Contacts of the helix formed by residues 144 - 157 (chain D) in PDB entry 2IHU
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 GLU 144 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A HIS* 3.8 7.6 - - - +
327B ARG* 3.2 44.1 + - + +
139D LEU* 4.5 1.6 - - + -
140D GLN* 5.2 1.4 + - - +
141D ARG* 2.7 64.0 + - - +
143D HIS* 1.3 95.5 + - + +
145D ILE* 1.3 63.5 + - - +
146D THR 3.1 2.5 - - - -
147D ASP* 3.0 19.2 + - - +
148D LEU* 3.0 25.6 + - + +
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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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14D ALA* 3.9 10.3 - - + +
17D ALA* 3.6 30.3 - - + -
18D LEU* 3.9 32.5 - - + +
21D ARG* 5.7 0.2 - - - -
139D LEU* 3.9 18.4 - - + +
142D PRO 3.3 18.9 + - - +
143D HIS 4.6 1.3 - - - +
144D GLU* 1.3 77.1 - - - +
146D THR* 1.3 58.2 + - - +
148D LEU* 4.2 6.7 - - + -
149D VAL* 2.9 30.1 + - - +
166D ILE* 4.0 19.3 - - + -
168D LEU* 3.8 28.7 - - + -
173D LEU* 6.3 0.4 - - + -
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Residues in contact with THR 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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330B ARG* 4.2 10.1 - - - +
17D ALA* 4.3 20.3 + - - +
21D ARG* 3.6 38.7 - - - +
143D HIS 3.9 11.1 + - - -
144D GLU 3.1 0.4 - - - -
145D ILE* 1.3 78.9 - - - +
147D ASP* 1.3 61.7 + - - +
149D VAL* 3.5 2.6 + - - +
150D ASP* 3.1 23.6 + - - +
185D ASN* 4.2 20.7 + - + +
186D PRO* 5.1 5.6 - - + -
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Residues in contact with ASP 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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115A PHE* 5.4 0.7 - - - -
326B PRO* 4.1 3.5 - - + +
327B ARG* 3.0 71.3 + - - +
330B ARG* 3.8 20.2 - - - +
143D HIS* 5.8 0.2 - - - -
144D GLU* 3.0 27.2 + - - +
146D THR* 1.3 76.0 - - - +
148D LEU* 1.3 66.0 + - - +
150D ASP* 3.4 2.9 + - - +
151D SER* 3.0 33.4 + - - -
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Residues in contact with LEU 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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115A PHE* 6.2 0.7 - - + -
327B ARG* 3.5 25.8 - - - +
135D TYR* 3.5 24.9 + - - +
137D VAL* 4.0 26.7 - - + -
138D GLU 4.7 0.4 - - - +
139D LEU* 3.9 41.7 - - + +
140D GLN 5.2 0.7 - - - +
144D GLU* 3.0 17.9 + - + +
145D ILE* 3.6 9.2 - - + +
147D ASP* 1.3 77.7 + - - +
149D VAL* 1.3 59.2 + - - +
151D SER* 3.4 1.1 + - - -
152D ALA* 2.9 30.0 + - - +
166D ILE* 3.9 19.3 - - + -
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Residues in contact with VAL 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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18D LEU* 3.6 31.2 - - + +
21D ARG* 3.8 28.3 - - + +
22D LEU* 4.1 21.5 - - + -
25D HIS* 3.9 15.0 - - + -
103D ILE* 5.4 2.5 - - + -
145D ILE* 2.9 22.0 + - + +
146D THR 3.7 4.9 - - - +
148D LEU* 1.3 75.7 - - - +
150D ASP* 1.3 58.0 + - - +
152D ALA* 3.2 2.9 + - - +
153D VAL* 2.8 32.9 + - + +
166D ILE* 4.0 14.6 - - + -
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Residues in contact with ASP 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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326B PRO* 4.5 7.4 - - + -
330B ARG* 2.7 39.9 + - - +
21D ARG* 2.8 25.9 + - - +
25D HIS* 2.8 31.3 + - + +
146D THR 3.1 10.3 + - - +
147D ASP* 3.7 9.4 - - - +
148D LEU 3.3 0.2 - - - -
149D VAL* 1.3 74.8 - - - +
151D SER* 1.3 58.5 + - - +
153D VAL* 3.4 2.3 + - - +
154D ASN* 2.9 37.0 + - - +
188D ALA 5.4 1.6 - - - -
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Residues in contact with SER 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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323B ASN 5.0 1.0 + - - -
324B PRO* 4.4 6.8 + - - +
326B PRO* 3.4 23.6 - - - +
135D TYR* 3.6 30.9 - - - -
147D ASP* 3.0 18.8 + - - -
148D LEU* 3.9 0.4 - - - -
150D ASP* 1.3 73.4 - - - +
152D ALA* 1.3 65.8 + - - +
154D ASN* 3.5 10.2 + - - +
155D ALA* 3.1 25.5 + - - +
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Residues in contact with ALA 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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103D ILE* 3.9 12.3 - - + -
135D TYR* 3.7 13.2 - - + -
148D LEU 2.9 17.9 + - - +
149D VAL* 3.4 6.5 - - - +
151D SER* 1.3 77.9 - - - +
153D VAL* 1.3 56.3 + - - +
156D ALA* 3.0 16.8 + - - +
164D SER* 2.6 42.1 + - - -
166D ILE* 4.2 15.7 - - + -
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Residues in contact with VAL 153 (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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22D LEU* 5.9 0.7 - - + -
25D HIS* 3.8 45.5 - - + +
74D PRO* 4.2 22.4 - - + -
103D ILE* 3.8 23.8 - - + -
149D VAL* 2.8 22.1 + - + +
150D ASP 3.7 4.7 - - - +
152D ALA* 1.3 73.9 - - - +
154D ASN* 1.3 67.0 + - - +
156D ALA* 3.3 1.6 + - - +
157D MET* 3.0 28.3 + - + +
190D THR* 4.4 7.6 - - + -
191D PRO* 4.4 8.3 - - + -
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Residues in contact with ASN 154 (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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322B VAL* 3.5 26.3 - - + +
323B ASN* 3.6 25.0 + - - +
326B PRO* 4.8 7.7 - - - +
25D HIS* 6.2 0.2 - - - -
150D ASP* 2.9 25.3 + - - +
151D SER* 3.6 9.4 - - - +
153D VAL* 1.3 80.6 - - - +
155D ALA* 1.3 60.0 + - - +
157D MET* 3.6 7.9 + - - +
158D THR* 2.8 22.2 + - - -
189D ASN 5.6 1.0 - - - +
191D PRO* 5.2 11.1 - - - +
195D VAL* 5.7 0.9 - - - +
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Residues in contact with ALA 155 (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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134D LYS* 3.0 42.0 + - + +
135D TYR* 3.7 29.2 - - + -
151D SER 3.1 17.2 + - - +
154D ASN* 1.3 72.8 - - - +
156D ALA* 1.3 63.3 + - - +
157D MET 3.4 0.3 + - - -
158D THR* 3.4 8.5 + - - -
164D SER* 3.9 0.9 - - - +
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Residues in contact with ALA 156 (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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74D PRO* 5.9 0.4 - - + -
101D PRO* 3.8 17.5 - - + +
102D VAL 4.4 1.3 - - - +
103D ILE* 4.1 15.5 - - + -
134D LYS* 4.4 0.4 - - - -
152D ALA 3.0 18.5 + - - +
153D VAL* 3.6 4.3 - - - +
155D ALA* 1.3 78.1 - - - +
157D MET* 1.3 57.3 + - + +
158D THR 3.3 0.2 - - - -
161D VAL* 3.3 13.0 - - - +
162D GLY 3.2 42.6 + - - +
164D SER* 3.5 7.3 + - - +
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Residues in contact with MET 157 (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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72D GLY 4.2 14.8 - - - +
74D PRO* 4.0 25.1 - - + -
101D PRO* 3.4 30.1 - - + -
153D VAL* 3.0 23.6 + - + +
154D ASN 3.9 2.2 - - - +
155D ALA 3.3 0.4 - - - -
156D ALA* 1.3 75.6 - - + +
158D THR* 1.3 59.8 + - - +
161D VAL* 4.1 8.7 - - - -
191D PRO* 3.5 41.3 - - + +
193D LYS* 3.8 25.6 - - - +
194D PRO* 3.3 11.4 - - + +
195D VAL* 2.8 28.4 + - + +
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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