Contacts of the helix formed by residues 144 - 157 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LEU* 4.4 1.6 - - + -
140B GLN* 5.3 1.6 + - - +
141B ARG* 2.6 65.8 + - - +
143B HIS* 1.3 94.4 + - + +
145B ILE* 1.3 63.4 + - - +
146B THR 3.1 3.1 - - - -
147B ASP* 3.0 17.6 + - - +
148B LEU* 3.0 25.8 + - + +
112C HIS* 3.8 6.8 - - - +
327D ARG* 3.2 45.4 + - + +
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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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14B ALA* 3.8 12.3 - - + +
17B ALA* 3.8 28.3 - - + -
18B LEU* 3.9 34.1 - - + +
21B ARG* 5.8 0.2 - - - -
139B LEU* 3.8 18.8 - - + +
142B PRO 3.3 18.8 + - - +
143B HIS 4.7 1.1 - - - +
144B GLU* 1.3 77.2 - - - +
146B THR* 1.3 59.9 + - - +
148B LEU* 3.2 4.2 + - + -
149B VAL* 2.9 36.1 + - - +
166B ILE* 4.0 20.6 - - + -
168B LEU* 3.7 29.8 - - + -
173B LEU* 6.3 0.4 - - + -
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Residues in contact with THR 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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17B ALA* 4.3 21.1 + - - +
21B ARG* 3.6 38.5 - - - +
143B HIS 3.9 11.7 + - - -
144B GLU 3.1 0.6 + - - -
145B ILE* 1.3 81.5 - - - +
147B ASP* 1.3 60.8 + - - +
149B VAL* 3.5 2.8 + - - +
150B ASP* 3.2 23.4 + - - +
185B ASN* 4.3 18.1 + - - +
186B PRO* 5.1 6.7 - - + -
330D ARG* 4.4 9.0 - - - +
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Residues in contact with ASP 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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144B GLU* 3.0 25.4 + - - +
146B THR* 1.3 77.1 - - - +
148B LEU* 1.3 66.3 + - - +
150B ASP* 3.4 2.7 + - - +
151B SER* 3.0 34.1 + - - -
115C PHE* 5.4 1.4 - - - -
326D PRO* 4.1 3.0 - - + +
327D ARG* 3.0 73.7 + - - +
330D ARG* 3.9 17.0 - - - +
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Residues in contact with LEU 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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135B TYR* 3.5 23.1 + - - +
137B VAL* 4.2 24.2 - - + -
138B GLU 4.7 2.0 - - - +
139B LEU* 3.8 44.9 - - + +
140B GLN 5.1 0.4 - - - +
144B GLU* 3.0 19.1 + - + +
145B ILE* 3.7 10.8 - - + +
147B ASP* 1.3 87.8 - - - +
149B VAL* 1.3 59.5 + - - +
151B SER* 3.4 0.9 + - - -
152B ALA* 2.9 30.1 + - - +
166B ILE* 3.8 15.8 - - + +
115C PHE* 6.2 0.7 - - + -
327D ARG* 3.5 14.8 - - - +
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.6 31.6 - - + +
21B ARG* 3.8 28.5 - - + -
22B LEU* 4.2 19.5 - - + -
25B HIS* 3.9 14.4 - - + -
103B ILE* 5.4 2.9 - - + -
145B ILE* 2.9 22.9 + - + +
146B THR 3.8 4.7 - - - +
147B ASP 3.4 0.2 - - - -
148B LEU* 1.3 75.1 - - - +
150B ASP* 1.3 56.7 + - - +
152B ALA* 3.3 3.1 + - - +
153B VAL* 2.9 32.7 + - + +
166B ILE* 4.0 13.5 - - + -
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Residues in contact with ASP 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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21B ARG* 2.8 25.1 + - - +
25B HIS* 2.8 31.1 + - + +
146B THR 3.2 10.5 + - - +
147B ASP* 3.7 7.6 - - - +
148B LEU 3.3 0.2 - - - -
149B VAL* 1.3 76.6 - - - +
151B SER* 1.3 57.1 + - - +
153B VAL* 3.3 2.9 + - - +
154B ASN* 2.9 37.5 + - - +
188B ALA 5.3 2.2 - - - -
326D PRO* 4.6 7.2 - - + -
330D ARG* 2.6 43.5 + - - +
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Residues in contact with SER 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TYR* 3.5 32.7 - - - -
147B ASP* 3.0 18.8 + - - -
148B LEU* 5.7 0.4 - - - +
150B ASP* 1.3 73.2 - - - +
152B ALA* 1.3 64.6 - - - +
154B ASN* 3.4 10.4 + - - +
155B ALA* 3.1 24.9 + - - +
115C PHE* 6.2 0.2 - - - -
323D ASN 5.0 0.5 + - - -
324D PRO* 4.3 6.6 + - - -
326D PRO* 3.4 23.4 - - - +
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Residues in contact with ALA 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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103B ILE* 3.9 12.6 - - + -
135B TYR* 3.6 13.2 - - + -
148B LEU 2.9 18.6 + - - +
149B VAL* 3.4 9.2 - - - +
150B ASP 3.2 0.2 - - - -
151B SER* 1.3 76.6 - - - +
153B VAL* 1.3 56.5 + - - +
155B ALA 3.4 0.3 + - - -
156B ALA* 2.9 15.8 + - - +
164B SER* 2.6 42.7 + - - -
166B ILE* 4.2 12.3 - - + -
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 6.0 0.4 - - + -
25B HIS* 3.6 47.1 - - + +
74B PRO* 4.2 22.0 - - + -
103B ILE* 3.8 25.1 - - + -
149B VAL* 2.9 23.5 + - + +
150B ASP 3.7 4.3 - - - +
152B ALA* 1.3 73.7 - - - +
154B ASN* 1.3 66.8 + - - +
156B ALA* 3.7 1.1 - - - +
157B MET* 3.0 26.0 + - + +
190B THR* 4.2 7.9 - - + -
191B PRO* 4.4 10.3 - - + -
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Residues in contact with ASN 154 (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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25B HIS* 6.1 0.5 - - - -
150B ASP* 2.9 26.6 + - - +
151B SER* 3.6 10.1 - - - +
153B VAL* 1.3 81.6 - - - +
155B ALA* 1.3 59.2 + - - +
157B MET* 3.6 3.4 + - - -
158B THR* 2.8 26.2 + - - -
189B ASN 5.6 1.4 - - - +
191B PRO* 5.1 12.2 - - - +
195B VAL* 5.6 1.2 - - - +
322D VAL* 3.5 27.0 - - + +
323D ASN* 3.6 24.2 + - - +
326D PRO* 4.9 6.9 - - - +
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Residues in contact with ALA 155 (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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134B LYS* 2.9 40.2 + - + +
135B TYR* 3.6 28.9 - - + -
151B SER 3.1 16.6 + - - +
154B ASN* 1.3 74.5 - - - +
156B ALA* 1.3 63.5 + - - +
157B MET 3.4 0.5 + - - -
158B THR* 3.4 9.3 + - - -
164B SER* 3.8 1.6 - - - +
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Residues in contact with ALA 156 (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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74B PRO* 5.9 0.4 - - + -
101B PRO* 3.8 17.2 - - + +
102B VAL 4.5 0.7 - - - +
103B ILE* 4.1 15.9 - - + -
134B LYS* 4.3 0.4 - - - -
152B ALA 2.9 18.6 + - - +
153B VAL* 3.7 5.2 - - - +
155B ALA* 1.3 77.2 - - - +
157B MET* 1.3 57.4 + - + +
158B THR 3.3 0.2 - - - -
161B VAL* 3.2 27.7 - - - +
162B GLY 3.2 30.0 + - - +
164B SER* 3.4 7.7 + - - +
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Residues in contact with MET 157 (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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72B GLY 4.0 17.3 - - - +
74B PRO* 4.0 23.3 - - + -
101B PRO* 3.5 33.4 - - + -
153B VAL* 3.0 23.1 + - + +
154B ASN 3.9 2.5 - - - +
155B ALA 3.2 0.2 - - - -
156B ALA* 1.3 75.9 - - + +
158B THR* 1.3 55.2 + - - +
161B VAL* 4.0 10.3 - - - -
191B PRO* 3.5 41.5 - - + +
193B LYS* 3.9 23.3 - - - +
194B PRO* 3.3 7.6 - - + +
195B VAL* 2.8 33.6 + - - +
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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