Contacts of the helix formed by residues 185 - 194 (chain A) in PDB entry 4LIR
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 SER 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A PHE* 4.5 3.4 - - - -
182A PRO* 3.0 26.5 + - - +
184A ALA* 1.3 78.8 - - - +
186A ALA* 1.3 56.2 + - - +
187A SER 3.4 2.2 - - - -
188A TYR* 3.2 14.5 + - - +
189A ILE* 3.0 30.4 + - - +
236A ILE* 3.5 31.5 - - - +
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Residues in contact with ALA 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 PHE* 4.0 26.2 - - + -
182A PRO 3.6 2.4 + - - -
183A GLN* 3.1 17.7 + - - +
184A ALA 3.5 0.4 - - - -
185A SER* 1.3 75.2 - - - +
187A SER* 1.3 58.2 + - - +
189A ILE 3.5 0.6 + - - +
190A LEU* 3.0 24.6 + - - +
204A MSE 4.4 15.3 - - + -
211A MSE 3.3 15.8 - - + +
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Residues in contact with SER 187 (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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184A ALA 5.1 4.6 + - - -
185A SER 3.4 0.4 - - - -
186A ALA* 1.3 76.0 - - - +
188A TYR* 1.4 59.7 + - - +
190A LEU* 3.5 8.6 + - - +
191A LEU* 3.1 31.1 + - - +
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Residues in contact with TYR 188 (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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184A ALA 5.8 0.4 - - - +
185A SER* 3.2 15.6 + - - +
187A SER* 1.4 79.5 + - - +
189A ILE* 1.4 80.1 - - + +
191A LEU* 3.4 12.1 + - + +
192A GLN* 3.0 57.9 + - - +
232A PHE* 4.2 15.2 - - + +
233A GLY* 3.7 23.0 + - - -
236A ILE* 4.8 11.7 - - + -
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Residues in contact with ILE 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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178A VAL* 3.6 30.5 - - + -
181A PHE* 3.8 32.8 - - + -
185A SER* 3.0 21.4 + - - +
186A ALA 4.0 3.6 - - - +
188A TYR* 1.4 94.7 - - + +
190A LEU* 1.4 60.0 + - - +
192A GLN* 3.3 3.5 + - + +
193A PHE* 2.9 41.8 + - + -
211A MSE 4.5 5.2 - - + -
232A PHE* 4.3 14.8 - - + -
236A ILE* 4.5 8.1 - - + -
238A ILE* 3.9 21.8 - - + -
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Residues in contact with LEU 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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186A ALA 3.0 18.2 + - - +
187A SER* 3.9 8.5 - - - +
189A ILE* 1.4 74.7 - - - +
191A LEU* 1.4 58.9 + - - +
193A PHE* 3.2 4.2 + - - -
194A ALA* 3.0 26.0 + - + +
199A ILE* 3.8 21.8 - - + -
202A HIS* 3.5 55.4 - - + +
211A MSE 4.0 21.3 - - + +
213A ILE* 4.1 4.0 - - + -
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Residues in contact with LEU 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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187A SER 3.1 19.0 + - - +
188A TYR* 3.7 11.2 - - + +
190A LEU* 1.4 72.0 - - - +
192A GLN* 1.3 68.1 + - - +
194A ALA* 3.3 23.6 + - + +
195A GLN* 3.8 12.7 + - - +
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Residues in contact with GLN 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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188A TYR* 3.0 46.3 + - + +
189A ILE* 3.4 9.6 - - - +
191A LEU* 1.3 81.7 - - - +
193A PHE* 1.3 62.0 + - + +
195A GLN* 3.3 46.4 + - - +
196A TYR* 3.6 11.0 + - - +
232A PHE* 3.4 39.7 - - + -
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Residues in contact with PHE 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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178A VAL* 3.8 33.9 - - + -
189A ILE* 2.9 35.6 + - + +
190A LEU 3.2 2.8 + - - +
192A GLN* 1.3 75.3 - - + +
194A ALA* 1.4 58.4 + - - +
195A GLN 3.1 5.6 + - - -
196A TYR* 3.3 26.7 + + - -
199A ILE* 3.9 2.7 - - - -
213A ILE* 3.8 16.6 - - + -
215A TYR* 2.7 40.1 + - - +
224A ALA* 3.8 14.8 - - + -
227A LYS* 4.2 1.6 - - + -
232A PHE* 3.9 23.8 - + - -
238A ILE* 3.7 26.5 - - + -
240A VAL* 3.7 16.6 - - + -
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Residues in contact with ALA 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 LEU* 3.0 13.5 + - + +
191A LEU* 3.5 20.4 - - + +
192A GLN 3.3 0.8 - - - -
193A PHE* 1.4 75.1 - - - +
195A GLN* 1.3 59.0 + - + +
196A TYR 3.3 0.4 - - - -
197A GLY 3.0 20.3 + - - +
199A ILE* 3.7 17.5 - - + +
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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