Contacts of the helix formed by residues 178 - 193 (chain B) in PDB entry 4S0H
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 THR 178 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B LEU* 1.3 73.8 - - - +
179B SER* 1.3 58.2 + - - +
180B THR* 3.0 14.9 - - - -
181B GLN* 3.0 53.2 + - - +
182B VAL* 3.4 5.9 + - - +
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 3.8 17.0 + - - -
169B ASP* 3.2 26.8 + - - -
172B ALA* 3.6 14.2 - - - +
177B LEU 3.4 2.4 + - - -
178B THR* 1.3 69.3 - - - +
180B THR* 1.3 68.1 + - - +
182B VAL* 3.8 5.9 - - - +
183B LYS* 3.1 22.0 + - - +
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Residues in contact with THR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 3.4 15.0 + - - -
179B SER* 1.3 80.1 + - - +
181B GLN* 1.3 58.8 + - + -
183B LYS* 3.0 22.1 + - - +
184B ILE* 2.9 43.2 + - + +
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Residues in contact with GLN 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PHE* 4.0 27.3 - - + -
153B LEU* 6.4 0.2 - - - -
177B LEU* 3.4 22.5 - - + +
178B THR* 3.0 43.0 + - - +
180B THR* 1.3 80.1 - - + +
182B VAL* 1.3 57.8 + - - +
184B ILE* 3.8 4.2 - - - +
185B TRP* 2.8 29.1 + - - +
15C A 3.0 40.0 + - - +
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Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 3.8 22.9 - - + -
163B LEU* 4.6 5.6 - - + -
168B ARG* 4.4 11.2 - - + +
171B LEU* 4.3 16.8 - - + -
172B ALA* 3.8 28.5 - - + -
175B LEU* 5.9 2.2 - - + -
177B LEU* 4.6 13.0 - - + +
178B THR 3.4 15.5 - - - +
179B SER* 3.8 4.9 - - - +
180B THR 3.2 0.2 - - - -
181B GLN* 1.3 74.6 - - - +
183B LYS* 1.3 64.1 + - - +
185B TRP* 3.6 5.0 - - - +
186B PHE* 3.0 41.7 + - + -
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Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 3.4 45.0 - - - +
179B SER 3.1 6.8 + - - +
180B THR* 3.0 24.0 + - - +
182B VAL* 1.3 78.4 - - - +
184B ILE* 1.3 73.0 + - + +
186B PHE* 3.3 5.8 + - - +
187B GLN* 3.0 29.2 + - + +
190B ARG* 5.1 1.2 + - - -
1D C 6.0 5.2 - - + -
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Residues in contact with ILE 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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180B THR* 2.9 29.3 + - + +
181B GLN* 3.9 7.0 - - - +
183B LYS* 1.3 87.9 - - + +
185B TRP* 1.3 62.8 + - - +
187B GLN* 3.7 26.0 - - - +
188B ASN* 2.8 48.2 + - - +
14C A 5.0 2.0 - - + -
15C A 4.0 27.6 - - + +
16C G 6.2 0.2 - - - +
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Residues in contact with TRP 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PHE* 3.9 17.6 - + + -
150B VAL* 4.8 9.8 - - + +
153B LEU* 3.5 64.7 - - + +
154B GLU* 4.0 20.0 - - + -
157B PHE* 4.0 10.8 - + + -
181B GLN 2.8 19.8 + - - +
182B VAL* 3.3 5.6 + - - +
184B ILE* 1.3 78.3 - - - +
186B PHE* 1.3 68.7 + + - +
188B ASN* 3.2 5.4 + - - +
189B ARG* 2.7 75.9 + - + +
192B LYS* 5.6 4.0 - - - +
14C A 3.2 40.6 + - - -
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Residues in contact with PHE 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 3.6 26.5 - - + -
156B ARG* 4.1 19.5 - - + -
157B PHE* 3.8 27.6 - + + -
160B GLN 3.6 22.2 - - - -
161B ARG 4.1 12.1 - - - -
162B TYR* 4.8 0.4 - - - -
163B LEU* 3.6 41.5 - - + -
168B ARG* 6.0 1.6 - - + -
171B LEU* 4.3 2.5 - - + -
182B VAL* 3.0 28.6 + - + +
183B LYS* 3.8 5.2 - - - +
185B TRP* 1.3 85.4 - + - +
187B GLN* 1.3 54.4 + - - +
189B ARG* 3.7 1.9 - - - +
190B ARG* 2.8 54.7 + - - +
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Residues in contact with GLN 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LYS* 3.0 19.8 + - + +
184B ILE* 3.7 25.0 + - - +
186B PHE* 1.3 78.1 - - - +
188B ASN* 1.3 69.1 + - - +
190B ARG* 3.4 18.1 + - - +
191B TYR* 3.1 23.1 + - + +
16C G 4.4 6.5 + - - -
17C T 4.6 3.4 + - - -
1D C 4.4 10.4 + - - -
2D C 3.0 51.3 + - + +
3D A 3.6 16.3 - - - +
4D C 5.1 0.8 - - - +
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Residues in contact with ASN 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ILE* 2.8 33.3 + - - +
185B TRP 3.7 2.9 - - - +
187B GLN* 1.3 78.4 + - - +
189B ARG* 1.3 58.0 + - - +
191B TYR* 3.6 6.6 - - - +
192B LYS* 2.9 36.2 + - - +
13C G 6.1 1.3 - - + -
14C A 3.7 28.3 + - - +
15C A 2.9 50.5 + - - +
16C G 4.6 1.0 - - - +
4D C 4.3 8.0 + - - -
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Residues in contact with ARG 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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140A ASP* 5.4 5.7 + - - -
154B GLU* 3.0 36.3 + - - -
157B PHE* 3.8 27.0 - - + -
185B TRP* 2.7 57.5 + - + +
186B PHE 3.7 2.9 - - - +
188B ASN* 1.3 70.3 - - - +
190B ARG* 1.3 64.1 + - - +
192B LYS* 3.9 30.7 - - - +
193B SER* 3.1 47.0 + - - +
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Residues in contact with ARG 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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157B PHE* 4.1 7.3 - - + -
161B ARG* 3.0 54.8 + - - +
162B TYR* 3.5 31.0 - - - +
163B LEU* 4.6 3.6 - - - +
168B ARG* 5.7 4.6 - - - +
183B LYS 5.1 1.4 + - - -
186B PHE* 2.8 45.9 + - - +
187B GLN* 3.4 25.9 - - - +
189B ARG* 1.3 71.0 - - - +
191B TYR* 1.3 65.8 + - - +
193B SER* 3.2 17.0 + - - +
194B LYS* 4.4 6.6 - - - +
1D C 4.0 14.7 + - - -
2D C 3.0 43.2 + - - +
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Residues in contact with TYR 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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187B GLN* 3.1 17.2 + - + +
188B ASN* 3.6 8.3 - - - +
190B ARG* 1.3 75.7 - - - +
192B LYS* 1.3 75.3 + - + +
193B SER 2.9 1.7 + - - -
194B LYS* 3.2 34.1 + - - +
2D C 5.5 0.2 - - - -
3D A 3.2 39.7 - + - +
4D C 2.7 68.7 + + - +
5D T 4.5 12.4 - - + +
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Residues in contact with LYS 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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154B GLU* 5.3 2.6 + - - -
185B TRP* 5.6 3.6 - - - +
188B ASN* 2.9 13.3 + - - +
189B ARG* 3.9 41.7 - - - +
191B TYR* 1.3 88.3 - - + +
193B SER* 1.3 53.1 + - - +
194B LYS* 2.8 19.3 + - - +
12C T 6.2 1.1 - - + -
13C G 3.7 46.2 + - + +
14C A 5.1 3.6 + - - -
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ARG* 4.0 17.7 + - - -
157B PHE* 4.2 6.1 - - - -
161B ARG* 4.0 15.3 + - - -
189B ARG* 3.1 31.3 + - - +
190B ARG* 3.2 16.6 + - - +
191B TYR 2.9 1.8 + - - -
192B LYS* 1.3 74.4 - - - +
194B LYS* 1.3 63.1 + - - +
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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