Contacts of the helix formed by residues 187 - 195 (chain A) in PDB entry 4AY1
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 GLY 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A SER* 3.0 10.9 + - - -
186A ALA* 1.3 77.3 - - - +
188A ARG* 1.3 69.7 + - - -
189A GLN 3.3 2.7 - - - -
190A MET* 3.0 8.3 + - - -
191A ILE* 2.9 22.7 + - - +
214A PHE* 5.3 3.4 - - - -
242A TYR 5.9 0.7 - - - -
243A TYR* 6.5 0.9 - - - -
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Residues in contact with ARG 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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186A ALA 3.8 4.0 + - - -
187A GLY* 1.3 70.2 - - - +
189A GLN* 1.3 64.0 + - - +
191A ILE* 3.3 12.4 + - - +
192A ASP* 3.0 33.8 + - - +
242A TYR* 3.4 51.8 + - + +
247A TYR* 2.9 38.4 + - + -
251A TYR* 3.0 38.1 + - + -
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Residues in contact with GLN 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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187A GLY 3.3 0.6 - - - -
188A ARG* 1.3 81.4 - - - +
190A MET* 1.3 59.0 + - + +
192A ASP* 3.4 11.1 + - - +
193A ASN* 3.0 62.7 + - - +
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Residues in contact with MET 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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146A TYR* 3.6 51.8 - - + -
148A ASP* 3.5 33.0 - - - +
185A SER* 3.4 18.2 - - - +
187A GLY* 3.0 5.2 + - - +
189A GLN* 1.3 76.1 - - + +
191A ILE* 1.3 60.0 + - - +
193A ASN* 4.3 4.3 - - - +
194A SER* 2.8 56.5 + - - +
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Residues in contact with ILE 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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185A SER* 3.3 23.1 + - - +
186A ALA 3.8 8.3 - - - +
187A GLY 2.9 26.8 + - - +
188A ARG* 3.5 7.9 - - - +
190A MET* 1.3 73.6 - - - +
192A ASP* 1.3 67.0 + - - +
193A ASN 3.3 0.3 + - - -
195A TYR* 3.3 34.2 + - + +
197A VAL* 4.6 6.3 - - + -
248A ALA* 5.1 1.8 - - + +
251A TYR* 4.0 29.8 - - + -
252A TRP* 3.3 45.5 - - + +
255A LYS* 4.5 11.2 - - + -
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Residues in contact with ASP 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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152A ASN* 4.8 1.9 + - - -
188A ARG* 3.0 33.5 + - - +
189A GLN* 3.7 14.9 + - - +
191A ILE* 1.3 77.4 - - - +
193A ASN* 1.3 64.0 + - - +
195A TYR 4.5 6.5 - - - +
251A TYR* 2.5 33.9 + - - -
255A LYS* 3.1 23.6 + - - +
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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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148A ASP* 3.1 41.0 + - - +
149A GLN* 3.7 29.4 - - + +
152A ASN* 3.0 20.1 + - - +
189A GLN* 3.0 47.4 + - - +
190A MET* 3.7 9.1 - - - +
191A ILE 3.2 0.2 - - - -
192A ASP* 1.3 79.8 - - - +
194A SER* 1.3 58.5 + - - +
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Residues in contact with SER 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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147A PRO* 3.8 11.4 - - - +
148A ASP 2.8 31.4 + - - -
152A ASN* 3.4 28.7 + - - +
155A PHE* 4.3 3.1 - - - -
156A THR* 4.8 0.2 + - - -
190A MET* 2.8 39.0 + - - +
193A ASN* 1.3 73.3 - - - +
195A TYR* 1.3 86.4 + - - +
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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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144A TRP 4.3 6.6 + - - -
146A TYR* 4.4 2.9 - - - -
147A PRO* 4.0 16.0 - - + +
152A ASN* 3.7 5.3 + - - +
155A PHE* 3.7 30.5 - + - -
156A THR* 5.3 0.7 - - - -
183A GLY 4.4 0.3 + - - -
184A VAL* 3.4 17.6 - - + -
185A SER* 3.0 31.7 + - - -
191A ILE* 3.3 31.6 + - - +
192A ASP 4.5 4.5 - - - +
194A SER* 1.3 100.0 - - - +
196A GLN* 1.3 64.5 + - - +
197A VAL* 3.6 20.2 + - + +
200A LEU* 4.0 11.9 - - + -
252A TRP* 3.5 31.2 - + - -
255A LYS* 5.6 3.1 + - - -
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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