Contacts of the helix formed by residues 116 - 130 (chain C) in PDB entry 2IGT
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 GLN 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C PHE* 3.0 24.8 + - + +
115C GLU* 1.3 71.7 - - - +
117C ILE* 1.3 65.2 + - - +
118C VAL 3.0 2.7 - - - -
119C HIS* 2.8 41.6 + - - +
120C TRP* 2.9 34.1 + - + +
211C ASP* 5.6 2.7 - - - +
251C THR* 3.6 20.3 + - - +
253C TYR* 3.0 40.7 + - + +
282C LEU* 3.5 16.5 - - - +
301C SER* 3.8 3.4 + - - -
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Residues in contact with ILE 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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18C SER* 3.4 23.1 - - - +
19C SER 4.2 7.4 - - - +
21C ALA* 4.5 22.2 - - + +
95C LEU* 4.5 9.9 - - + -
96C LEU* 4.1 36.6 - - + +
114C PRO 3.0 19.3 + - - +
115C GLU 3.0 1.3 - - - +
116C GLN* 1.3 77.9 - - - +
118C VAL* 1.3 60.4 + - + +
120C TRP* 3.3 23.9 - - + -
121C GLU* 2.8 45.1 + - + +
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Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 3.8 37.9 - - + -
17C GLU 4.1 6.1 - - - +
18C SER* 3.7 32.8 - - - +
19C SER 5.2 0.2 - - - +
115C GLU 3.2 7.5 + - - +
116C GLN 3.0 1.0 + - - -
117C ILE* 1.3 77.8 - - + +
119C HIS* 1.3 60.9 + - + +
121C GLU* 3.5 16.6 + - - +
122C TRP* 3.3 19.2 + - - +
282C LEU* 3.8 17.7 - - + -
305C ARG* 5.9 0.8 + - - +
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Residues in contact with HIS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 3.7 25.1 - - + +
116C GLN* 2.8 36.5 + - - +
118C VAL* 1.3 74.0 - - - +
120C TRP* 1.3 64.6 + - + +
122C TRP* 3.2 10.9 + - + +
123C LEU* 2.9 27.4 + - - +
209C LEU* 6.0 2.7 - - + +
249C VAL* 4.2 18.6 - - + +
251C THR* 3.6 20.4 - - + +
282C LEU* 4.0 17.5 - - + +
303C PHE* 3.6 31.7 - + + +
305C ARG* 4.6 11.4 + - + +
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Residues in contact with TRP 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LEU* 3.8 26.7 - - + -
96C LEU* 3.7 14.6 - - + -
112C VAL* 3.9 17.7 - - + -
113C PHE 3.8 15.3 - - - -
114C PRO* 4.5 0.2 - - + -
116C GLN* 2.9 38.2 + - + +
117C ILE* 3.3 26.9 - - + +
119C HIS* 1.3 81.2 - - + +
121C GLU* 1.3 54.1 + - - +
123C LEU* 3.3 7.9 + - + +
124C LYS* 2.8 36.6 + - - +
145C VAL* 3.5 39.7 - - + -
146C ALA* 3.7 31.4 - - + +
149C VAL* 3.6 17.4 - - + +
209C LEU* 6.0 0.4 - - + -
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Residues in contact with GLU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LEU* 3.9 29.2 - - + +
117C ILE* 2.8 33.3 + - + +
118C VAL* 3.6 18.9 - - - +
120C TRP* 1.3 74.9 - - - +
122C TRP* 1.3 63.6 + - - +
124C LYS* 3.9 3.1 - - - +
125C ASN* 3.0 26.5 + - - +
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Residues in contact with TRP 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C VAL 3.3 9.3 + - - +
119C HIS* 3.2 14.0 + - + +
121C GLU* 1.3 77.3 - - - +
123C LEU* 1.3 84.4 + - + +
125C ASN* 3.4 6.0 + - - +
126C ALA* 3.0 35.0 + - + +
207C ILE* 3.7 39.3 - - + -
209C LEU* 4.3 4.0 - - + -
246C LEU* 3.7 19.3 - - + -
247C GLY* 3.9 15.7 - - - -
249C VAL* 3.7 20.6 - - + -
305C ARG* 3.9 33.9 - - - +
307C GLU* 3.0 32.3 + - + -
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Residues in contact with LEU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C HIS 2.9 13.3 + - - +
120C TRP* 3.4 10.5 - - - +
122C TRP* 1.3 84.6 - - + +
124C LYS* 1.3 60.3 + - - +
126C ALA* 3.2 2.3 + - - +
127C VAL* 2.9 35.9 + - + +
136C VAL* 4.1 17.5 - - + -
146C ALA* 3.4 31.6 - - + +
149C VAL* 4.5 4.5 - - + -
150C ALA* 3.9 17.0 - - + +
207C ILE* 3.9 35.7 - - + -
209C LEU* 3.7 26.2 - - + -
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Residues in contact with LYS 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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96C LEU* 3.9 37.0 - - + +
120C TRP 2.8 20.2 + - - +
121C GLU* 3.9 4.5 - - - +
123C LEU* 1.3 72.9 - - - +
125C ASN* 1.3 58.6 + - - +
127C VAL* 3.4 1.6 + - - +
128C GLU* 3.0 59.5 + - - +
149C VAL* 3.8 16.1 - - + +
153C ALA* 4.2 19.1 - - + +
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Residues in contact with ASN 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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121C GLU 3.0 18.0 + - - +
122C TRP* 3.8 5.8 - - - +
124C LYS* 1.3 76.6 - - - +
126C ALA* 1.3 58.6 + - - +
128C GLU* 3.8 14.3 + - - +
129C THR* 2.7 59.3 + - - +
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Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C TRP* 3.0 33.9 + - + +
123C LEU* 3.2 4.9 + - - +
125C ASN* 1.3 79.7 + - - +
127C VAL* 1.3 64.0 + - - +
129C THR* 3.8 3.4 + - - -
130C ALA* 3.3 24.6 + - - +
134C LEU* 4.3 1.8 - - - -
207C ILE* 3.9 20.4 - - + -
246C LEU* 3.8 16.2 - - + +
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Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LEU* 2.9 30.2 + - + +
126C ALA* 1.3 77.9 - - - +
128C GLU* 1.3 62.4 + - - +
129C THR 3.3 0.5 + - - -
130C ALA* 3.4 17.7 + - - +
132C ARG 5.0 1.6 - - - +
134C LEU* 3.9 18.1 - - + +
136C VAL* 4.2 25.1 - - + -
150C ALA* 4.7 3.4 - - - -
153C ALA* 3.4 40.8 - - + +
154C GLY 4.2 2.0 - - - -
155C ALA* 3.8 20.9 - - + +
207C ILE* 4.3 1.1 - - + -
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Residues in contact with GLU 128 (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 LYS* 3.0 48.7 + - - +
125C ASN* 3.8 21.8 + - - +
127C VAL* 1.3 76.8 - - - +
129C THR* 1.3 67.1 + - + +
130C ALA 3.6 3.6 - - - +
153C ALA* 4.4 16.9 - - + +
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Residues in contact with THR 129 (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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125C ASN* 2.7 45.8 + - - +
126C ALA* 3.8 4.5 + - - -
128C GLU* 1.3 86.1 - - + +
130C ALA* 1.3 66.1 + - - +
131C ASP* 3.5 4.9 + - - +
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Residues in contact with ALA 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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126C ALA 3.3 20.7 + - - +
127C VAL 3.4 12.6 + - - +
128C GLU 4.3 3.6 - - - +
129C THR* 1.3 78.9 + - - +
131C ASP* 1.3 61.5 + - - +
132C ARG* 3.2 15.3 + - + +
134C LEU* 3.8 29.2 - - + -
246C LEU* 4.3 7.9 - - + -
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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