Contacts of the helix formed by residues 188 - 199 (chain A) in PDB entry 1I4A
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 ASP 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A ALA* 3.1 29.9 + - + +
183A LYS* 4.4 7.5 - - + +
185A TRP* 3.7 27.6 - - + -
186A GLY 3.4 2.2 + - - -
187A THR* 1.3 69.2 - - - +
189A GLU* 1.3 62.6 + - - +
190A VAL* 3.2 19.3 + - - +
191A LYS* 3.0 49.1 + - - +
192A PHE* 4.1 0.7 + - - -
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Residues in contact with GLU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A PHE* 4.7 7.3 - - - -
146A MET* 3.2 30.9 - - + +
185A TRP* 5.2 0.2 - - - -
187A THR* 2.8 36.5 + - + +
188A ASP* 1.3 71.1 - - - +
190A VAL* 1.3 61.9 + - - +
192A PHE* 3.1 21.0 + - - +
193A LEU* 3.2 8.7 + - - +
226A GLU 4.6 2.1 - - - +
227A THR* 4.0 13.5 - - - +
228A SER 4.9 1.6 + - - -
231A PHE* 3.5 37.6 - - + -
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A MET* 4.1 12.6 - - + +
149A ARG* 3.9 25.4 - - - +
188A ASP* 3.2 22.4 + - - +
189A GLU* 1.3 77.1 - - - +
191A LYS* 1.3 68.2 + - + +
193A LEU* 3.2 6.5 + - + +
194A THR* 2.9 43.9 + - - +
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Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ASP* 4.3 37.7 + - + +
177A LEU* 4.5 3.6 - - + -
180A ALA* 4.1 14.8 - - + -
188A ASP* 3.0 41.3 + - + +
190A VAL* 1.3 84.5 - - + +
192A PHE* 1.3 62.4 + - - +
194A THR* 3.4 5.2 + - - +
195A VAL* 3.0 30.0 + - - +
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Residues in contact with PHE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LEU* 4.1 25.4 - - + -
180A ALA* 4.1 12.1 - - + -
187A THR* 3.7 22.7 - - + -
188A ASP 4.4 2.5 - - - -
189A GLU* 3.1 13.8 + - - +
191A LYS* 1.3 78.1 - - + +
193A LEU* 1.3 63.9 + - - +
196A LEU* 2.9 42.1 + - + +
211A TYR* 5.5 0.9 - - - -
219A ILE* 3.8 27.6 - - + -
222A SER* 5.2 2.9 - - - -
223A ILE* 4.0 21.8 - - + -
226A GLU* 3.5 29.8 - - + -
227A THR* 4.6 8.7 - - + -
231A PHE* 4.5 0.4 - - + -
235A LEU* 3.8 23.1 - - + -
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A MET* 3.9 17.7 - - + -
149A ARG* 3.4 44.6 - - + +
150A VAL* 3.2 30.3 - - + +
153A SER* 4.6 4.0 - - - -
189A GLU 3.2 7.6 + - - +
190A VAL* 3.2 12.7 + - + +
192A PHE* 1.3 79.0 - - - +
194A THR* 1.3 64.9 + - - +
196A LEU* 5.2 0.4 - - - -
197A CYS* 3.0 62.8 + - + +
231A PHE* 4.7 3.0 - - + -
235A LEU* 5.4 1.8 - - - -
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Residues in contact with THR 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A VAL* 2.9 32.3 + - - +
191A LYS* 3.8 8.1 - - - +
193A LEU* 1.3 73.9 - - - +
195A VAL* 1.3 64.5 + - + +
198A SER* 2.8 37.9 + - - +
199A ARG* 4.5 18.8 - - - +
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASP* 3.6 41.7 - - + +
176A ASP* 5.3 4.5 - - + +
177A LEU* 3.3 34.1 - - + -
191A LYS* 3.0 11.3 + - - +
194A THR* 1.3 79.8 - - + +
196A LEU* 1.3 69.6 + - + +
197A CYS 3.4 0.3 + - - -
199A ARG* 3.3 31.8 + - + +
204A LEU* 3.4 22.8 - - + +
207A VAL* 4.4 3.4 - - + -
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ARG* 2.8 26.0 + - - -
177A LEU* 4.2 15.9 - - + -
192A PHE* 2.9 32.9 + - + +
193A LEU* 4.5 0.7 - - - +
195A VAL* 1.3 88.3 - - + +
197A CYS* 1.3 58.6 + - - +
204A LEU* 3.7 12.0 - - + +
208A PHE* 4.5 9.4 - - + -
219A ILE* 5.5 0.9 - - + -
223A ILE* 4.1 8.1 - - + -
235A LEU* 4.0 33.7 - - + +
238A ILE* 3.4 22.3 - - + +
239A VAL* 3.8 29.2 - - + -
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Residues in contact with CYS 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A VAL* 3.8 23.6 - - - -
153A SER* 3.2 26.7 + - - +
154A LEU* 4.3 8.7 - - + +
159A ARG* 3.4 34.3 + - - +
193A LEU* 3.0 46.1 + - + +
196A LEU* 1.3 77.2 - - - +
198A SER* 1.3 60.1 + - - +
235A LEU* 6.1 0.7 - - - -
238A ILE* 4.0 12.8 - - - -
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Residues in contact with SER 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A SER* 5.2 1.6 + - - -
158A GLY 5.1 0.2 - - - +
159A ARG* 3.8 3.5 - - - +
160A ASP* 3.1 30.0 + - - +
194A THR* 2.8 28.3 + - - +
197A CYS* 1.3 81.2 - - - +
199A ARG* 1.3 78.5 + - - +
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Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ARG* 2.8 31.4 + - - +
160A ASP* 4.7 2.2 - - - -
169A LEU* 3.7 28.0 - - - +
173A ASP* 2.7 39.9 + - - +
194A THR* 4.3 17.6 + - - +
195A VAL* 3.3 31.8 + - + +
198A SER* 1.3 98.3 + - - +
200A ASN* 1.3 64.2 + - - +
201A ARG 3.9 0.2 + - - -
203A HIS* 3.4 30.5 - - + -
204A LEU* 3.8 11.3 - - + +
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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