Contacts of the helix formed by residues 185 - 194 (chain A) in PDB entry 4A8W
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 LYS 185 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 2.8 25.8 + - + +
183A GLN* 3.9 45.0 + - + +
184A GLY* 1.4 75.2 - - - +
186A PHE* 1.3 59.2 + - - +
187A ASP 3.4 2.7 - - - +
188A ASP* 3.7 29.3 - - + +
189A ALA* 3.1 26.3 + - - +
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Residues in contact with PHE 186 (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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181A MET* 3.7 38.1 - - + -
184A GLY* 3.2 26.0 + - - -
185A LYS* 1.3 72.5 - - - +
187A ASP* 1.3 60.7 + - - +
189A ALA* 3.3 7.3 + - - +
190A TYR* 3.0 29.3 + - - +
195A MET 4.4 1.7 - - - +
196A GLY* 5.7 0.5 - - - -
355A LYS* 3.9 15.7 - - - -
359A THR* 3.7 27.6 - - + -
382A PRO 3.7 13.2 - - - +
383A SER 3.3 25.9 + - - +
384A ASN* 4.2 14.4 - - - -
385A PRO* 3.6 26.5 - - + -
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Residues in contact with ASP 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 4.6 1.9 + - - -
185A LYS* 3.4 0.8 - - - +
186A PHE* 1.3 76.1 - - - +
188A ASP* 1.3 59.6 + - - +
190A TYR* 3.3 6.9 + - - +
191A GLN* 2.8 49.6 + - - +
382A PRO* 4.2 6.2 - - - +
383A SER* 2.8 43.0 + - - +
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Residues in contact with ASP 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.2 15.9 - - + +
185A LYS* 3.4 38.2 + - + +
186A PHE 3.3 0.2 - - - -
187A ASP* 1.3 77.6 - - - +
189A ALA* 1.4 59.5 + - - +
191A GLN* 4.5 12.4 + - - +
192A LEU* 2.9 42.8 + - + +
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Residues in contact with ALA 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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177A ALA* 3.7 26.9 - - + +
180A LEU* 4.0 11.4 - - + +
181A MET* 3.9 15.3 - - + -
185A LYS 3.1 14.2 + - - +
186A PHE 3.3 8.0 + - - +
188A ASP* 1.4 75.5 - - - +
190A TYR* 1.3 57.1 + - - +
193A HIS* 2.9 34.7 + - - +
194A GLN 3.5 1.0 + - - -
195A MET* 3.6 14.2 + - - +
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Residues in contact with TYR 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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16A MET* 2.7 44.9 + - + -
17A LEU* 3.3 15.4 - - + -
153A ILE* 3.5 10.3 - - + +
154A PRO* 3.3 22.1 - - + +
186A PHE 3.0 17.2 + - - +
187A ASP* 3.7 7.4 - - - +
189A ALA* 1.3 74.4 - - - +
191A GLN* 1.3 72.3 + - + +
194A GLN* 2.7 47.8 + - + +
195A MET 3.5 10.7 + - - +
196A GLY* 3.5 9.4 - - - -
197A GLY* 3.5 34.3 - - - +
382A PRO* 6.3 2.0 - - + -
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Residues in contact with GLN 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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16A MET* 3.7 31.2 - - + +
187A ASP* 2.8 37.6 + - - +
188A ASP* 4.0 13.2 + - - +
190A TYR* 1.3 79.8 - - + +
192A LEU* 1.3 63.6 + - + +
194A GLN* 3.5 10.6 + - - -
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Residues in contact with LEU 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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169A ARG* 5.4 3.1 + - - -
176A GLU* 4.3 7.2 - - - +
180A LEU* 3.9 21.1 - - + -
188A ASP* 2.9 26.9 + - + +
191A GLN* 1.3 81.1 - - + +
193A HIS* 1.3 84.6 + - + +
194A GLN* 3.6 9.6 + - - +
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Residues in contact with HIS 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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169A ARG* 4.6 9.9 + - - +
170A ALA* 5.8 0.3 - - - -
173A LYS* 3.4 39.3 - - + +
176A GLU* 2.9 32.6 + - - +
177A ALA* 3.9 34.3 - - + -
180A LEU* 4.5 5.2 - - + -
189A ALA 2.9 12.9 + - - +
192A LEU* 1.3 99.2 + - + +
194A GLN* 1.4 79.1 + - - +
195A MET* 3.1 15.1 + - + +
278A ALA* 3.4 13.7 - - - +
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Residues in contact with GLN 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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153A ILE 4.6 1.6 - - - +
154A PRO* 3.6 35.7 - - + -
155A TYR* 3.4 31.5 + - + +
169A ARG* 6.0 2.4 - - - +
190A TYR* 2.7 35.5 + - + +
191A GLN 3.5 20.8 + - - -
192A LEU 3.6 9.4 + - - +
193A HIS* 1.4 79.9 - - - +
195A MET* 1.4 57.9 + - - +
196A GLY 3.7 3.3 + - - -
276A PRO* 4.2 13.7 - - - +
278A ALA* 3.4 17.7 + - + +
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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