Contacts of the strand formed by residues 183 - 188 (chain A) in PDB entry 3RCH
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 LEU 183 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ARG* 3.9 28.3 - - + -
163A VAL* 4.1 16.8 - - + -
164A ILE* 4.9 1.6 - - + -
179A ILE* 3.1 37.5 - - + +
180A MET* 3.4 23.6 + - + +
182A LYS* 1.3 79.2 - - - +
184A VAL* 1.3 56.8 + - - +
204A VAL* 3.7 20.1 - - + +
205A LYS* 3.4 27.3 + - - +
235A ILE* 3.4 23.8 - - + -
237A PHE* 3.7 17.9 - - + -
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Residues in contact with VAL 184 (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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182A LYS 3.5 0.2 - - - +
183A LEU* 1.3 74.7 - - - +
185A ALA* 1.3 64.3 + - - +
186A TYR* 4.0 22.0 - - + +
205A LYS* 3.5 18.6 - - + +
207A LYS* 3.8 31.2 - - + -
229A ASP* 4.2 1.8 - - + +
234A LEU* 3.3 34.5 - - + -
235A ILE 2.7 22.6 + - - +
236A PRO* 3.4 4.8 - - + +
237A PHE* 3.0 30.6 + - - -
238A PHE 3.9 0.3 + - - +
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Residues in contact with ALA 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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156A LEU* 4.6 4.3 - - + -
184A VAL* 1.3 74.4 - - - +
186A TYR* 1.3 69.5 + - - +
199A GLY* 6.1 0.2 - - - -
204A VAL* 4.6 5.4 - - + -
205A LYS 2.8 13.5 + - - +
206A LEU* 3.7 11.7 - - + -
207A LYS* 2.9 25.5 + - - +
237A PHE* 4.0 16.8 - - + -
238A PHE* 3.0 27.8 - - + +
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Residues in contact with TYR 186 (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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184A VAL* 4.0 23.5 - - + +
185A ALA* 1.3 79.8 - - - +
187A SER* 1.3 61.0 + - - +
195A VAL* 4.6 0.2 - - - +
206A LEU* 3.9 4.4 - - - +
207A LYS* 3.3 26.0 - - + -
209A ILE* 3.4 31.2 - - + -
222A LEU* 4.8 3.1 - - + -
225A ALA* 4.1 9.7 + - + -
226A LEU* 3.6 28.4 - - + +
228A ARG* 4.9 0.2 - - - -
229A ASP* 2.7 39.3 + - - +
236A PRO* 4.2 11.7 - - + +
238A PHE* 2.9 17.8 + - - +
239A MET* 3.4 20.5 - - + -
240A VAL* 2.8 33.8 + - - +
266A ILE* 5.2 2.5 - - + -
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Residues in contact with SER 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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186A TYR* 1.3 78.9 - - - +
188A SER* 1.3 63.4 + - - +
191A ALA* 3.5 23.3 - - - +
195A VAL* 3.8 21.6 - - - +
206A LEU* 3.9 10.6 - - - +
207A LYS 3.3 4.2 + - - -
208A ALA* 3.4 5.5 - - - +
209A ILE* 2.8 26.3 + - - +
217A MET* 3.6 7.6 - - - -
240A VAL* 3.7 15.9 - - - -
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Residues in contact with SER 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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187A SER* 1.3 80.2 + - - +
189A ASP* 1.3 62.6 + - - +
190A GLN* 2.6 33.8 + - - +
191A ALA* 2.8 28.8 + - - +
208A ALA* 4.5 1.7 - - - +
209A ILE 3.7 5.6 - - - -
211A SER* 4.3 6.3 - - - -
215A PHE 4.8 0.7 + - - -
217A MET* 3.3 25.5 - - - +
240A VAL 4.4 1.4 + - - -
242A THR* 5.4 2.4 + - - -
252A ASP* 3.9 20.9 + - - -
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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