Contacts of the helix formed by residues 196 - 204 (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 GLN 196 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152C ASN* 2.5 30.8 + - - +
153C THR* 4.3 10.5 + - - +
156C THR* 3.2 27.0 + - - +
194C SER 4.4 0.2 + - - -
195C TYR* 1.3 71.8 - - - +
197C VAL* 1.3 63.7 + - - +
198C GLU* 3.4 2.7 - - - -
199C LYS* 3.0 43.0 + - + +
200C LEU* 3.0 25.2 + - - +
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Residues in contact with VAL 197 (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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191C ILE* 4.6 4.7 - - + -
195C TYR* 3.5 15.0 + - + +
196C GLN* 1.3 72.0 - - - +
198C GLU* 1.3 57.1 + - - +
200C LEU* 3.2 9.0 + - - +
201C ALA* 2.8 28.9 + - - +
252C TRP* 3.8 34.8 - - + +
255C LYS* 3.4 59.2 - - + +
257C MET* 3.7 18.1 - - + +
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Residues in contact with GLU 198 (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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196C GLN 3.4 0.4 - - - -
197C VAL* 1.3 77.5 - - - +
199C LYS* 1.3 63.6 + - + +
201C ALA* 3.5 13.1 + - - +
202C LYS* 3.6 20.1 + - - +
255C LYS 3.9 15.4 - - - +
256C GLY* 4.7 8.5 - - - +
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Residues in contact with LYS 199 (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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156C THR* 4.4 21.0 - - + +
160C HIS* 6.3 0.7 - - - +
196C GLN* 3.0 45.0 + - + +
198C GLU* 1.3 77.2 - - + +
200C LEU* 1.3 64.5 + - + +
202C LYS* 3.1 24.5 + - - +
203C ASP* 3.3 22.8 + - - +
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Residues in contact with LEU 200 (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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155C PHE* 3.9 23.6 - - + -
156C THR* 5.0 11.2 - - + +
159C ILE* 4.1 24.2 - - + -
184C VAL* 5.5 1.3 - - + -
195C TYR* 3.7 42.0 - - + -
196C GLN 3.0 15.3 + - - +
197C VAL* 3.5 9.4 - - - +
199C LYS* 1.3 80.3 - - + +
201C ALA* 1.3 56.8 + - - +
203C ASP* 4.5 3.1 - - - +
204C LEU* 2.9 51.2 + - + +
252C TRP* 4.5 10.5 - - + -
257C MET* 4.2 9.9 - - + -
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Residues in contact with ALA 201 (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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197C VAL 2.8 18.8 + - - +
198C GLU* 3.7 8.5 - - - +
199C LYS 3.3 0.4 - - - -
200C LEU* 1.3 73.5 - - - +
202C LYS* 1.3 55.4 + - + +
256C GLY 3.7 21.3 - - - +
257C MET* 3.8 15.4 - - + +
258C PRO* 3.8 16.9 - - + +
261C LYS* 2.7 33.7 + - - -
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Residues in contact with LYS 202 (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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198C GLU* 3.6 15.8 + - - +
199C LYS* 3.1 17.6 + - - +
201C ALA* 1.3 78.7 - - + +
203C ASP* 1.3 70.0 + - - +
204C LEU 3.6 1.7 - - - +
261C LYS* 4.6 2.6 + - - +
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Residues in contact with ASP 203 (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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156C THR* 4.8 1.9 - - - +
159C ILE* 3.5 21.9 - - + +
160C HIS* 3.4 47.5 + - - +
163C ALA* 3.7 27.4 - - + +
164C GLU* 5.4 0.3 - - - +
177C ARG* 5.8 1.4 + - - -
180C LEU* 3.9 9.4 - - - +
199C LYS* 3.5 22.0 - - - +
200C LEU* 3.2 3.7 + - - +
202C LYS* 1.3 86.3 - - - +
204C LEU* 1.3 62.7 + - - +
205C ASP* 4.0 1.7 + - - +
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Residues in contact with LEU 204 (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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159C ILE* 3.7 29.4 - - + -
180C LEU* 3.6 22.2 - - + +
181C THR 4.1 10.5 - - - +
182C ALA* 3.7 20.0 - - + -
184C VAL* 5.3 0.2 - - + -
200C LEU* 2.9 33.4 + - + +
201C ALA* 3.8 1.0 - - - +
202C LYS 4.6 0.3 - - - +
203C ASP* 1.3 79.4 - - - +
205C ASP* 1.3 56.5 + - - +
206C PHE* 3.9 13.9 - - - +
207C ILE* 3.5 31.2 - - + -
257C MET* 5.6 0.9 - - + -
261C LYS* 2.6 35.0 + - + +
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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