Contacts of the helix formed by residues 181 - 196 (chain A) in PDB entry 5Y36
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 VAL 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ASN* 3.1 36.8 + - - +
179A SER 4.2 0.2 - - - -
180A ASP* 1.3 70.8 - - - +
182A ASP* 1.4 66.2 + - - +
183A LYS 3.3 0.4 - - - -
184A LEU* 3.1 26.4 + - - +
185A PHE* 3.9 23.7 - - + -
209A LYS* 4.2 23.3 - - + +
296A LEU* 4.6 3.6 - - + -
299A ALA* 4.0 33.0 - - + +
300A ILE* 5.2 2.5 - - + +
303A SER* 5.1 5.2 - - - -
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Residues in contact with ASP 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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180A ASP* 3.6 5.3 - - - +
181A VAL* 1.4 73.9 - - - +
183A LYS* 1.3 62.3 + - - +
184A LEU 3.3 0.7 + - - -
185A PHE* 3.4 16.4 + - - +
186A ILE* 3.6 20.0 + - + +
209A LYS* 2.7 43.3 + - - +
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Residues in contact with LYS 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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180A ASP* 3.4 35.9 + - + +
182A ASP* 1.3 77.4 - - - +
184A LEU* 1.3 60.6 + - + +
186A ILE* 3.3 11.1 + - - +
187A GLN* 2.9 58.9 + - + +
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Residues in contact with LEU 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 4.4 7.9 - - - +
181A VAL* 3.1 17.0 + - - +
183A LYS* 1.3 79.6 - - + +
185A PHE* 1.4 57.3 + - - +
187A GLN* 4.0 5.9 - - + +
188A LEU* 3.1 37.7 + - + +
292A ALA* 4.7 21.6 - - + +
295A ASN* 4.4 11.0 - - + +
296A LEU* 3.8 42.2 - - + +
299A ALA* 4.0 15.7 - - + -
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Residues in contact with PHE 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 VAL* 3.9 16.8 - - + -
182A ASP* 3.8 7.6 - - - +
183A LYS 3.4 0.6 - - - -
184A LEU* 1.4 75.0 - - - +
186A ILE* 1.4 64.9 + - + +
188A LEU* 3.7 7.0 + - + +
189A VAL* 3.4 27.5 + - - +
208A ALA* 3.7 23.8 - - + -
209A LYS* 3.4 35.2 - - + -
212A LEU* 3.8 30.7 - - + -
225A LEU* 6.1 1.6 - - + -
296A LEU* 3.7 38.4 - - + -
300A ILE* 3.9 8.7 - - + -
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Residues in contact with ILE 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 ASP* 3.6 17.9 + - + +
183A LYS* 3.3 11.3 + - + +
185A PHE* 1.4 75.5 - - + +
187A GLN* 1.4 63.3 + - - +
189A VAL* 3.3 7.2 + - - +
190A GLN* 2.9 54.7 + - + +
203A ALA* 6.1 4.7 - - + -
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Residues in contact with GLN 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 LYS* 2.9 47.2 + - + +
184A LEU* 4.0 8.3 - - + +
186A ILE* 1.4 80.9 - - - +
188A LEU* 1.3 54.5 + - + +
190A GLN* 3.2 24.8 + - - +
191A THR* 2.6 44.0 + - - +
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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 LEU 3.1 19.6 + - - +
185A PHE* 4.0 7.2 - - + +
186A ILE 3.4 0.2 - - - -
187A GLN* 1.3 74.0 - - - +
189A VAL* 1.4 59.9 + - + +
191A THR* 4.5 0.7 - - - -
192A TYR* 3.0 30.5 + - - +
238A PHE* 5.2 6.9 - - + -
241A LEU* 6.4 1.3 - - + -
289A LEU* 3.7 37.8 - - + +
292A ALA* 3.6 28.0 - - + -
293A ALA* 4.2 8.7 - - + +
296A LEU* 3.4 36.8 - - + -
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Residues in contact with VAL 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 PHE 3.4 13.9 + - - +
186A ILE* 3.3 9.7 + - - +
188A LEU* 1.4 77.2 - - + +
190A GLN* 1.4 58.7 + - + +
192A TYR* 3.5 5.0 + - - +
193A ASN* 3.0 36.9 + - - +
201A ILE* 3.5 33.9 - - + +
203A ALA* 4.5 21.5 - - + +
229A LEU* 4.9 9.6 - - + -
238A PHE* 4.1 28.0 - - + -
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Residues in contact with GLN 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 ILE* 2.9 34.6 + - + +
187A GLN* 3.2 31.1 + - - +
189A VAL* 1.4 74.5 - - + +
191A THR* 1.3 59.3 + - - +
193A ASN* 3.3 10.1 + - - +
194A GLN* 2.9 43.8 + - - +
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Residues in contact with THR 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 GLN* 2.6 35.5 + - - +
188A LEU* 4.5 0.4 - - - -
190A GLN* 1.3 70.3 - - - +
192A TYR* 1.3 62.4 + - - +
194A GLN* 3.4 13.0 + - - +
195A LEU* 3.0 34.7 + - + +
285A GLN 5.5 0.7 - - - +
288A ASP* 4.2 25.1 + - + +
289A LEU* 3.6 30.5 - - + +
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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 LEU 3.0 19.2 + - - +
189A VAL* 3.6 6.1 - - - +
191A THR* 1.3 76.3 - - - +
193A ASN* 1.3 61.3 + - - +
195A LEU 3.3 0.7 + - - -
196A PHE* 2.7 78.8 + + + +
199A ASN 4.5 10.2 + - - -
201A ILE* 3.6 30.5 - - + +
231A GLY 5.1 1.6 + - - -
232A GLU* 3.5 22.9 + - - +
237A LEU* 3.9 21.7 - - + +
238A PHE* 4.2 24.2 - + + -
241A LEU* 4.8 9.6 - - + -
289A LEU* 4.0 11.6 - - + +
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Residues in contact with ASN 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 VAL* 3.0 27.0 + - - +
190A GLN* 3.3 10.0 + - - +
192A TYR* 1.3 81.4 - - - +
194A GLN* 1.3 60.1 + - + +
196A PHE 3.5 19.8 - - - +
197A GLU* 3.6 12.0 - - - +
200A PRO* 3.3 19.5 - - + +
201A ILE* 2.7 47.1 + - - +
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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 GLN* 2.9 31.6 + - + +
191A THR* 3.7 11.8 + - - +
193A ASN* 1.3 73.4 - - + +
195A LEU* 1.3 61.8 + - + +
197A GLU* 3.8 20.5 - - - +
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Residues in contact with LEU 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 THR* 3.0 27.3 + - + +
194A GLN* 1.3 76.8 - - + +
196A PHE* 1.3 78.0 + - + +
197A GLU* 3.9 2.1 + - - +
285A GLN* 3.5 46.4 - - + +
286A TYR* 3.7 25.3 + - + +
289A LEU* 3.7 30.1 - - + -
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Residues in contact with PHE 196 (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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192A TYR* 2.7 62.0 + + + +
193A ASN* 3.5 11.2 - - - +
195A LEU* 1.3 87.9 - - + +
197A GLU* 1.4 59.7 + - - +
198A GLU* 3.2 13.9 + - + +
199A ASN 3.8 9.9 + - - +
200A PRO* 4.1 8.1 - - - +
237A LEU* 3.5 31.9 - - + -
256A PHE* 5.7 4.9 - + - -
286A TYR* 4.0 25.8 - + - -
289A LEU* 4.7 9.4 - - + -
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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