Contacts of the helix formed by residues 185 - 192 (chain A) in PDB entry 4LXZ
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 GLY 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A HIS* 3.5 11.9 - - - -
177A TYR* 4.7 4.8 - - - -
179A ASP* 3.2 24.4 + - - -
183A HIS 3.5 1.6 + - - -
184A HIS* 1.3 72.5 + - - +
186A ASP* 1.3 57.5 + - - -
187A GLY 3.5 2.2 - - - -
188A VAL* 3.6 5.6 + - - +
189A GLU* 3.0 29.3 + - - +
200A THR* 5.8 0.2 - - - -
202A SER* 3.3 15.7 + - - -
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Residues in contact with ASP 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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146A HIS* 2.6 34.3 + - - +
148A LYS* 2.8 27.1 + - - +
153A SER* 4.9 1.0 + - - -
184A HIS* 2.9 18.4 + - + +
185A GLY* 1.3 69.3 - - - +
187A GLY* 1.3 62.0 + - - -
189A GLU* 3.4 1.8 + - - +
190A GLU* 2.8 37.0 + - - +
211A PRO* 3.7 19.5 - - - +
213A THR* 3.4 25.3 + - + +
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Residues in contact with GLY 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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72A TYR* 4.0 5.4 + - - -
145A HIS 3.0 13.9 + - - -
146A HIS 4.1 0.9 - - - -
147A ALA 3.9 14.4 - - - -
148A LYS* 4.0 15.0 - - - -
159A ASN* 3.8 6.1 - - - -
162A VAL* 4.1 0.9 - - - +
186A ASP* 1.3 85.3 + - - +
188A VAL* 1.3 56.0 + - - +
190A GLU* 3.7 1.9 - - - +
191A ALA* 3.1 28.4 + - - +
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Residues in contact with VAL 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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145A HIS* 3.4 14.6 + - + +
159A ASN* 3.9 12.1 - - - +
161A ILE* 3.8 29.4 - - + -
162A VAL* 3.9 7.6 - - + -
165A ILE* 3.8 25.6 - - + -
177A TYR* 3.6 36.6 - - + +
185A GLY 3.6 2.0 + - - +
186A ASP 3.3 0.2 - - - -
187A GLY* 1.3 70.8 - - - +
189A GLU* 1.4 66.0 + - - +
190A GLU 3.4 0.2 + - - -
191A ALA 3.4 1.4 + - - -
192A PHE* 3.3 34.9 + - + +
200A THR* 4.0 6.5 - - + +
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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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184A HIS* 2.8 29.3 + - - +
185A GLY 3.0 19.6 + - - +
186A ASP 3.7 3.2 - - - +
188A VAL* 1.4 75.5 - - - +
190A GLU* 1.3 55.7 + - - +
192A PHE 3.4 1.6 + - - -
193A TYR* 2.9 61.3 + - + +
200A THR* 3.8 27.6 + - - +
202A SER* 5.5 0.3 - - - -
213A THR* 5.4 1.0 - - - -
218A ASP* 4.5 7.3 - - - +
228A ALA* 4.2 5.0 - - + +
229A VAL 4.9 1.2 - - - +
230A ASN* 2.8 32.2 + - - +
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Residues in contact with GLU 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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72A TYR* 4.5 6.1 + - - +
148A LYS* 3.5 37.7 - - - +
149A LYS* 5.0 2.8 + - - +
186A ASP 2.8 22.5 + - - +
187A GLY* 3.7 4.7 - - - +
189A GLU* 1.3 73.2 - - - +
191A ALA* 1.3 64.1 + - - +
192A PHE 3.2 1.0 + - - -
193A TYR* 3.3 19.6 + - - +
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Residues in contact with ALA 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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72A TYR* 3.6 37.2 + - + +
162A VAL* 3.7 23.1 - - + -
187A GLY 3.1 13.7 + - - +
188A VAL 3.4 2.9 + - - +
190A GLU* 1.3 77.2 - - - +
192A PHE* 1.4 62.0 + - + +
193A TYR 4.0 0.2 + - - -
194A THR* 5.4 0.9 + - - -
195A THR* 5.2 0.2 - - - +
404A PG4 3.1 24.5 - - - +
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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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162A VAL* 3.8 37.0 - - + -
165A ILE* 3.7 37.9 - - + -
166A LEU* 3.9 14.1 - - + -
169A LEU* 4.0 2.0 - - + -
188A VAL* 3.3 26.7 + - + +
189A GLU 3.5 3.4 - - - +
190A GLU 3.2 0.6 - - - -
191A ALA* 1.4 77.6 - - - +
193A TYR* 1.3 58.3 + - - +
194A THR 3.2 3.1 - - - -
195A THR* 3.2 16.3 + - + +
198A VAL* 3.7 42.2 - - + -
200A THR* 4.6 3.1 - - + -
403A NA 2.4 29.8 - - - -
404A PG4 3.7 34.5 - - - -
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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