24.5 + - - +
141C VAL* 3.0 27.9 + - - +
151C VAL* 4.5 4.3 - - + -
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Residues in contact with VAL 138 (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 ILE 2.7 31.0 + - - +
135C LYS* 3.6 5.2 - - - +
137C ALA* 1.3 74.5 - - - +
139C GLN* 1.3 51.8 + - - +
141C VAL* 3.1 8.0 + - - +
142C MET* 2.7 47.1 + - + +
149C ALA* 4.4 15.9 - - + +
151C VAL* 3.9 21.8 - - + +
168C ALA* 3.6 30.1 - - + +
169C ALA 4.5 2.7 - - - +
170C GLN* 4.3 24.9 - - + +
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Residues in contact with GLN 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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135C LYS 3.1 15.0 + - - +
136C GLN* 2.6 16.6 + - - +
138C VAL* 1.3 72.7 - - - +
140C ARG* 1.3 57.5 + - - +
142C MET* 2.8 11.8 + - - +
143C GLU* 2.5 46.9 + - - +
170C GLN* 3.9 20.0 + - - +
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Residues in contact with ARG 140 (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 ASN* 3.5 26.9 + - - +
116C VAL* 5.0 2.9 + - - +
119C ARG* 2.8 47.1 - - - +
123C GLN* 2.8 32.9 + - - +
136C GLN* 2.7 34.6 + - + +
137C ALA* 3.4 34.7 - - - +
139C GLN* 1.3 76.4 - - - +
141C VAL* 1.3 66.0 + - + +
143C GLU* 2.9 16.8 + - - +
144C SER* 2.9 17.7 + - - -
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Residues in contact with VAL 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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110C ASN* 3.1 29.6 - - + +
111C LEU* 4.0 1.5 - - + +
116C VAL* 3.6 24.5 - - + -
137C ALA 3.0 16.2 - - - +
138C VAL* 3.2 7.0 - - - +
140C ARG* 1.3 84.1 - - + +
142C MET* 1.3 62.5 + - - +
144C SER* 3.4 17.0 - - - +
146C ALA* 3.3 13.0 - - + +
149C ALA* 3.6 15.3 - - + -
151C VAL* 5.9 0.9 - - + -
202C ILE* 3.4 35.0 - - + -
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Residues in contact with MET 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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138C VAL* 2.7 26.1 + - + +
139C GLN* 2.8 19.0 + - - +
141C VAL* 1.3 72.9 - - - +
143C GLU* 1.3 59.0 + - - +
145C GLY 2.6 20.0 - - - +
146C ALA* 4.0 19.2 - - - +
147C LYS 4.8 1.1 - - - -
148C GLY* 3.8 10.8 - - - +
149C ALA* 3.8 26.0 - - + -
170C GLN* 3.8 45.1 - - + +
171C GLY* 4.3 5.4 - - - +
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Residues in contact with GLU 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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139C GLN* 2.5 29.2 + - - +
140C ARG* 3.4 8.0 - - - +
142C MET* 1.3 73.7 - - - +
144C SER* 1.3 59.0 + - - +
145C GLY 3.0 7.8 + - - -
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Residues in contact with SER 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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108C ASN* 3.3 20.0 + - - -
110C ASN* 3.2 26.1 + - - +
111C LEU* 3.0 25.6 - - - +
140C ARG 2.9 15.3 + - - -
141C VAL 3.5 3.5 + - - -
143C GLU* 1.3 74.9 - - - +
145C GLY* 1.3 57.2 + - - +
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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