Contacts of the helix formed by residues 177 - 191 (chain A) in PDB entry 5E2Q
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 THR 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A LEU* 3.8 11.9 - - - +
164A GLY* 4.3 18.8 - - - +
165A LYS* 6.4 1.3 - - + -
175A ASN 4.4 6.1 - - - +
176A CYS* 1.3 80.3 - - - +
178A MET* 1.3 66.4 + - - +
179A GLU* 3.6 19.2 + - - +
180A ASP* 2.7 31.8 + - - +
181A ALA 3.1 9.4 + - - -
202A LYS* 5.6 0.7 - - - +
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Residues in contact with MET 178 (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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163A LEU* 3.8 32.7 - - + +
164A GLY 5.3 0.2 - - - +
177A THR* 1.3 75.5 - - - +
179A GLU* 1.3 67.0 + - + +
181A ALA* 3.2 1.4 + - - +
182A LYS* 2.9 30.6 + - + +
321A PRO* 4.0 8.3 - - + +
322A PHE* 3.8 23.8 - - + -
501A THR* 3.8 31.6 - - + -
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Residues in contact with GLU 179 (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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177A THR* 3.8 13.2 - - - +
178A MET* 1.3 88.5 - - + +
180A ASP* 1.3 62.9 + - - +
182A LYS* 3.4 7.1 + - - +
183A LEU* 3.1 23.6 + - - +
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Residues in contact with ASP 180 (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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175A ASN 3.8 0.2 - - - +
176A CYS* 3.3 10.9 - - + -
177A THR* 2.7 38.5 + - - +
179A GLU* 1.3 78.5 - - - +
181A ALA* 1.3 56.7 + - - +
183A LEU* 3.4 5.2 + - - +
184A ALA* 3.0 29.8 + - - +
200A LEU* 3.9 5.1 - - + +
202A LYS* 3.1 31.9 + - - -
212A TYR* 2.7 37.6 + - + -
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Residues in contact with ALA 181 (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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163A LEU* 3.8 24.2 - - + -
172A PHE* 3.8 23.3 - - + -
177A THR 3.1 4.9 + - - -
178A MET 3.2 6.3 + - - +
180A ASP* 1.3 76.9 - - - +
182A LYS* 1.3 57.3 + - - +
184A ALA* 3.5 4.2 + - - +
185A GLN* 3.1 28.2 + - - +
200A LEU* 4.7 0.2 - - - +
322A PHE* 3.5 29.2 - - + -
325A ARG* 4.8 2.9 + - - +
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Residues in contact with LYS 182 (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 MET* 2.9 17.8 + - + +
179A GLU* 3.7 8.1 - - - +
180A ASP 3.2 0.2 - - - -
181A ALA* 1.3 75.1 - - - +
183A LEU* 1.3 64.3 + - - +
185A GLN* 3.2 3.7 + - - +
186A ASP* 3.1 44.6 + - - +
322A PHE* 3.9 22.7 - - + -
497A SER 4.3 16.0 + - - -
498A LYS 5.5 3.0 + - - -
500A SER* 5.6 2.6 - - - -
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Residues in contact with LEU 183 (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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179A GLU 3.1 16.8 + - - +
180A ASP* 3.4 5.4 + - - +
182A LYS* 1.3 75.6 - - - +
184A ALA* 1.3 61.8 + - - +
186A ASP* 3.4 6.0 + - - +
187A PHE* 3.1 20.6 + - - +
212A TYR* 4.0 25.6 - - + +
239A PHE* 3.7 25.6 - - + +
240A ARG* 3.9 23.3 - - + +
242A SER* 3.9 25.4 - - - +
244A PHE* 4.0 9.2 - - + -
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Residues in contact with ALA 184 (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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180A ASP 3.0 17.1 + - - +
181A ALA 3.7 4.9 - - - +
182A LYS 3.2 0.2 - - - -
183A LEU* 1.3 78.4 - - - +
185A GLN* 1.3 57.9 + - - +
187A PHE* 3.1 4.0 + - - +
188A LEU* 2.8 36.5 + - + +
200A LEU* 3.6 31.9 - - + -
214A VAL* 5.4 0.7 - - + -
244A PHE* 3.9 14.8 - - + -
325A ARG* 3.9 13.0 - - - +
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Residues in contact with GLN 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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181A ALA 3.1 17.5 + - - +
182A LYS* 3.2 6.5 + - - +
184A ALA* 1.3 76.9 - - - +
186A ASP* 1.3 60.0 + - - +
188A LEU* 4.1 10.9 - - - +
189A ASP* 2.9 57.4 + - - +
193A LEU 5.7 0.4 + - - -
195A ALA* 4.0 14.6 - - - +
322A PHE* 3.5 25.9 - - + -
324A SER* 2.9 31.8 + - - -
325A ARG* 4.4 3.1 + - - +
494A THR* 5.2 0.8 + - - -
497A SER* 3.3 29.1 - - - +
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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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182A LYS* 3.1 48.4 + - - +
183A LEU* 3.7 4.6 - - - +
185A GLN* 1.3 76.0 - - - +
187A PHE* 1.3 62.8 + - - +
189A ASP* 3.7 9.6 + - - +
190A SER* 3.1 26.0 + - - -
239A PHE* 3.4 9.8 - - + -
240A ARG* 2.8 38.6 + - - +
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Residues in contact with PHE 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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183A LEU 3.1 12.0 + - - +
184A ALA 3.1 8.0 + - - +
186A ASP* 1.3 76.4 - - - +
188A LEU* 1.3 78.4 + - + +
190A SER* 2.5 19.8 + - - -
191A GLN* 3.2 36.0 + - + +
193A LEU* 5.5 0.9 - - + -
214A VAL* 4.2 7.9 - - + -
237A TYR* 3.7 49.1 - + + -
238A GLU 5.9 0.2 - - - -
239A PHE* 3.5 36.0 - + + -
244A PHE* 3.5 35.0 - + + -
246A VAL* 4.2 16.8 - - + -
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Residues in contact with LEU 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* 2.8 24.0 + - + +
185A GLN* 3.8 18.4 - - - +
187A PHE* 1.3 87.0 - - + +
189A ASP* 1.3 60.6 + - - +
191A GLN* 3.3 1.5 + - - -
192A ASN 3.1 3.5 + - - -
193A LEU* 2.9 63.8 + - + +
194A SER 5.0 1.8 - - - +
195A ALA* 3.7 31.4 - - + -
198A THR* 4.4 4.7 - - - +
214A VAL* 3.9 27.4 - - + -
325A ARG* 4.3 15.3 - - - +
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Residues in contact with ASP 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 GLN* 2.9 43.1 + - - +
186A ASP* 4.0 9.8 - - - +
188A LEU* 1.3 77.0 - - - +
190A SER* 1.3 62.4 + - - +
192A ASN* 3.3 12.0 + - - +
193A LEU 5.4 1.0 - - - +
491A CYS 4.4 4.4 - - - +
492A GLY* 3.2 38.8 - - - +
493A GLU* 4.5 10.6 - - + +
494A THR* 5.3 0.2 + - - -
497A SER* 3.4 24.3 + - - +
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Residues in contact with SER 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 3.1 16.5 + - - -
187A PHE* 2.5 26.5 + - - -
189A ASP* 1.3 76.9 - - - +
191A GLN* 1.3 68.9 + - - +
192A ASN* 3.3 1.2 + - - +
239A PHE* 3.5 17.7 - - - -
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Residues in contact with GLN 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 PHE* 3.2 41.0 + - + +
188A LEU* 3.3 3.5 + - - +
189A ASP 3.3 0.2 - - - -
190A SER* 1.3 83.3 + - - +
192A ASN* 1.3 69.4 + - - +
193A LEU* 3.1 12.2 + - + -
233A LYS* 3.4 19.0 + - - +
237A TYR* 3.5 35.3 + - + +
239A PHE* 5.9 1.6 - - - -
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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