Contacts of the helix formed by residues 179 - 184 (chain C) in PDB entry 4P9O
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 SER 179 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C GLN* 4.2 6.5 - - - -
177C LEU 3.2 3.8 + - - -
178C GLU* 1.4 91.3 + - - +
180C TRP* 1.3 59.6 + - - +
181C SER 3.3 2.9 - - - -
182C MET* 5.7 1.1 - - - -
183C GLY* 2.8 43.8 + - - -
184C ILE* 3.3 3.3 + - - +
178D GLU* 3.4 22.3 + - - +
179D SER* 5.1 2.1 + - - -
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Residues in contact with TRP 180 (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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174C VAL* 4.2 30.7 - - + +
177C LEU* 3.3 37.9 + - + +
178C GLU 2.9 5.4 + - - -
179C SER* 1.3 75.8 - - - +
181C SER* 1.4 62.9 + - - +
184C ILE* 3.5 5.5 + - - +
185C VAL* 2.8 55.8 + - + +
199C PHE* 5.4 0.9 - - + -
200C ILE* 4.3 6.5 - - + -
203C ILE* 3.5 24.2 - - + -
169D TYR* 3.7 31.2 - + - -
172D PHE* 3.6 38.8 - + - -
173D GLN* 3.8 12.6 - - + -
176D THR* 2.8 28.9 + - - +
178D GLU* 3.4 14.8 - - + +
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Residues in contact with SER 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C TRP* 1.4 92.2 - - - +
182C MET* 1.3 63.8 + - - -
183C GLY 3.3 1.3 + - - -
185C VAL* 3.8 1.0 + - - -
186C ARG* 2.9 32.7 + - - +
169D TYR* 2.7 31.3 + - - -
173D GLN* 2.8 33.3 + - - -
178D GLU* 3.0 12.5 + - - -
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Residues in contact with MET 182 (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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179C SER* 5.6 1.1 - - - -
181C SER* 1.3 72.6 - - - +
183C GLY* 1.3 58.8 + - - +
186C ARG* 3.8 18.4 - - - +
187C PRO* 3.7 13.9 - - - +
160D TRP* 4.4 10.8 - - + +
173D GLN* 3.4 34.1 - - - +
178D GLU* 2.6 13.6 + - - +
179D SER* 3.5 22.2 - - - +
183D GLY* 3.7 32.5 - - - +
184D ILE* 3.8 9.6 - - + -
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Residues in contact with GLY 183 (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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160C TRP* 3.3 24.3 - - - -
173C GLN* 5.6 0.4 - - - -
179C SER* 2.8 32.2 + - - -
182C MET* 1.3 75.7 - - - +
184C ILE* 1.4 62.5 + - - -
187C PRO* 3.5 6.9 - - - +
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Residues in contact with ILE 184 (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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160C TRP* 3.5 51.1 - - + +
161C PHE* 3.8 26.7 - - + -
170C THR* 4.0 14.8 - - + -
173C GLN* 3.8 28.0 - - - +
174C VAL* 4.8 10.3 - - + -
179C SER 3.3 6.8 + - - +
180C TRP* 3.8 4.7 - - - +
183C GLY* 1.4 78.3 - - - +
185C VAL* 1.4 70.1 + - + +
186C ARG 3.5 2.5 - - - -
187C PRO* 3.0 14.2 - - - +
188C VAL* 3.1 22.0 + - + +
199C PHE* 5.0 4.5 - - + -
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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
------------------------------------------------------------
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