Contacts of the helix formed by residues 184 - 194 (chain A) in PDB entry 3ETL
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 ASN 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A ALA* 3.5 2.1 - - - +
183A TYR* 1.3 82.5 - - - +
185A SER* 1.3 58.8 + - - +
186A ASP* 3.0 18.7 - - - +
187A MET* 2.7 52.0 - - - +
188A GLN* 2.9 28.6 + - - +
216A THR* 3.7 12.1 - - - +
220A GLU* 3.6 16.4 - - + +
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Residues in contact with SER 185 (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 ASN* 1.3 71.5 - - - +
186A ASP* 1.3 60.7 + - - +
188A GLN* 3.6 4.6 - - - +
189A MET* 2.9 30.0 + - - +
216A THR* 3.5 16.9 - - - -
217A PHE* 4.0 26.2 - - - -
220A GLU* 2.6 34.3 + - - -
221A PHE* 4.4 1.4 - - - -
233A LYS* 2.6 32.4 + - - +
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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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184A ASN* 3.0 12.7 + - - +
185A SER* 1.3 76.3 + - - +
187A MET* 1.3 58.6 + - + +
189A MET* 3.6 4.6 + - - +
190A LEU* 3.0 30.1 + - - +
220A GLU* 4.5 6.2 - - - +
233A LYS* 2.8 28.3 + - - +
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Residues in contact with MET 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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181A ARG 3.6 23.1 - - - +
182A ALA* 4.1 7.9 - - + -
183A TYR* 3.6 33.7 - - + +
184A ASN* 2.7 31.7 - - - +
186A ASP* 1.3 69.6 - - + +
188A GLN* 1.3 67.6 + - - +
190A LEU* 3.8 8.0 - - + +
191A PHE* 2.9 46.9 + - + -
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Residues in contact with GLN 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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148A ILE* 4.1 11.5 - - + +
150A THR* 3.6 19.9 + - - +
182A ALA* 3.8 12.9 - - + +
184A ASN 2.9 15.6 + - - +
185A SER 3.6 4.5 - - - +
187A MET* 1.3 78.2 - - - +
189A MET* 1.3 62.8 + - - +
191A PHE* 3.3 3.5 + - - +
192A ALA* 3.2 20.4 + - - +
210A ILE* 3.4 20.1 - - + +
212A SER 4.0 2.9 - - - +
213A LEU* 3.1 23.7 + - - +
216A THR* 2.8 27.7 + - - +
217A PHE* 3.9 6.5 - - - -
237A HIS* 2.8 32.9 + - + +
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Residues in contact with MET 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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185A SER 2.9 16.2 + - - +
186A ASP* 3.9 4.3 - - - +
188A GLN* 1.3 78.6 - - + +
190A LEU* 1.3 60.2 + - - +
192A ALA* 3.4 4.5 + - - +
193A GLU* 3.2 38.0 + - - +
217A PHE* 4.2 9.6 - - + -
233A LYS* 3.5 51.6 - - - +
236A ARG* 3.2 38.6 - - + +
237A HIS* 3.8 36.9 - - + +
240A THR* 6.0 0.9 - - - +
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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 ASP 3.0 20.2 + - - +
187A MET* 3.8 8.7 - - + +
189A MET* 1.3 73.0 - - - +
191A PHE* 1.3 70.5 + - + +
193A GLU* 3.1 19.3 + - + +
194A LYS* 2.9 53.2 + - + +
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Residues in contact with PHE 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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146A VAL* 5.7 0.3 - - - +
148A ILE* 3.6 21.9 - - + +
180A ALA* 3.6 31.4 - - + -
181A ARG 3.3 29.6 - - - -
182A ALA* 4.0 12.8 - - + -
187A MET* 2.9 40.7 + - + +
188A GLN 3.3 1.5 + - - +
190A LEU* 1.3 78.5 - - + +
192A ALA* 1.3 62.6 + - - +
194A LYS* 3.2 29.6 + - + +
195A ILE* 3.3 16.1 + - - +
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Residues in contact with ALA 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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148A ILE* 3.7 8.2 - - + +
188A GLN 3.2 10.2 + - - +
189A MET 3.6 9.0 - - - +
190A LEU 3.1 0.6 - - - -
191A PHE* 1.3 80.1 - - - +
193A GLU* 1.3 58.9 + - - +
194A LYS 3.5 0.3 + - - -
195A ILE* 3.6 26.8 + - + +
196A GLU* 4.9 1.4 + - - +
237A HIS* 3.9 21.5 - - + +
240A THR* 4.2 9.4 - - + +
241A LEU* 4.2 17.3 - - + -
244A LEU* 3.7 11.3 - - - +
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Residues in contact with GLU 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 MET* 3.2 32.6 + - - +
190A LEU* 3.1 27.1 + - + +
192A ALA* 1.3 76.8 - - - +
194A LYS* 1.3 60.9 + - - +
195A ILE 3.3 1.0 + - - -
196A GLU* 3.9 21.6 + - - +
197A ASP* 5.1 0.7 - - - +
236A ARG* 4.9 4.7 + - - -
240A THR* 4.3 23.9 + - + +
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Residues in contact with LYS 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* 2.9 47.5 + - + +
191A PHE* 3.6 21.4 - - + +
192A ALA 3.2 0.8 - - - -
193A GLU* 1.3 76.6 - - - +
195A ILE* 1.3 58.9 + - - +
196A GLU 3.0 2.9 - - - -
197A ASP* 2.9 44.6 + - + +
198A LEU* 3.6 6.5 + - - +
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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