Contacts of the helix formed by residues 184 - 190 (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 ILE 184 (chain C).
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Specific contacts
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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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Residues in contact with VAL 185 (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* 5.0 2.9 - - + -
180C TRP* 2.8 44.8 + - + +
181C SER* 4.2 0.2 - - - -
184C ILE* 1.4 71.8 - - + +
186C ARG* 1.4 57.3 + - - +
188C VAL* 3.3 7.3 + - - +
189C MET* 2.9 38.1 + - + +
195C ALA* 5.2 0.4 - - + -
196C TRP* 4.8 5.2 - - - -
199C PHE* 3.8 44.4 - - + -
200C ILE* 6.1 0.2 - - + -
169D TYR* 3.2 31.9 - - + +
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Residues in contact with ARG 186 (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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181C SER* 2.9 30.0 + - - +
182C MET* 3.8 19.9 - - - +
185C VAL* 1.4 68.6 - - - +
187C PRO* 1.4 67.3 - - + +
189C MET* 3.0 24.0 + - + +
190C ASN* 3.2 20.3 + - - +
300C 2CV 5.2 4.9 + - - -
159D GLU* 4.0 12.8 + - - -
160D TRP* 3.6 25.3 - - - +
166D LYS* 6.3 0.6 - - - +
169D TYR* 3.5 21.4 - - + +
170D THR* 3.0 44.1 + - - +
173D GLN* 3.0 27.5 + - - -
184D ILE* 4.4 0.6 - - - +
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Residues in contact with PRO 187 (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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159B GLU* 5.3 0.2 - - - +
157C PHE* 3.2 19.6 - - + -
160C TRP* 3.9 17.3 - - + -
182C MET 3.7 15.9 - - - +
183C GLY 3.5 17.3 - - - +
184C ILE 3.0 19.7 - - - +
186C ARG* 1.4 86.5 - - + +
188C VAL* 1.4 58.6 + - - +
190C ASN* 3.4 27.2 + - - +
191C VAL* 4.0 1.6 + - - +
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Residues in contact with VAL 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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153C TYR* 3.6 37.0 - - + -
157C PHE* 3.6 22.7 - - + -
160C TRP* 4.0 16.8 - - + -
161C PHE* 4.5 8.3 - - + -
184C ILE* 3.1 24.1 + - + +
185C VAL* 3.7 9.2 - - - +
187C PRO* 1.4 71.6 - - - +
189C MET* 1.4 53.1 + - - +
191C VAL* 3.1 4.2 + - - +
192C HIS* 2.7 40.8 + - + +
195C ALA* 3.8 11.0 - - + -
199C PHE* 4.5 5.8 - - + -
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Residues in contact with MET 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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185C VAL* 2.9 14.7 + - + +
186C ARG* 3.0 19.3 + - + +
188C VAL* 1.4 69.9 - - - +
190C ASN* 1.4 60.4 + - - +
191C VAL 3.1 6.5 + - - -
192C HIS 3.0 27.0 - - - +
193C PRO* 3.2 24.4 - - + +
195C ALA* 3.8 13.7 - - + -
196C TRP* 3.8 30.3 - - - +
300C 2CV 4.0 21.3 - - - +
169D TYR* 3.5 39.0 - - + +
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Residues in contact with ASN 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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190A ASN* 3.3 41.5 - - - +
186C ARG* 3.2 19.3 + - - +
187C PRO* 3.5 19.4 + - - +
188C VAL 3.3 0.4 - - - -
189C MET* 1.4 74.6 - - - +
191C VAL* 1.3 60.8 + - + +
193C PRO* 5.6 1.0 - - - +
159D GLU* 5.4 5.2 - - - +
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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