Contacts of the helix formed by residues 112 - 127 (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 SER 112 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C ALA* 3.5 19.0 - - - +
106C VAL* 4.1 16.2 - - - -
108C ASN 3.7 2.4 + - - -
109C PRO 3.9 1.1 - - - -
110C ASN 3.3 1.0 - - - -
111C LEU* 1.3 76.2 - - - +
113C ALA* 1.3 52.5 + - - +
114C PRO* 3.1 3.4 - - - +
115C LEU* 2.6 66.4 + - - +
116C VAL* 2.9 12.1 + - - +
183C ASP* 3.9 5.8 - - - -
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Residues in contact with ALA 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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111C LEU 2.7 9.5 + - - -
112C SER* 1.3 69.0 - - - +
114C PRO* 1.3 73.3 - - + +
115C LEU 2.8 1.6 + - - -
116C VAL* 3.0 2.3 + - - -
117C ALA* 2.9 21.5 + - - +
183C ASP* 3.1 34.9 + - + +
184C TYR 4.0 6.7 - - - -
185C GLY* 4.0 3.1 - - - +
200C ALA* 3.5 13.5 - - + +
202C ILE* 3.4 23.8 - - + -
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Residues in contact with PRO 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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16C ARG* 5.2 5.4 - - - +
52C LEU 5.0 1.6 - - - +
53C ALA* 4.3 26.7 - - + +
112C SER* 3.2 11.4 - - - +
113C ALA* 1.3 93.5 - - + +
115C LEU* 1.3 56.0 + - - +
117C ALA* 3.8 3.3 - - - +
118C GLN* 3.1 29.0 + - - +
183C ASP* 2.9 26.2 - - - +
184C TYR 3.9 8.5 - - - +
185C GLY* 3.9 12.8 - - - -
186C PHE 4.7 3.7 - - - +
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C GLY* 3.6 33.7 - - - +
52C LEU 4.2 3.8 - - - +
53C ALA* 4.8 1.6 - - + -
71C ALA* 4.3 10.8 - - + -
106C VAL* 4.5 7.2 - - + -
109C PRO* 3.4 33.7 - - + +
112C SER* 2.6 43.3 + - - +
114C PRO* 1.3 68.3 - - - +
116C VAL* 1.3 53.6 + - - +
117C ALA 2.9 1.8 - - - -
118C GLN* 2.5 53.8 + - + +
119C ARG* 2.6 18.7 + - - -
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Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C PRO 3.9 3.8 - - - +
110C ASN* 3.1 35.0 - - - +
112C SER 2.9 16.1 + - - +
113C ALA 3.6 5.2 - - - +
115C LEU* 1.3 74.3 - - - +
117C ALA* 1.3 61.7 + - - +
119C ARG* 3.2 9.6 - - - +
120C VAL* 3.2 23.9 + - - +
137C ALA* 4.3 18.4 - - + +
140C ARG* 5.4 2.5 - - - +
141C VAL* 3.6 23.1 - - + -
151C VAL* 4.3 9.9 - - + -
200C ALA* 4.1 13.7 - - + -
202C ILE* 3.7 8.7 - - + -
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Residues in contact with ALA 117 (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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113C ALA 2.9 14.7 + - - +
114C PRO 3.8 5.2 - - - +
115C LEU 2.7 4.2 + - - -
116C VAL* 1.3 72.1 - - - +
118C GLN* 1.3 66.9 + - - +
119C ARG 3.1 0.3 + - - -
120C VAL* 3.3 3.5 + - - +
121C ALA* 2.9 24.4 + - - +
151C VAL* 5.8 0.4 - - - -
185C GLY 3.9 21.3 - - - +
186C PHE* 3.9 6.5 - - - -
187C ALA* 3.3 18.6 - - + +
198C VAL* 3.9 12.6 - - + +
200C ALA* 3.9 10.0 - - + +
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Residues in contact with GLN 118 (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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48C TYR* 3.8 25.7 + - + -
51C GLY* 5.2 0.6 - - - -
52C LEU* 3.4 37.9 + - - +
114C PRO* 3.1 19.7 + - - +
115C LEU* 2.5 43.4 + - + +
117C ALA* 1.3 76.0 - - - +
119C ARG* 1.3 51.0 + - - +
121C ALA* 3.3 3.5 + - - +
122C GLU* 2.8 46.9 + - - +
186C PHE 5.4 2.0 - - - +
187C ALA* 3.5 13.0 - - + +
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Residues in contact with ARG 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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115C LEU 2.6 14.5 + - - +
116C VAL* 3.2 15.3 - - - +
118C GLN* 1.3 71.1 - - - +
120C VAL* 1.3 55.2 + - - +
122C GLU* 2.5 51.8 + - - +
123C GLN* 3.0 38.1 + - - +
126C ARG* 4.6 16.3 - - - +
128C PHE* 5.8 3.4 - - - -
140C ARG* 2.8 45.8 - - - +
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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
----------------------------------------------------------
116C VAL* 3.2 15.4 + - + +
117C ALA 3.9 3.6 - - - +
119C ARG* 1.3 79.4 - - - +
121C ALA* 1.3 64.6 + - - +
123C GLN* 3.1 15.2 + - - +
124C ILE* 2.9 38.9 + - + +
133C ALA* 4.2 18.2 - - + +
134C ILE* 4.4 6.7 - - + -
137C ALA* 3.4 30.7 - - + -
140C ARG* 4.6 0.4 - - - +
151C VAL* 4.5 12.6 - - + -
153C VAL* 4.3 8.7 - - + -
198C VAL* 4.0 12.3 - - + -
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Residues in contact with ALA 121 (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 ALA 2.9 19.0 + - - +
118C GLN* 3.3 5.4 - - - +
120C VAL* 1.3 76.8 - - - +
122C GLU* 1.3 63.8 + - - +
124C ILE* 3.3 6.0 + - - +
125C GLU* 3.0 28.9 + - - +
187C ALA* 3.4 12.6 - - + -
188C LEU 3.1 27.6 - - - +
189C ALA* 4.1 2.0 - - + +
198C VAL* 3.7 12.1 - - + +
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Residues in contact with GLU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C TYR* 3.2 30.9 + - - +
118C GLN* 2.8 27.4 + - - +
119C ARG* 2.5 36.0 + - - +
121C ALA* 1.3 67.8 - - - +
123C GLN* 1.3 64.8 - - - +
125C GLU* 3.0 15.2 + - - +
126C ARG* 3.0 38.2 + - - +
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Residues in contact with GLN 123 (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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119C ARG* 3.0 26.8 + - - +
120C VAL* 3.1 17.0 + - - +
122C GLU* 1.3 74.8 - - - +
124C ILE* 1.3 55.4 + - - +
126C ARG* 2.7 33.6 + - - +
127C ARG 2.9 10.2 + - - -
128C PHE* 3.2 50.1 + - + +
133C ALA* 3.6 29.6 + - + +
136C GLN* 4.1 4.5 + - - +
140C ARG* 2.8 40.2 + - - +
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Residues in contact with ILE 124 (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* 2.9 25.7 + - + +
121C ALA* 3.5 7.9 - - - +
123C GLN* 1.3 76.8 - - + +
125C GLU* 1.3 64.5 + - - +
127C ARG* 2.9 18.2 + - - +
128C PHE* 4.5 6.7 - - + +
130C VAL* 4.3 24.9 - - + -
133C ALA* 5.6 1.1 - - + -
153C VAL* 3.6 43.1 - - + -
189C ALA* 4.6 9.2 - - + -
191C THR* 4.8 4.8 + - - +
193C TYR* 4.7 10.2 + - - +
196C LEU* 4.2 26.0 - - + -
198C VAL* 4.3 10.5 - - + -
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Residues in contact with GLU 125 (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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421A U 5.3 6.1 + - - +
48C TYR* 4.9 7.1 + - - -
121C ALA* 3.0 19.3 + - - +
122C GLU* 3.0 15.2 + - - +
124C ILE* 1.3 76.2 - - - +
126C ARG* 1.3 58.4 + - - +
127C ARG* 3.2 8.4 + - - +
189C ALA* 3.9 13.0 - - + -
190C ARG* 3.1 50.1 + - - +
191C THR* 4.9 2.5 - - - +
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Residues in contact with ARG 126 (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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119C ARG* 4.6 18.8 - - - +
122C GLU* 3.0 30.8 + - - +
123C GLN* 2.7 16.2 + - - +
125C GLU* 1.3 76.9 - - - +
127C ARG* 1.3 71.0 + - - +
128C PHE* 3.5 35.2 - - + -
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Residues in contact with ARG 127 (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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421A U 3.8 30.2 + - - +
123C GLN 2.9 4.6 + - - -
124C ILE 2.9 13.0 + - - +
125C GLU 4.2 8.5 + - - +
126C ARG* 1.3 84.1 - - - +
128C PHE* 1.3 64.9 + - - +
191C THR* 4.3 5.2 - - - +
192C THR* 2.6 40.0 + - - +
193C TYR* 3.7 27.9 + - - -
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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