Contacts of the helix formed by residues 179 - 188 (chain A) in PDB entry 1YQA
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 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A LEU* 1.3 77.5 - - - +
180A TYR* 1.3 55.3 + - - +
181A LYS* 3.7 12.9 + - - +
182A GLU* 3.0 33.7 + - + +
183A MET* 2.7 33.5 + - - +
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Residues in contact with TYR 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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178A LEU 4.5 1.8 - - - -
179A THR* 1.3 73.5 - - - +
181A LYS* 1.3 62.8 + - - +
183A MET* 3.3 28.6 + - + +
184A ILE* 3.2 27.8 + - + +
212A ILE* 5.7 4.0 - - + +
213A VAL* 4.5 5.9 - - + +
216A ALA* 5.0 6.1 - - - +
219A PHE* 3.2 42.1 - + + +
222A LEU* 3.4 49.9 - - + +
223A PHE* 4.6 1.6 - - + -
226A ALA* 3.8 17.7 - - + -
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Residues in contact with LYS 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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179A THR* 3.7 11.2 - - - +
180A TYR* 1.3 78.2 - - - +
182A GLU* 1.3 85.9 + - - +
184A ILE* 3.2 6.5 + - - +
185A LEU* 2.9 37.3 + - + +
226A ALA* 4.2 7.6 - - + +
229A LYS* 5.9 3.8 - - + -
230A CYS* 3.5 28.8 - - - +
233A ASN* 5.0 11.9 - - - +
235A GLU* 2.7 35.3 + - + +
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Residues in contact with GLU 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 LEU* 3.7 24.9 - - + +
179A THR* 3.0 33.0 + - + +
181A LYS* 1.3 106.3 + - - +
183A MET* 1.3 56.7 + - - +
185A LEU* 3.2 19.1 + - - +
186A LYS* 2.8 32.2 + - - +
235A GLU* 4.4 0.2 - - - +
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Residues in contact with MET 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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177A SER 4.7 0.7 - - - +
178A LEU* 3.2 32.3 - - + +
179A THR 2.7 17.4 + - - +
180A TYR* 3.4 31.0 - - + +
181A LYS 3.2 0.2 - - - -
182A GLU* 1.3 73.4 - - - +
184A ILE* 1.3 60.1 + - + +
187A SER* 2.8 24.5 + - - -
206A VAL* 4.7 9.2 - - + -
210A TYR* 3.2 49.0 + - + -
212A ILE* 3.6 30.7 - - + -
213A VAL* 3.5 25.1 - - + -
219A PHE* 5.3 0.7 - - - -
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Residues in contact with ILE 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 TYR 3.3 14.8 - - - +
181A LYS 3.2 6.6 + - - +
183A MET* 1.3 72.2 - - + +
185A LEU* 1.3 59.2 + - - +
186A LYS 3.0 1.8 - - - -
187A SER* 3.0 6.8 + - - -
188A MET* 2.7 52.9 + - + +
202A LEU* 3.5 15.7 - - + -
206A VAL* 4.6 4.7 - - + -
223A PHE* 3.6 35.2 - - + -
226A ALA* 4.3 11.7 - - + -
227A ILE* 3.8 23.6 - - + -
230A CYS* 5.0 1.1 - - - -
236A LEU* 3.4 28.3 - - + -
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Residues in contact with LEU 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 LYS* 2.9 29.6 + - + +
182A GLU* 3.2 37.4 + - - +
184A ILE* 1.3 75.7 - - - +
186A LYS* 1.3 56.8 - - - +
189A PRO* 3.0 22.0 - - - +
235A GLU* 3.5 46.0 - - + +
236A LEU* 3.8 20.4 - - + -
248A LEU* 3.9 17.0 - - + +
250A LYS* 5.3 21.4 - - + +
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Residues in contact with LYS 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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172A ALA* 3.9 23.3 - - - +
173A SER 3.3 23.1 + - - -
174A SER* 4.2 5.8 - - - +
175A PRO* 3.5 27.8 - - + -
178A LEU* 4.6 4.3 - - + -
182A GLU 2.8 12.2 + - - +
185A LEU* 1.3 78.5 - - - +
187A SER* 1.3 60.8 + - - +
189A PRO* 3.3 3.4 - - + +
190A GLN* 2.9 33.9 + - - +
210A TYR* 3.3 17.5 - - - +
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Residues in contact with SER 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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174A SER* 4.8 7.4 - - - -
183A MET 2.8 19.2 + - - -
184A ILE* 3.0 15.8 + - - -
186A LYS* 1.3 75.9 - - - +
188A MET* 1.3 64.2 + - - +
190A GLN* 3.0 21.2 + - - +
191A LEU* 3.0 16.3 + - - +
202A LEU* 3.7 14.4 - - - +
205A TYR* 3.6 24.9 - - - -
206A VAL* 3.7 8.5 - - - +
210A TYR* 4.8 3.1 - - - -
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Residues in contact with MET 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 ILE* 2.7 42.6 + - + +
187A SER* 1.3 72.0 + - - +
189A PRO* 1.4 64.2 - - + +
191A LEU* 2.9 35.4 + - + +
194A GLY* 3.1 6.7 - - - -
196A GLY* 4.4 5.6 - - - +
197A SER* 3.1 31.2 - - - +
202A LEU* 4.5 4.5 - - + -
236A LEU* 3.7 9.2 - - + -
246A ILE* 3.4 39.3 - - - +
247A LYS 3.8 0.4 - - - -
248A LEU* 3.5 33.0 - - + +
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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