Contacts of the helix formed by residues 187 - 195 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C SER* 3.0 10.8 + - - -
186C ALA* 1.3 76.3 - - - +
188C ARG* 1.3 67.5 + - - -
189C GLN 3.3 2.9 - - - -
190C MET* 2.9 17.1 + - - +
191C ILE* 3.0 12.9 + - - +
214C PHE* 5.3 2.9 - - - -
242C TYR 5.7 0.2 - - - -
243C TYR* 5.4 11.9 - - - -
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Residues in contact with ARG 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C ALA 3.8 4.4 + - - -
187C GLY* 1.3 70.3 - - - +
189C GLN* 1.3 65.5 + - - +
191C ILE* 3.3 11.4 + - - +
192C ASP* 3.0 31.7 + - - +
242C TYR* 3.5 53.5 + - + +
243C TYR* 5.4 2.2 - - - -
247C TYR* 2.7 48.4 + - + -
251C TYR* 3.4 36.9 + - + -
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Residues in contact with GLN 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C GLY 3.3 1.0 - - - -
188C ARG* 1.3 80.5 - - - +
190C MET* 1.3 64.1 + - + +
192C ASP* 3.3 13.4 + - - +
193C ASN* 2.8 52.5 + - - +
242C TYR* 5.5 1.0 - - - -
243C TYR* 6.2 0.8 - - - -
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Residues in contact with MET 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C TYR* 3.6 47.1 - - + -
148C ASP* 3.5 32.1 - - - +
185C SER* 3.4 23.3 - - - +
187C GLY* 2.9 5.5 + - - +
189C GLN* 1.3 78.3 - - + +
191C ILE* 1.3 57.7 + - - +
193C ASN* 3.4 5.8 + - - +
194C SER* 2.9 55.9 + - - +
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Residues in contact with ILE 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C SER 3.3 22.4 - - - +
186C ALA 3.8 7.9 - - - +
187C GLY 3.0 26.2 + - - +
188C ARG* 3.6 9.9 - - - +
190C MET* 1.3 76.4 - - - +
192C ASP* 1.3 63.8 + - - +
195C TYR* 3.2 42.6 + - + +
197C VAL* 4.6 7.2 - - + -
248C ALA* 5.1 2.2 - - - +
251C TYR* 4.0 27.6 - - + -
252C TRP* 3.3 38.4 - - + +
255C LYS* 4.6 11.1 + - + -
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Residues in contact with ASP 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ASN* 4.6 3.3 + - - -
188C ARG* 3.0 30.3 + - - +
189C GLN* 3.6 20.3 + - - +
191C ILE* 1.3 79.0 - - - +
193C ASN* 1.3 63.7 + - - +
195C TYR 4.4 5.0 + - - +
251C TYR* 2.6 31.6 + - - -
255C LYS* 3.1 22.7 + - - +
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Residues in contact with ASN 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ASP* 2.8 44.7 + - - +
149C GLN* 3.6 34.0 + - + +
152C ASN* 3.0 16.3 + - - -
189C GLN* 2.8 44.8 + - - +
190C MET* 3.7 12.5 - - - +
192C ASP* 1.3 75.6 - - - +
194C SER* 1.3 58.5 + - - +
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Residues in contact with SER 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C PRO* 3.8 10.4 - - - +
148C ASP* 2.8 32.8 + - - -
152C ASN* 3.3 30.2 + - - +
155C PHE* 4.6 2.8 - - - -
156C THR* 5.2 0.2 + - - -
190C MET* 2.9 31.8 + - - +
191C ILE 3.2 0.6 + - - -
193C ASN* 1.3 74.4 - - - +
195C TYR* 1.3 87.3 + - - +
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Residues in contact with TYR 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C TRP 4.4 3.7 + - - -
146C TYR* 4.3 5.4 - - - -
147C PRO* 4.1 17.1 - - + +
152C ASN* 3.5 4.4 + - - +
155C PHE* 3.8 20.4 - + - -
156C THR* 5.5 0.2 - - - -
183C GLY 4.5 0.6 + - - -
184C VAL* 3.4 18.2 - - + -
185C SER* 3.0 31.7 + - - -
191C ILE* 3.2 33.4 + - + +
192C ASP 4.6 3.6 - - - +
193C ASN 3.8 0.2 - - - -
194C SER* 1.3 99.3 - - - +
196C GLN* 1.3 65.1 + - - +
197C VAL* 3.5 18.0 + - + +
200C LEU* 3.7 24.2 - - + -
252C TRP* 3.4 30.3 - + + -
255C LYS* 5.1 5.5 + - - -
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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