Contacts of the helix formed by residues 184 - 189 (chain A) in PDB entry 3ORP
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 184 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TYR 3.8 2.0 + - - -
183A LEU* 1.3 76.3 - - - +
185A PRO* 1.3 73.1 - - - +
186A GLU* 3.2 36.4 + - - +
187A GLN* 3.0 26.5 + - - +
188A ALA* 3.0 10.8 + - - +
197A SER* 3.6 23.1 - - - -
200A TYR* 3.5 15.0 - - - -
201A SER* 4.0 1.6 + - - -
228A HIS* 5.0 0.2 - - - -
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Residues in contact with PRO 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LEU 3.9 0.4 - - - +
184A SER* 1.3 86.7 - - - +
186A GLU* 1.3 65.4 + - - +
188A ALA* 3.2 12.2 + - + +
189A ARG* 3.2 45.4 + - - +
200A TYR* 3.6 30.5 - - + +
228A HIS* 3.4 26.7 - - + +
229A VAL* 4.2 11.2 - - + +
257A LYS* 4.1 22.2 - - + +
262A ARG* 4.3 0.9 - - - +
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Residues in contact with GLU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A SER* 3.1 21.7 + - - +
185A PRO* 1.3 76.3 - - - +
187A GLN* 1.3 57.2 + - - +
189A ARG* 3.4 12.3 + - - +
190A GLY 3.3 4.2 + - - -
191A ASP* 2.8 43.7 + - + +
192A SER 3.6 21.1 - - - +
193A VAL* 4.4 2.2 - - + -
194A ASP* 4.9 2.1 - - - +
197A SER* 2.7 25.2 + - - +
257A LYS 4.7 0.5 - - - +
259A PRO* 4.2 16.0 - - + +
262A ARG* 2.6 39.3 + - - -
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Residues in contact with GLN 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ARG* 3.1 36.0 + - - +
183A LEU* 3.2 40.3 - - + +
184A SER* 3.0 25.2 + - - +
186A GLU* 1.3 76.1 - - - +
188A ALA* 1.3 59.3 + - - +
190A GLY* 3.0 20.4 + - - +
191A ASP 4.6 1.3 - - - +
193A VAL* 3.3 29.7 - - + +
197A SER* 5.2 3.6 - - - -
201A SER* 4.6 4.2 + - - -
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LEU* 5.0 6.2 - - + +
184A SER 3.0 11.8 + - - +
185A PRO* 3.2 12.7 + - + +
187A GLN* 1.3 76.0 - - - +
189A ARG* 1.3 58.9 + - - +
190A GLY 3.4 0.8 + - - -
225A ALA* 4.0 29.4 - - + +
228A HIS* 4.9 2.9 - - + -
229A VAL* 3.7 22.7 - - + -
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Residues in contact with ARG 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A PRO* 3.2 34.9 + - - +
186A GLU* 3.4 6.1 + - - +
187A GLN 3.2 0.4 - - - -
188A ALA* 1.3 77.5 - - - +
190A GLY* 1.3 65.1 + - - +
191A ASP* 2.8 27.4 + - - +
229A VAL* 3.6 37.4 + - + +
230A ARG* 5.2 6.7 - - - +
257A LYS* 5.2 5.9 + - - +
259A PRO* 6.2 1.8 - - - +
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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