Contacts of the helix formed by residues 187 - 195 (chain A) in PDB entry 1LWT
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 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ASN* 1.3 81.2 - - - +
188A HIS* 1.3 58.9 + - - +
189A PHE 3.0 3.6 - - - -
190A PHE* 2.6 56.5 + - - +
191A ASP* 2.7 29.6 + - - +
310A ASP* 3.1 4.7 - - - -
311A ASN* 3.5 24.4 + - - +
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Residues in contact with HIS 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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186A ASN* 4.1 7.3 - - + +
187A ASP* 1.3 76.4 - - - +
189A PHE* 1.3 64.9 + - - +
191A ASP* 4.2 8.8 + - - -
192A TYR* 2.8 31.7 + + + +
293A LEU* 3.9 24.4 - - + +
306A PHE* 3.7 38.6 - + + +
310A ASP* 2.8 8.7 + - - +
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Residues in contact with PHE 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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187A ASP 3.0 0.8 - - - -
188A HIS* 1.3 81.1 + - - +
190A PHE* 1.3 59.1 + - + +
192A TYR* 3.3 5.1 - - - +
193A MSE 3.0 32.9 + - + +
205A PRO* 3.0 45.8 - - + -
208A LEU* 3.7 26.7 - - + -
209A ALA* 3.7 13.7 - - + -
212A LEU* 3.8 19.1 - - + -
293A LEU* 3.9 21.5 - - + -
295A PHE* 5.8 2.7 - + - -
306A PHE* 4.2 14.5 - + + -
307A LEU* 5.5 2.2 - - + -
310A ASP* 3.2 19.3 + - - +
311A ASN* 6.1 0.2 - - + -
314A THR* 3.6 29.2 - - + +
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Residues in contact with PHE 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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187A ASP* 2.6 38.0 + - - +
189A PHE* 1.3 77.4 - - + +
191A ASP* 1.3 85.1 + - - +
193A MSE 3.0 8.9 + - - +
194A GLN* 2.9 69.7 + - + +
205A PRO* 4.7 17.0 - - + -
310A ASP* 4.5 0.4 + - - -
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Residues in contact with ASP 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 ASP* 2.7 33.9 + - - +
188A HIS* 4.1 6.5 + - - +
190A PHE* 1.3 94.2 - - - +
192A TYR* 1.3 62.9 + - - +
194A GLN* 3.3 3.9 + - - +
195A LYS* 2.7 25.6 + - - +
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Residues in contact with TYR 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 HIS* 2.8 26.3 + + + +
189A PHE 3.3 4.5 - - - +
191A ASP* 1.3 75.8 - - - +
193A MSE 1.3 67.7 + - + +
195A LYS* 2.6 64.7 + - + +
196A SER* 3.4 14.9 + - - -
208A LEU* 5.8 1.6 - - + -
288A ASP* 2.5 40.0 + - - -
289A ALA* 4.2 11.2 - - + -
292A GLY* 3.3 19.3 - - - -
293A LEU* 3.2 42.8 - - + -
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Residues in contact with MSE 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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189A PHE* 3.0 19.0 + - + +
190A PHE* 3.0 9.8 + - - +
192A TYR* 1.3 89.9 - - + +
194A GLN* 1.3 66.1 + - + +
196A SER* 3.3 16.2 + - - +
198A PHE 4.3 7.1 - - - +
199A HIS* 5.5 0.2 + - - -
200A LEU* 4.8 15.5 - - + -
204A GLY* 3.3 28.5 - - - -
205A PRO* 3.1 38.1 - - + -
208A LEU* 3.2 37.5 - - + -
285A PRO* 6.1 0.4 - - + -
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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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190A PHE* 2.9 61.6 + - + +
191A ASP* 3.6 5.6 - - - +
193A MSE 1.3 78.7 - - - +
195A LYS* 1.3 58.2 + - - +
196A SER 2.8 15.1 + - - +
199A HIS* 3.8 20.8 - - + -
205A PRO* 5.8 3.2 - - - +
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Residues in contact with LYS 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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191A ASP 2.7 15.1 + - - +
192A TYR* 2.6 53.1 + - + +
194A GLN* 1.3 69.8 - - - +
196A SER* 1.3 68.9 + - - -
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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