Contacts of the helix formed by residues 140 - 152 (chain B) in PDB entry 4IRP
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B GLN* 2.7 11.1 + - - -
138B ARG 3.1 0.4 + - - -
139B PHE* 1.3 72.3 - - - +
141B ARG* 1.3 63.7 + - - +
142B ALA* 3.6 7.8 + - - +
143B ALA* 3.1 25.5 + - - +
144B LEU* 3.0 24.6 + - - +
219B ASN* 2.9 27.7 + - - +
221B PHE* 5.5 0.5 - - - +
222B TRP* 3.2 50.2 + - + +
223B GLY 4.8 1.1 - - - +
227B GLU* 4.6 2.9 - - - +
314B LEU* 3.8 12.1 - - + -
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Residues in contact with ARG 141 (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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100B PRO* 3.8 22.7 - - + +
139B PHE* 3.8 19.4 + - + -
140B ASN* 1.3 72.3 + - - +
142B ALA* 1.3 56.4 + - - +
144B LEU* 3.3 13.1 + - - +
145B ILE* 2.9 52.8 + - + +
161B MET 5.3 8.9 - - - +
163B ASP* 3.8 15.1 + - - -
200B VAL 5.4 1.2 + - - -
201B GLY* 4.7 1.8 - - - -
202B GLY 4.5 13.5 - - - +
204B LEU* 6.2 2.4 - - - +
217B MET* 4.2 7.5 - - - +
227B GLU* 3.2 25.3 + - - +
228B ASP* 2.5 40.1 + - - -
401B UDP 4.0 17.9 - - - -
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Residues in contact with ALA 142 (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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140B ASN* 3.2 3.5 - - - +
141B ARG* 1.3 74.3 - - - +
143B ALA* 1.3 64.1 + - - +
145B ILE* 3.2 5.5 + - - +
146B ASN* 3.1 23.3 + - - -
217B MET* 3.7 33.2 - - + +
218B SER 3.1 25.8 - - - +
221B PHE* 5.5 0.2 - - + -
227B GLU* 2.8 30.2 + - + +
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Residues in contact with ALA 143 (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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140B ASN* 3.1 31.6 + - - +
142B ALA* 1.3 80.2 - - - +
144B LEU* 1.3 61.1 + - - +
146B ASN* 3.1 5.1 + - - +
147B VAL* 3.0 27.2 + - - +
218B SER 4.3 0.4 + - - -
219B ASN* 3.5 26.9 + - + +
222B TRP* 5.8 0.4 - - + -
290B VAL* 4.0 6.1 - - + +
314B LEU* 3.8 18.4 - - + -
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Residues in contact with LEU 144 (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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100B PRO* 4.3 6.1 - - + -
131B LEU* 3.9 25.5 - - + +
133B GLN* 3.3 33.2 - - + +
139B PHE* 3.3 39.9 - - + -
140B ASN 3.0 17.2 + - - +
141B ARG* 3.4 7.6 - - - +
143B ALA* 1.3 75.2 - - - +
145B ILE* 1.3 57.2 + - - +
147B VAL* 3.1 7.5 + - - +
148B GLY* 2.8 25.5 + - - -
312B ILE* 4.0 26.7 - - + -
314B LEU* 4.0 12.1 - - + -
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Residues in contact with ILE 145 (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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98B LEU* 3.7 19.3 - - + +
100B PRO* 4.6 17.3 - - + -
131B LEU* 4.6 8.1 - - + -
141B ARG* 2.9 44.6 + - + +
142B ALA 3.5 7.9 - - - +
144B LEU* 1.3 72.5 - - - +
146B ASN* 1.3 65.3 + - - +
148B GLY 4.3 0.7 - - - +
149B PHE* 2.9 23.6 + - - +
159B ILE* 5.2 2.2 - - + -
161B MET 5.3 12.8 - - - +
211B TYR* 3.5 22.7 - - + +
217B MET* 3.9 20.4 - - - -
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Residues in contact with ASN 146 (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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142B ALA 3.1 11.6 + - - -
143B ALA 3.1 9.4 + - - +
145B ILE* 1.3 74.6 - - - +
147B VAL* 1.3 63.6 + - - +
149B PHE* 3.3 4.6 + - - +
150B LEU* 3.1 27.0 + - - +
211B TYR* 2.6 27.7 + - - -
216B GLY* 3.4 6.1 - - - -
217B MET 2.7 37.9 + - - +
219B ASN* 3.0 19.0 + - - -
286B GLY 3.5 6.3 - - - -
287B LEU* 3.7 15.5 - - + +
290B VAL* 3.9 18.2 - - + -
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Residues in contact with VAL 147 (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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143B ALA 3.0 19.0 + - - +
144B LEU* 3.1 6.5 + - - +
146B ASN* 1.3 73.9 - - - +
148B GLY* 1.3 59.9 + - - +
150B LEU* 3.1 6.2 + - - -
151B GLU* 2.8 37.7 + - + +
290B VAL* 4.0 5.4 - - + -
292B TYR* 3.5 52.3 - - + -
294B VAL* 4.7 0.4 - - + -
310B LEU* 5.4 0.7 - - + -
312B ILE* 3.6 27.8 - - + -
314B LEU* 3.7 19.5 - - + -
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Residues in contact with GLY 148 (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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98B LEU* 3.9 15.7 - - - +
129B TYR* 5.4 1.0 - - - -
131B LEU* 3.7 26.8 - - - +
144B LEU 2.8 15.7 + - - -
145B ILE 3.3 2.4 + - - -
147B VAL* 1.3 73.2 - - - +
149B PHE* 1.3 56.9 + - - +
151B GLU* 4.8 3.1 - - - -
152B SER* 2.9 35.0 + - - -
310B LEU* 4.9 1.0 - - - +
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Residues in contact with PHE 149 (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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98B LEU* 3.5 10.9 - - + +
145B ILE 2.9 13.7 + - - +
146B ASN 3.4 8.7 - - - +
148B GLY* 1.3 75.2 - - - +
150B LEU* 1.3 72.0 + - + +
152B SER* 2.8 23.4 + - - +
159B ILE* 4.2 15.5 - - + -
208B LYS* 3.5 51.1 + - + -
211B TYR* 3.4 30.5 - + + -
212B ARG* 4.0 24.0 - - + -
287B LEU* 3.8 28.9 - - + -
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Residues in contact with LEU 150 (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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146B ASN 3.1 12.0 + - - +
147B VAL 3.1 6.3 + - - +
149B PHE* 1.3 91.4 - - + +
151B GLU* 1.3 64.2 + - - +
152B SER 4.2 3.6 - - - +
287B LEU* 3.6 30.1 - - + +
290B VAL* 3.7 30.5 - - + +
292B TYR* 3.7 26.5 - - + +
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Residues in contact with GLU 151 (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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129B TYR* 4.4 7.7 - - - -
147B VAL* 2.8 31.8 + - + +
148B GLY 4.4 0.2 - - - +
150B LEU* 1.3 76.4 - - - +
152B SER* 1.3 65.4 + - - +
153B SER* 3.8 0.7 + - - -
292B TYR* 2.4 32.8 + - - +
294B VAL* 3.7 18.7 - - + +
297B ARG* 3.6 25.7 + - - -
310B LEU* 3.7 23.8 - - + +
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Residues in contact with SER 152 (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 ALA* 3.9 17.0 - - - -
98B LEU* 4.7 0.2 - - - -
129B TYR* 3.7 17.0 - - - -
148B GLY 2.9 17.1 + - - -
149B PHE* 2.8 21.5 + - - +
150B LEU 4.2 4.9 - - - +
151B GLU* 1.3 81.8 - - - +
153B SER* 1.3 64.8 + - - +
154B ASN* 3.5 2.1 + - - -
156B THR* 3.9 9.9 - - - -
208B LYS* 2.8 26.2 + - - -
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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