Contacts of the helix formed by residues 184 - 193 (chain A) in PDB entry 1YH7
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 ILE 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ASP* 4.4 2.0 + - - +
52A VAL* 6.2 0.9 - - + -
167A ALA* 4.8 7.0 - - + -
168A GLN* 4.6 15.7 - - + -
171A GLN* 3.3 29.0 + - - +
183A GLY* 1.3 70.3 - - - -
185A MET* 1.3 69.9 + - - +
187A GLN* 3.2 13.4 - - + +
188A PHE* 2.9 42.6 + - + +
201A ILE* 5.4 5.2 - - + -
203A CYS* 4.7 23.1 - - + +
206A LEU* 3.6 32.8 - - + -
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Residues in contact with MET 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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37A ARG* 4.0 15.5 - - - +
39A ASN* 3.6 41.7 - - + +
42A GLY 5.3 0.2 - - - +
43A GLU* 4.3 12.3 - - - +
44A HIS 5.7 1.6 - - - -
46A ASP* 2.7 38.9 + - - +
52A VAL* 4.6 13.5 - - + -
54A PRO* 4.6 8.4 - - + +
182A CYS* 4.7 9.0 - - - -
183A GLY 3.2 3.8 - - - -
184A ILE* 1.3 84.6 - - - +
186A ASP* 1.3 85.0 + - - +
188A PHE* 3.5 3.4 + - - +
189A ILE* 3.2 22.9 + - - +
345A GLY* 5.4 5.6 - - - -
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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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37A ARG* 2.7 41.5 + - - +
140A SER* 2.8 31.4 + - - +
142A SER* 5.3 2.8 + - - -
143A ALA* 3.5 9.8 - - + +
182A CYS* 4.8 10.9 - - - -
183A GLY 4.7 0.6 + - - -
184A ILE 3.4 0.6 - - - -
185A MET* 1.3 89.9 - - - +
187A GLN* 1.3 70.7 + - - +
189A ILE* 3.0 21.2 - - - +
190A SER* 3.0 9.9 + - - -
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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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142A SER* 5.5 0.8 + - - -
143A ALA* 4.0 11.0 - - + +
146A GLU* 3.7 15.4 + - - -
147A VAL* 4.6 1.1 - - + +
167A ALA* 3.5 18.2 - - + +
170A CYS* 3.1 28.7 + - + -
171A GLN* 3.5 30.3 - - - +
174A GLU* 4.3 10.7 - - - +
182A CYS* 5.4 4.5 - - - +
183A GLY 3.4 10.1 + - - +
184A ILE* 3.2 23.8 - - + +
186A ASP* 1.3 77.8 + - - +
188A PHE* 1.3 53.3 + - - +
190A SER* 2.9 6.9 + - - -
191A LEU* 2.6 40.9 + - - +
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Residues in contact with PHE 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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54A PRO* 5.9 1.6 - - + -
164A ALA* 6.1 5.4 - - + -
167A ALA* 4.8 2.2 - - + -
184A ILE* 2.9 44.6 + - + +
185A MET* 3.9 4.3 - - - +
187A GLN* 1.3 77.2 - - - +
189A ILE* 1.3 55.4 + - - +
191A LEU* 4.1 13.9 - - + -
192A MET* 2.6 74.5 + - + +
199A LEU* 3.4 11.7 - - + -
201A ILE* 4.3 20.0 - - + -
206A LEU* 4.8 14.1 - - + -
208A THR* 3.0 30.7 - - + -
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Residues in contact with ILE 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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37A ARG* 2.9 36.6 - - + -
54A PRO* 3.2 36.8 - - + +
55A MET* 2.9 11.2 - - - +
56A ALA* 2.8 34.0 - - + +
185A MET 3.2 11.0 + - - +
186A ASP 3.0 14.6 - - - +
188A PHE* 1.3 79.4 - - - +
190A SER* 1.3 59.6 + - - +
193A GLY* 2.7 35.8 + - - -
197A HIS 5.6 1.1 - - - +
199A LEU* 4.1 13.7 - - + -
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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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34A ALA* 6.0 0.2 - - - -
35A PRO* 4.0 24.7 - - - +
36A GLY 5.1 2.0 - - - -
37A ARG* 5.5 1.1 - - - -
56A ALA* 4.7 7.6 - - - -
140A SER* 6.0 0.2 - - - -
143A ALA* 4.3 4.6 + - - +
144A SER* 5.0 1.3 - - - -
147A VAL* 3.0 28.6 - - - +
186A ASP 3.0 9.9 + - - -
187A GLN* 2.9 11.1 + - - -
189A ILE* 1.3 81.7 - - - +
191A LEU* 1.3 69.7 + - - +
386A GLY* 2.8 29.0 - - - -
387A ALA* 2.9 7.7 + - - -
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Residues in contact with LEU 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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147A VAL* 4.7 9.6 - - + -
163A ILE* 2.7 80.0 - - + +
164A ALA* 3.8 3.4 - - - +
166A ARG* 3.1 30.3 - - + +
167A ALA* 2.9 21.5 - - + +
187A GLN 2.6 25.0 + - - +
188A PHE* 3.6 11.9 - - + +
190A SER* 1.3 78.7 + - - +
192A MET* 1.3 60.6 + - + +
193A GLY 3.7 0.5 + - - +
386A GLY* 4.1 5.4 - - - -
387A ALA 4.2 6.2 + - - +
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Residues in contact with MET 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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163A ILE* 5.2 2.5 - - - -
188A PHE* 2.6 51.0 + - + +
191A LEU* 1.3 76.1 - - + +
193A GLY* 1.4 66.2 + - - +
194A GLN* 3.5 7.8 + - - +
199A LEU* 2.9 33.2 - - + +
208A THR* 3.7 13.2 - - + +
210A LEU* 3.0 43.1 - - + +
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Residues in contact with GLY 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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56A ALA* 4.0 9.9 - - - -
189A ILE* 2.7 28.8 + - - -
191A LEU 3.4 3.1 - - - +
192A MET* 1.4 78.5 - - - +
194A GLN* 1.4 66.2 + - - -
197A HIS 5.7 0.4 - - - -
199A LEU* 5.2 2.2 - - - -
385A ASP* 3.5 2.9 - - - +
386A GLY* 2.6 33.6 + - - -
388A LYS* 5.1 2.1 - - - -
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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