Contacts of the helix formed by residues 140 - 152 (chain D) in PDB entry 4IRQ
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 ASN 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133D GLN* 2.9 8.3 + - - -
138D ARG 4.0 0.2 - - - +
139D PHE* 1.3 71.7 - - - +
141D ARG* 1.3 63.7 + - - +
142D ALA* 3.7 4.9 + - - +
143D ALA* 3.0 26.7 + - - +
144D LEU* 3.1 24.7 + - - +
219D ASN 3.1 26.2 + - - +
221D PHE 3.0 19.8 + - - +
222D TRP* 3.3 45.1 - - + -
314D LEU* 3.8 9.6 - - + -
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Residues in contact with ARG 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D PRO* 3.8 21.9 - - + +
139D PHE* 3.8 23.8 + - + -
140D ASN* 1.3 73.9 - - - +
142D ALA* 1.3 62.2 + - - +
144D LEU* 3.5 4.4 + - - +
145D ILE* 3.2 28.3 + - + +
161D MET* 4.2 34.0 - - - +
162D HIS 5.1 0.2 - - - +
163D ASP* 2.9 30.1 + - - +
200D VAL 5.4 0.2 + - - -
201D GLY* 4.3 2.6 - - - -
202D GLY 3.6 25.1 + - - +
204D LEU* 5.7 0.4 - - - +
217D MET* 4.5 6.1 - - - +
221D PHE 4.7 1.2 + - - -
223D GLY 5.8 0.4 + - - -
227D GLU* 2.9 28.7 + - - +
228D ASP* 4.6 6.1 - - - +
402D UDP 4.3 4.7 - - - -
403D TRS 3.3 34.2 + - - +
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Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D ASN* 3.3 3.8 + - - +
141D ARG* 1.3 76.4 - - - +
143D ALA* 1.3 65.7 + - - +
145D ILE* 3.2 3.8 + - - +
146D ASN* 3.1 24.9 + - - +
217D MET* 3.6 29.9 - - + +
218D SER 3.2 22.9 - - - +
221D PHE* 5.3 0.6 + - + -
227D GLU* 3.6 31.1 - - + +
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Residues in contact with ALA 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D ASN* 3.0 35.3 + - - +
142D ALA* 1.3 77.5 - - - +
144D LEU* 1.3 62.5 + - - +
146D ASN* 3.2 4.5 + - - +
147D VAL* 3.0 25.5 + - - +
218D SER 4.0 1.0 + - - -
219D ASN* 3.7 27.6 - - + +
222D TRP* 5.6 0.4 - - + -
290D VAL* 4.1 3.4 - - + +
314D LEU* 3.9 20.2 - - + -
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D PRO* 4.2 6.7 - - + -
101D PHE 4.0 2.2 - - - +
131D LEU* 3.2 41.7 - - + +
133D GLN* 3.7 24.2 - - + +
139D PHE* 3.6 35.9 - - + -
140D ASN 3.1 12.4 + - - +
141D ARG 3.7 5.6 - - - +
143D ALA* 1.3 75.0 - - - +
145D ILE* 1.3 53.7 + - - +
147D VAL* 3.3 5.5 + - - +
148D GLY 2.8 30.7 + - - -
312D ILE* 4.2 16.4 - - + -
314D LEU* 3.8 24.2 - - + -
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Residues in contact with ILE 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 3.7 40.2 - - + +
100D PRO* 3.9 17.3 - - + -
131D LEU* 4.2 6.5 - - + -
141D ARG* 3.2 20.9 - - + +
142D ALA 3.2 8.8 + - - +
144D LEU* 1.3 72.3 - - - +
146D ASN* 1.3 60.8 + - - +
148D GLY* 3.4 0.7 + - - -
149D PHE* 2.9 28.1 + - - +
159D ILE* 4.8 0.7 - - + -
161D MET* 3.6 33.2 - - + -
211D TYR* 3.4 23.6 - - + +
217D MET* 3.8 12.6 - - - -
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Residues in contact with ASN 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ALA 3.1 12.8 + - - -
143D ALA 3.4 8.3 - - - +
145D ILE* 1.3 76.2 - - - +
147D VAL* 1.3 62.5 + - - +
149D PHE* 3.2 5.1 + - - +
150D LEU* 3.0 27.3 + - - +
211D TYR* 2.5 30.2 + - - -
216D GLY* 3.7 2.6 - - - -
217D MET 2.8 35.5 + - - -
219D ASN* 2.6 29.4 + - - +
286D GLY 3.7 6.3 + - - -
287D LEU* 3.8 12.6 - - + +
290D VAL* 4.1 12.3 - - + -
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Residues in contact with VAL 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ALA 3.0 14.4 + - - +
144D LEU 3.6 7.4 - - - +
146D ASN* 1.3 71.8 - - - +
148D GLY* 1.3 67.6 + - - +
150D LEU* 3.1 8.0 + - - +
151D GLU* 2.8 31.1 + - + +
290D VAL* 4.1 5.4 - - + +
292D TYR* 3.5 53.2 - - + -
294D VAL* 5.0 0.7 - - + -
310D LEU* 5.2 0.7 - - + -
312D ILE* 3.5 27.6 - - + -
314D LEU* 3.9 17.9 - - + -
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Residues in contact with GLY 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 4.0 6.5 - - - -
129D TYR* 5.6 1.0 - - - -
131D LEU* 3.7 27.3 - - - +
144D LEU 2.8 19.6 + - - -
145D ILE 3.7 2.0 - - - -
147D VAL* 1.3 73.5 - - - +
149D PHE* 1.3 50.6 + - - +
151D GLU* 3.1 3.4 + - - +
152D SER* 2.2 44.5 + - - -
310D LEU* 5.2 0.4 - - - -
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Residues in contact with PHE 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 3.6 6.7 - - + +
145D ILE 2.9 17.3 + - - +
146D ASN 3.3 8.3 - - - +
148D GLY* 1.3 71.7 - - - +
150D LEU* 1.3 69.3 + - + +
152D SER* 3.3 20.2 + - - +
159D ILE* 3.8 19.7 - - + -
208D LYS* 3.8 45.5 + - + -
211D TYR* 3.4 39.5 - + + -
212D ARG* 3.7 47.3 - - + -
287D LEU* 3.7 21.1 - - + -
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Residues in contact with LEU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ASN 3.0 13.2 + - - +
147D VAL 3.5 7.2 - - - +
149D PHE* 1.3 79.0 - - + +
151D GLU* 1.3 61.6 + - - +
152D SER 3.6 2.6 + - - +
212D ARG* 4.2 20.2 - - - +
287D LEU* 3.6 26.2 - - + +
290D VAL* 3.7 30.5 - - + +
292D TYR* 3.8 24.7 - - + +
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Residues in contact with GLU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D TYR* 4.5 5.5 - - - -
147D VAL* 2.8 33.9 + - + +
148D GLY 3.9 1.3 - - - +
150D LEU* 1.3 72.3 - - - +
152D SER* 1.3 64.9 + - - +
153D SER* 3.1 5.9 + - - -
292D TYR* 2.8 32.1 + - - +
294D VAL* 3.5 15.7 - - + +
297D ARG* 3.7 24.4 + - - +
310D LEU* 3.8 24.7 - - + -
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Residues in contact with SER 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ALA* 3.8 16.8 - - - +
98D LEU* 3.4 12.5 - - - +
129D TYR* 3.9 14.5 - - - -
148D GLY 2.2 41.7 + - - -
149D PHE* 3.3 12.5 + - - +
150D LEU 4.4 2.9 - - - +
151D GLU* 1.3 70.4 - - - +
153D SER* 1.3 69.2 + - - +
154D ASN* 3.6 1.9 + - - +
156D THR* 3.5 12.6 - - - -
159D ILE* 5.1 0.8 - - - +
208D LYS* 3.0 15.7 + - - -
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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