Contacts of the helix formed by residues 182 - 193 (chain B) in PDB entry 4HI7
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 TYR 182 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B THR* 3.6 16.8 + - + +
139B TYR* 3.6 42.6 - + + +
140B ASP* 2.6 31.7 + - - -
143B GLU* 3.4 20.4 - - + +
177B VAL* 3.7 16.6 - - + -
178B ASP* 2.9 36.2 + - + +
179B ALA 3.6 2.9 - - - -
181B LYS* 1.3 117.3 + - + +
183B PRO* 1.3 64.7 - - - +
184B LYS 3.3 2.9 - - - -
185B LEU* 3.9 7.4 - - + -
186B SER* 2.9 24.1 + - - -
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Residues in contact with PRO 183 (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 GLU* 3.2 11.9 - - - +
179B ALA 3.5 13.0 - - - +
180B ALA 3.6 9.6 - - - +
181B LYS 3.2 10.1 - - - +
182B TYR* 1.3 89.6 - - - +
184B LYS* 1.3 62.5 + - + +
186B SER* 3.5 3.2 + - - -
187B ALA* 2.9 29.3 + - - +
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Residues in contact with LYS 184 (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 GLU* 2.9 23.6 + - - +
146B PHE* 3.7 37.6 - - + -
147B LYS* 2.9 28.9 + - - +
149B GLN 5.8 0.2 - - - +
183B PRO* 1.3 80.0 - - + +
185B LEU* 1.3 66.4 + - - +
187B ALA* 3.4 5.9 + - - +
188B TRP* 3.0 24.4 + - - +
191B ARG* 5.3 0.3 + - - -
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 4.0 45.1 - - + +
142B VAL* 3.8 22.2 - - + -
143B GLU* 2.8 21.4 + - - +
146B PHE* 3.8 9.3 - - + -
168B ILE* 4.2 10.1 - - + -
177B VAL* 4.1 22.9 - - + -
182B TYR* 3.9 8.1 - - + +
184B LYS* 1.3 76.1 - - - +
186B SER* 1.3 63.0 + - - +
188B TRP* 3.3 27.4 + - + +
189B ILE* 3.0 27.9 + - + +
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Residues in contact with SER 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B VAL* 3.4 14.1 + - - +
179B ALA* 3.3 32.3 - - - +
182B TYR 2.9 23.4 + - - -
183B PRO* 3.8 4.7 - - - -
185B LEU* 1.3 77.6 - - - +
187B ALA* 1.3 61.7 + - - +
189B ILE* 3.4 11.9 + - - +
190B LYS* 3.0 28.2 + - - +
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Residues in contact with ALA 187 (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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183B PRO 2.9 17.6 + - - +
184B LYS* 3.8 6.7 - - - +
186B SER* 1.3 78.0 - - - +
188B TRP* 1.3 57.6 + - - +
190B LYS* 3.3 8.2 + - - +
191B ARG* 2.9 46.0 + - - +
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Residues in contact with TRP 188 (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 VAL* 5.0 0.4 - - + -
146B PHE* 3.4 28.0 - + + -
150B THR 3.8 10.8 - - - -
151B TYR* 4.3 5.2 - + - -
152B VAL* 3.8 18.3 - - + +
161B ASP* 2.8 36.1 + - - -
164B LEU* 3.7 12.3 - - + -
165B ILE* 3.5 38.1 - - + -
168B ILE* 3.9 10.3 - - + -
184B LYS 3.0 16.4 + - - +
185B LEU* 3.6 31.2 - - + +
187B ALA* 1.3 74.9 - - - +
189B ILE* 1.3 78.4 + - + +
191B ARG* 3.2 16.1 + - - +
192B LEU* 3.0 52.5 + - + +
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Residues in contact with ILE 189 (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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165B ILE* 3.8 27.8 - - + -
168B ILE* 4.1 21.3 - - + -
169B SER* 6.2 2.2 - - - -
172B VAL* 5.3 3.8 - - + -
177B VAL* 4.2 19.3 - - + -
185B LEU* 3.0 24.9 + - + +
186B SER* 3.7 9.4 - - - +
188B TRP* 1.3 85.2 - - + +
190B LYS* 1.3 61.6 - - - +
192B LEU* 3.1 3.9 + - - +
193B GLU* 2.9 50.4 + - + +
198B TYR* 4.9 2.4 + - - +
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Residues in contact with LYS 190 (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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186B SER* 3.0 17.2 + - - +
187B ALA* 3.6 12.1 - - - +
189B ILE* 1.3 75.7 - - - +
191B ARG* 1.3 62.7 + - - +
193B GLU* 3.4 26.3 + - + +
194B GLN* 3.0 33.7 + - + +
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Residues in contact with ARG 191 (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 PHE* 5.5 0.4 - - - -
150B THR* 2.7 57.0 + - - +
151B TYR* 3.8 26.2 - - + +
184B LYS 5.3 0.4 + - - -
187B ALA* 2.9 35.0 + - - +
188B TRP* 3.4 26.5 - - - +
189B ILE 3.2 0.2 - - - -
190B LYS* 1.3 78.2 - - - +
192B LEU* 1.3 63.9 + - + +
194B GLN* 3.1 27.9 + - - +
195B LEU* 3.9 4.3 + - - +
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Residues in contact with LEU 192 (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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151B TYR* 4.2 15.0 - - + -
157B LEU* 3.6 30.1 - - + -
161B ASP* 4.1 6.1 - - + +
162B PHE* 5.7 1.6 - - + -
165B ILE* 3.6 32.5 - - + -
188B TRP* 3.0 53.4 + - + +
189B ILE 3.8 3.6 - - - +
191B ARG* 1.3 72.1 - - + +
193B GLU* 1.3 61.8 + - - +
194B GLN 2.9 6.8 + - - -
195B LEU* 3.0 28.7 + - + +
198B TYR* 3.1 27.7 - - + -
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Residues in contact with GLU 193 (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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189B ILE* 2.9 36.6 + - + +
190B LYS* 3.5 30.2 + - - +
191B ARG 3.2 0.4 - - - -
192B LEU* 1.3 76.8 - - - +
194B GLN* 1.3 61.4 + - + +
195B LEU 3.4 1.3 - - - +
198B TYR* 3.6 44.0 + - + +
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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