Contacts of the helix formed by residues 190 - 195 (chain A) in PDB entry 5LUA
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 GLU 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A GLY 3.9 0.7 - - - +
150A SER* 3.6 26.5 + - - +
151A THR* 3.8 15.5 - - - +
188A ALA 3.5 0.4 + - - -
189A CYS* 1.3 86.4 - - - +
191A SER* 1.3 54.5 + - - +
192A GLY 3.2 2.7 - - - -
193A SER* 2.7 41.0 + - - +
194A MET* 4.2 0.9 + - - +
210A ALA* 4.2 0.4 - - - +
211A ASN 3.5 8.5 - - - -
212A PRO 3.2 22.9 - - - +
213A ARG* 4.3 2.7 - - - +
214A GLU* 2.8 40.2 + - - +
215A SER* 4.1 4.7 + - - -
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Residues in contact with SER 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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154A LEU* 5.5 0.2 - - - -
186A ILE* 2.9 35.6 + - - +
188A ALA* 3.0 28.4 + - - -
189A CYS 3.1 2.7 - - - -
190A GLU* 1.3 76.4 - - - +
192A GLY* 1.3 63.3 + - - +
194A MET* 3.1 25.9 + - - +
208A THR* 3.6 15.0 - - - +
209A ALA 3.9 0.4 - - - -
210A ALA* 3.6 20.6 - - - +
211A ASN 4.0 2.0 + - - -
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Residues in contact with GLY 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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190A GLU 3.1 1.0 + - - -
191A SER* 1.3 73.1 - - - +
193A SER* 1.3 55.9 + - - +
194A MET 3.1 0.4 - - - -
195A MET 3.0 4.3 + - - -
196A ASN* 2.9 30.8 + - - +
208A THR* 3.7 7.2 + - - -
210A ALA 2.9 22.5 + - - -
212A PRO* 3.7 12.6 - - - -
270A TYR* 3.6 20.2 + - - -
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Residues in contact with SER 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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150A SER 3.4 4.9 + - - -
151A THR* 3.5 13.3 - - - -
152A GLY* 2.8 32.0 + - - -
163A VAL* 3.9 14.2 - - - +
190A GLU* 2.7 21.0 + - - -
192A GLY* 1.3 75.5 - - - +
194A MET* 1.3 61.8 + - - +
195A MET 3.4 0.7 - - - -
196A ASN* 3.4 20.2 - - - +
197A HIS* 5.4 1.9 - - - -
212A PRO* 3.8 17.5 - - - +
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Residues in contact with MET 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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150A SER 5.4 0.2 - - - +
152A GLY* 3.4 7.9 - - - -
153A ILE 3.4 34.3 - - - +
154A LEU* 3.7 34.1 - - + -
161A LEU* 4.2 8.5 - - + +
162A HIS 4.3 0.7 - - - -
163A VAL* 3.6 45.4 - - + +
166A LEU* 3.8 24.7 - - + +
186A ILE* 4.2 17.0 - - + -
190A GLU 5.0 0.4 - - - +
191A SER* 3.1 14.9 + - - +
193A SER* 1.3 80.0 - - - +
195A MET* 1.3 69.7 + - - +
196A ASN 3.9 0.2 - - - -
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Residues in contact with MET 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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166A LEU* 4.0 13.9 - - + -
170A ILE* 4.2 6.3 - - + -
184A PHE* 3.6 41.1 - - + -
186A ILE* 3.7 22.4 - - + -
192A GLY 3.0 3.5 + - - +
194A MET* 1.3 87.7 - - - +
196A ASN* 1.3 57.1 + - - +
197A HIS 3.2 5.6 - - - -
198A LEU* 3.1 47.6 + - - +
206A ALA* 3.7 23.6 - - + -
208A THR* 4.2 7.2 - - + -
270A TYR* 3.4 34.2 - - + +
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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