Contacts of the helix formed by residues 116 - 130 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PHE* 3.0 23.5 + - + +
115B GLU* 1.3 71.4 - - - +
117B ILE* 1.3 58.5 + - - +
118B VAL 3.0 2.7 - - - -
119B HIS* 2.8 34.5 + - - +
120B TRP* 2.8 49.1 + - + +
211B ASP* 5.9 1.6 - - - -
251B THR* 3.6 22.2 + - - +
253B TYR* 3.1 35.5 + - + +
282B LEU* 3.5 18.8 - - - +
301B SER* 3.8 7.1 + - - -
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B SER* 3.8 22.4 - - - +
95B LEU* 4.6 15.3 - - + -
96B LEU* 4.2 31.6 - - + +
114B PRO 3.1 18.5 + - - +
115B GLU 3.0 3.5 - - - +
116B GLN* 1.3 77.5 - - - +
118B VAL* 1.3 60.7 + - + +
120B TRP* 3.4 27.2 - - + -
121B GLU* 2.9 48.8 + - - +
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.9 35.4 - - + -
17B GLU 4.0 22.4 - - - +
18B SER* 4.1 11.2 - - - -
115B GLU 3.8 10.1 - - - +
116B GLN 3.0 1.2 + - - -
117B ILE* 1.3 79.0 - - + +
119B HIS* 1.3 62.0 + - + +
121B GLU* 3.4 16.1 + - - +
122B TRP* 3.3 20.6 + - - +
282B LEU* 3.8 19.1 - - + -
305B ARG* 6.0 1.8 - - - +
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Residues in contact with HIS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.8 18.7 - - + +
116B GLN* 2.8 33.6 + - - +
118B VAL* 1.3 71.3 - - - +
120B TRP* 1.3 69.9 + - + +
122B TRP* 3.3 11.6 + - + +
123B LEU* 3.0 23.1 + - - +
209B LEU* 5.9 3.4 - - + +
249B VAL* 3.9 25.1 - - + +
251B THR* 3.6 20.2 - - + +
282B LEU* 3.9 20.8 - - + +
302B LEU 5.4 0.2 - - - -
303B PHE* 3.6 32.3 - + + +
305B ARG* 4.6 13.0 - - - -
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Residues in contact with TRP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.7 27.4 - - + -
96B LEU* 3.6 16.4 - - + -
112B VAL* 3.8 22.7 - - + -
113B PHE* 3.8 11.4 - - + -
116B GLN* 2.8 39.5 + - + +
117B ILE* 3.3 26.7 + - + +
119B HIS* 1.3 79.4 - - + +
121B GLU* 1.3 52.2 + - - +
123B LEU* 3.3 7.8 + - + +
124B LYS* 2.7 36.0 + - - +
145B VAL* 3.5 39.5 - - + -
146B ALA* 3.6 31.8 - - + +
149B VAL* 3.7 15.3 - - + +
209B LEU* 6.1 0.2 - - + -
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 3.6 30.5 - - + +
117B ILE* 2.9 32.7 + - - +
118B VAL* 3.7 19.0 - - - +
120B TRP* 1.3 72.3 - - - +
122B TRP* 1.3 66.4 + - - +
124B LYS* 3.8 3.5 - - + +
125B ASN* 3.0 26.9 + - - +
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Residues in contact with TRP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL 3.3 10.5 + - - +
119B HIS* 3.3 12.8 + + + +
121B GLU* 1.3 78.5 - - - +
123B LEU* 1.3 82.0 + - + +
125B ASN* 3.8 6.5 - - - +
126B ALA* 3.0 33.6 + - + +
207B ILE* 3.8 31.6 - - + -
209B LEU* 4.2 4.5 - - + -
246B LEU* 3.7 20.2 - - + -
247B GLY* 3.9 19.5 - - - -
249B VAL* 3.7 24.9 - - + -
305B ARG* 3.9 33.4 - - - +
307B GLU* 2.8 31.6 + - + -
309B LYS* 4.2 11.1 - - - +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B HIS 3.0 13.3 + - - +
120B TRP* 3.4 9.2 - - + +
122B TRP* 1.3 84.5 - - + +
124B LYS* 1.3 65.8 + - - +
126B ALA* 3.2 3.7 + - - +
127B VAL* 2.9 35.6 + - + +
136B VAL* 4.0 22.7 - - + -
146B ALA* 3.5 32.1 - - + +
149B VAL* 4.4 6.1 - - + -
150B ALA* 4.0 15.5 - - + +
207B ILE* 4.1 26.9 - - + -
209B LEU* 3.8 22.2 - - + -
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Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LEU* 3.9 37.7 - - + +
120B TRP 2.7 20.0 + - - +
121B GLU* 3.8 4.9 - - - +
123B LEU* 1.3 73.1 - - - +
125B ASN* 1.3 57.6 + - - +
127B VAL* 3.4 1.8 + - - +
128B GLU* 2.7 71.0 + - + +
149B VAL* 3.8 16.4 - - + +
153B ALA* 4.1 12.7 - - + +
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Residues in contact with ASN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B GLU 3.0 18.1 + - - +
122B TRP* 3.8 6.3 - - - +
124B LYS* 1.3 75.8 - - - +
126B ALA* 1.3 67.6 + - - +
128B GLU* 4.4 8.0 + - - -
129B THR* 2.9 55.2 + - - +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B TRP* 3.0 33.0 + - + +
123B LEU* 3.5 5.6 - - - +
125B ASN* 1.3 78.4 + - - +
127B VAL* 1.3 61.9 + - - +
129B THR* 3.8 4.8 + - - -
130B ALA* 3.3 22.7 + - - +
134B LEU* 4.3 2.0 - - - -
207B ILE* 3.9 21.3 - - + -
246B LEU* 3.7 17.9 - - + +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU* 2.9 37.6 + - + +
126B ALA* 1.3 74.5 - - - +
128B GLU* 1.3 65.3 + - - +
130B ALA* 3.3 18.0 + - - +
132B ARG 5.0 1.0 - - - +
134B LEU* 3.8 23.0 - - + +
136B VAL* 4.1 11.2 - - + -
150B ALA* 4.8 2.9 - - + -
153B ALA* 3.5 40.8 - - + +
154B GLY 4.2 0.9 - - - -
155B ALA* 3.8 21.5 - - + +
207B ILE* 4.1 4.7 - - + -
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LYS* 2.7 60.1 + - - +
125B ASN* 3.9 7.9 + - - +
127B VAL* 1.3 78.8 - - - +
129B THR* 1.3 66.5 + - + +
130B ALA 3.5 5.5 + - - +
153B ALA* 4.0 21.4 - - + +
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Residues in contact with THR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ASN* 2.9 46.5 + - - +
126B ALA* 3.8 5.0 + - - -
128B GLU* 1.3 78.9 - - + +
130B ALA* 1.3 64.8 + - - +
131B ASP* 3.4 2.8 + - - +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ALA 3.3 15.2 + - - +
127B VAL 3.3 15.3 + - - +
128B GLU 3.2 7.4 - - - +
129B THR* 1.3 78.3 - - - +
131B ASP* 1.3 72.0 + - - +
132B ARG* 3.4 20.0 + - - +
134B LEU* 3.7 20.2 - - + -
246B LEU* 4.6 6.1 - - + -
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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