Contacts of the helix formed by residues 184 - 200 (chain A) in PDB entry 1YCH
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 ASP 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A VAL* 1.3 78.7 - - - +
185A ALA* 1.3 66.8 + - - +
186A GLY* 3.1 19.8 + - - -
187A LEU* 3.0 44.2 - - + +
188A ILE* 3.1 20.1 + - - +
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Residues in contact with ALA 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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180A ASP 5.8 1.1 - - - -
183A VAL 3.3 4.9 + - - -
184A ASP* 1.3 74.5 + - - +
186A GLY* 1.3 62.9 + - - +
188A ILE* 3.6 7.9 - - - +
189A MET* 3.1 28.3 + - + +
238A ARG* 3.5 29.2 - - - +
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Residues in contact with GLY 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 ASP* 3.1 9.8 + - - -
185A ALA* 1.3 77.9 - - - +
187A LEU* 1.3 66.5 + - - +
189A MET* 3.7 4.9 + - - +
190A ASP* 3.2 23.6 + - - +
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Residues in contact with LEU 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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33A ARG* 4.8 21.3 - - - +
173A ILE* 6.1 0.2 - - - -
183A VAL* 5.6 2.0 - - + -
184A ASP* 3.0 38.9 + - + +
186A GLY* 1.3 76.0 - - - +
188A ILE* 1.3 66.1 + - - +
190A ASP* 3.3 6.4 + - - +
191A GLU* 3.2 28.3 + - - +
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Residues in contact with ILE 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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171A GLN* 3.7 30.3 - - + +
173A ILE* 3.8 29.8 - - + -
180A ASP* 5.5 4.7 - - + +
183A VAL* 3.6 29.4 - - + +
184A ASP 3.1 9.6 + - - +
185A ALA* 3.6 13.7 - - - +
187A LEU* 1.3 74.8 - - - +
189A MET* 1.3 66.3 + - + +
191A GLU* 3.4 5.3 + - + +
192A ALA* 3.0 26.2 + - - +
230A ILE* 4.1 15.7 - - + -
232A TRP* 3.8 24.2 - - + -
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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 ALA 3.1 16.6 + - - +
186A GLY* 4.1 6.1 - - - +
188A ILE* 1.3 83.3 - - + +
190A ASP* 1.3 58.7 + - - +
192A ALA* 3.4 9.6 - - - +
193A ALA* 3.1 24.3 + - - +
232A TRP* 4.5 15.7 - - + -
238A ARG* 4.0 41.5 - - + +
239A ILE* 4.5 4.5 - - - +
242A ALA* 4.1 11.9 - - - -
245A ARG* 5.4 4.3 - - - +
246A TRP* 4.0 23.1 - - + -
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Residues in contact with ASP 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 GLY 3.2 18.5 + - - +
187A LEU* 3.6 8.1 - - - +
188A ILE 3.2 0.6 - - - -
189A MET* 1.3 76.5 - - - +
191A GLU* 1.3 63.0 + - + +
193A ALA* 3.1 8.4 + - - +
194A LYS* 3.0 26.7 + - - +
299A LYS* 2.8 37.7 + - - +
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Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PHE* 5.6 0.9 - - - -
32A HIS* 5.8 2.1 - - - +
33A ARG* 3.5 31.9 + - - +
171A GLN* 4.0 16.9 - - + +
172A HIS 4.2 17.8 + - - +
173A ILE* 4.6 16.8 - - + -
187A LEU 3.2 18.7 + - - +
188A ILE* 3.7 8.5 - - + +
189A MET 3.3 0.2 - - - -
190A ASP* 1.3 78.4 - - + +
192A ALA* 1.3 64.5 + - - +
194A LYS* 3.2 23.8 + - - +
195A TYR* 3.0 23.9 + - - +
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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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169A PHE 5.7 0.7 - - - +
170A GLY 4.3 3.5 - - - +
171A GLN* 3.9 19.9 - - + +
188A ILE 3.0 17.8 + - - +
189A MET* 3.4 11.9 - - - +
191A GLU* 1.3 79.9 - - - +
193A ALA* 1.3 56.4 + - - +
195A TYR* 3.3 5.8 - - - +
196A TYR* 3.0 27.4 + - - +
232A TRP* 4.6 4.0 - - + -
239A ILE* 4.4 22.4 - - + -
243A TYR* 5.0 3.1 + - + -
246A TRP* 4.2 6.0 - - + -
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Residues in contact with ALA 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 3.1 13.0 + - - +
190A ASP* 3.1 13.5 + - - +
192A ALA* 1.3 75.1 - - - +
194A LYS* 1.3 59.1 + - - +
195A TYR 3.1 1.6 - - - -
196A TYR* 4.4 1.1 - - - +
197A ALA* 2.9 32.6 + - - +
246A TRP* 3.6 26.9 - - + -
299A LYS* 4.3 11.1 - - + +
302A LEU* 3.9 11.1 - - + +
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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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29A PHE* 3.7 14.7 - - + -
30A SER* 3.1 39.0 + - - -
32A HIS* 3.6 15.3 + - + +
190A ASP 3.0 12.3 + - - +
191A GLU* 3.4 26.7 + - - +
193A ALA* 1.3 76.0 - - - +
195A TYR* 1.3 62.0 + - - +
198A ASN* 2.5 38.8 + - - +
293A ASP* 3.5 3.4 + - - -
295A ASN* 3.6 24.2 - - - +
296A ASP* 3.3 25.9 + - - +
299A LYS* 3.8 20.8 - - + +
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Residues in contact with TYR 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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29A PHE* 4.0 8.0 - - + -
167A ASP* 3.2 48.5 + - + +
170A GLY 3.1 27.8 - - - +
171A GLN* 4.3 1.1 - - - -
172A HIS* 3.6 49.1 + + - +
191A GLU 3.0 13.2 + - - +
192A ALA 3.3 9.0 - - - +
194A LYS* 1.3 74.4 - - - +
196A TYR* 1.3 67.6 + - - +
198A ASN 3.3 1.4 + - - -
199A ILE* 3.1 49.7 + - + +
200A LEU* 4.7 8.5 - - + -
228A HIS* 3.5 15.9 - + - -
243A TYR* 4.1 11.0 - - - -
501A FEO 4.5 0.2 - - - -
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Residues in contact with TYR 196 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A ALA 3.0 13.7 + - - +
193A ALA* 4.0 3.4 - - - +
195A TYR* 1.3 81.8 - - - +
197A ALA* 1.3 63.5 + - - +
200A LEU* 2.9 45.8 + - + -
201A MET* 3.1 22.9 + - - -
204A SER* 3.4 19.7 - - - -
207A ILE* 4.0 7.7 - - + +
243A TYR* 3.6 46.0 - + + -
246A TRP* 3.9 39.3 - + + -
247A ALA* 3.3 24.0 - - - +
302A LEU* 3.8 21.1 - - + -
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Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A ALA 2.9 19.0 + - - +
194A LYS 4.1 2.0 - - - +
195A TYR 3.3 0.2 - - - -
196A TYR* 1.3 83.6 - - - +
198A ASN* 1.3 57.3 + - - +
201A MET* 3.3 23.4 - - + +
298A ILE* 3.4 22.9 - - + +
299A LYS* 3.7 26.5 - - - -
302A LEU* 4.0 16.6 - - + -
332A LEU* 3.4 5.0 - - - +
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Residues in contact with ASN 198 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PHE* 3.8 20.2 - - + -
194A LYS* 2.5 38.4 + - - +
196A TYR 3.3 0.4 - - - -
197A ALA* 1.3 79.8 - - - +
199A ILE* 1.3 62.1 + - - +
295A ASN* 3.4 42.6 + - - +
298A ILE* 3.3 29.0 - - - +
328A ASP* 4.8 2.9 - - - +
332A LEU* 3.6 19.6 - - - +
315B ASN* 4.9 3.5 + - - -
711B FMN 6.0 1.2 - - - +
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Residues in contact with ILE 199 (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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25A HIS* 4.3 21.5 - - + +
29A PHE* 4.1 18.8 - - + -
148A HIS* 4.0 28.6 + - + +
167A ASP* 5.8 1.8 - - + -
172A HIS* 4.3 6.3 - - - +
195A TYR* 3.1 55.6 + - + +
198A ASN* 1.3 84.5 - - - +
200A LEU* 1.3 76.0 + - + +
201A MET 3.6 1.1 - - - -
202A PRO* 3.4 14.7 - - - +
203A PHE* 4.0 12.1 - - - -
315B ASN* 5.0 3.3 - - - +
711B FMN 5.4 5.2 - - + +
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Residues in contact with LEU 200 (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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147A LEU* 4.6 4.5 - - + +
148A HIS* 4.4 16.4 - - + +
167A ASP* 6.5 0.7 - - + -
168A ALA* 4.5 13.9 - - + +
195A TYR* 4.7 6.7 - - + -
196A TYR* 2.9 36.8 + - + +
199A ILE* 1.3 89.1 - - + +
201A MET* 1.3 63.6 + - - +
202A PRO* 3.1 4.3 - - - -
203A PHE* 2.9 31.6 + - + -
204A SER 3.6 6.4 + - - -
207A ILE* 4.5 15.9 - - + -
243A TYR* 3.4 40.8 - - + +
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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