Contacts of the helix formed by residues 184 - 190 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182C MET* 3.8 17.3 - - + -
160D TRP* 3.6 52.0 - - + +
161D PHE* 3.7 26.7 - - + -
170D THR* 4.1 13.9 - - + -
173D GLN* 3.9 17.9 - - - +
174D VAL* 4.7 11.2 - - + -
179D SER 3.3 6.5 + - - +
180D TRP* 3.8 4.9 - - - +
183D GLY* 1.4 78.3 - - - +
185D VAL* 1.4 69.5 + - + +
186D ARG 3.5 1.6 - - - -
187D PRO* 3.0 13.8 - - - +
188D VAL* 3.1 21.1 + - + +
199D PHE* 4.9 5.6 - - + -
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Residues in contact with VAL 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D VAL* 5.1 2.9 - - + -
180D TRP* 2.8 55.3 + - + +
181D SER* 4.2 2.7 - - - +
184D ILE* 1.4 71.7 - - + +
186D ARG* 1.4 56.8 + - - +
188D VAL* 3.3 7.7 + - - +
189D MET* 2.9 50.2 + - + +
195D ALA* 5.3 0.2 - - + -
196D TRP* 4.8 8.1 - - + -
199D PHE* 3.7 46.0 - - + -
200D ILE* 6.0 1.1 - - + -
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Residues in contact with ARG 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D SER* 2.9 41.3 + - - +
182D MET* 3.8 30.4 - - - +
185D VAL* 1.4 68.7 - - - +
187D PRO* 1.4 67.0 - - + +
189D MET* 3.0 34.7 + - + +
190D ASN* 3.1 20.1 + - - +
302D 2CV 5.2 7.5 + - - -
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Residues in contact with PRO 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D PHE* 3.3 17.9 - - + -
160D TRP* 3.8 17.3 - - + -
182D MET 3.7 17.3 - - - +
183D GLY 3.5 17.9 - - - +
184D ILE 3.0 19.5 - - - +
186D ARG* 1.4 85.7 - - + +
188D VAL* 1.4 59.2 + - - +
190D ASN* 3.4 25.0 + - - +
191D VAL* 4.0 2.1 + - - +
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Residues in contact with VAL 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D TYR* 3.6 37.9 - - + -
157D PHE* 3.5 29.2 - - + -
160D TRP* 3.9 13.2 - - + -
161D PHE* 4.4 8.1 - - + -
184D ILE* 3.1 25.0 + - + +
185D VAL* 3.7 5.6 - - - +
187D PRO* 1.4 71.3 - - - +
189D MET* 1.4 53.7 + - - +
191D VAL* 3.1 3.6 + - - +
192D HIS* 2.7 40.1 + - + -
195D ALA* 3.9 9.4 - - + -
199D PHE* 4.3 5.8 - - + -
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Residues in contact with MET 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D VAL* 2.9 23.6 + - + +
186D ARG* 3.0 35.6 + - + +
188D VAL* 1.4 69.3 - - - +
190D ASN* 1.4 60.4 + - - +
191D VAL 3.1 5.6 + - - -
192D HIS 3.0 27.2 - - - +
193D PRO* 3.2 24.8 - - + +
195D ALA* 3.8 13.0 - - + -
196D TRP* 3.9 29.8 - - - +
302D 2CV 4.0 24.9 - - - +
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Residues in contact with ASN 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D ARG* 3.1 28.5 + - - +
187D PRO* 3.5 14.8 - - - +
188D VAL 3.3 0.6 - - - -
189D MET* 1.4 74.1 - - - +
191D VAL* 1.3 62.3 + - + +
193D PRO* 5.6 1.2 - - - +
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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