Contacts of the strand formed by residues 183 - 189 (chain A) in PDB entry 5E6J
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 LYS 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A SER 3.9 7.9 - - - +
182A ALA* 1.3 75.4 - - - +
184A ARG* 1.3 66.6 + - - +
185A VAL* 4.3 19.7 - - + -
199A THR* 4.5 11.4 - - + -
200A LEU 3.6 6.7 - - - +
201A THR* 4.9 5.8 - - + -
205A ALA* 4.1 2.4 - - - +
237A GLN* 4.0 12.4 + - - +
238A GLN* 3.6 2.6 - - - +
239A GLU* 2.7 69.4 + - + +
240A SER* 4.8 0.4 - - - -
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Residues in contact with ARG 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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183A LYS* 1.3 74.7 - - - +
185A VAL* 1.3 67.0 + - - +
186A LEU* 3.9 32.6 - - + +
199A THR* 3.5 0.5 - - - +
200A LEU* 2.7 47.2 + - + +
204A GLU 4.2 4.3 + - - -
205A ALA* 3.4 34.3 + - + +
206A VAL* 4.1 6.3 - - - +
207A MET 3.1 26.5 + - - +
208A TYR* 3.9 17.2 - - - -
214A TYR* 5.4 0.2 - - - -
217A LEU* 4.3 12.4 - - - +
235A LEU* 4.0 4.2 - - + +
237A GLN 3.4 4.7 - - - -
238A GLN* 2.7 25.0 + - - +
243A VAL* 3.3 32.5 - - - +
245A MET* 4.5 3.0 - - - -
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Residues in contact with VAL 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 LYS* 4.3 14.6 - - + -
184A ARG* 1.3 77.5 - - - +
186A LEU* 1.3 63.3 + - - +
197A THR* 4.9 5.2 - - - +
198A THR 3.2 4.9 - - - +
199A THR* 3.3 34.8 - - + +
235A LEU* 3.8 2.1 - - - +
236A VAL* 2.9 33.6 + - + +
237A GLN* 2.8 56.6 + - + +
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Residues in contact with LEU 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 ARG* 3.9 22.2 - - + +
185A VAL* 1.3 74.4 - - - +
187A ASN* 1.3 62.7 + - - +
188A VAL* 5.7 2.0 - - + -
197A THR* 3.0 8.7 + - - -
198A THR* 2.8 37.5 + - + +
200A LEU* 4.2 20.4 - - + -
208A TYR* 5.0 9.0 - - + -
217A LEU* 4.8 9.4 - - + -
233A GLN* 4.2 29.2 - - + +
234A TYR 3.7 6.1 - - - +
235A LEU* 3.6 40.4 - - + +
236A VAL* 3.7 3.0 - - - +
46B ALA 5.3 1.8 - - - +
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Residues in contact with ASN 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 LEU* 1.3 78.7 - - - +
188A VAL* 1.3 63.3 + - - +
189A VAL* 3.3 31.9 - - - +
195A GLN* 3.0 38.0 + - - +
196A LYS 3.7 3.4 - - - -
197A THR* 3.4 10.7 - - - -
232A THR 3.5 1.9 - - - +
233A GLN* 3.6 1.3 - - - -
234A TYR* 3.2 53.4 + - + -
236A VAL* 3.4 19.4 - - + +
317A PRO* 5.3 2.0 - - - +
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Residues in contact with VAL 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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186A LEU* 5.7 1.1 - - + -
187A ASN* 1.3 76.5 - - - +
189A VAL* 1.3 68.3 + - - +
194A GLY 3.7 1.2 - - - +
195A GLN* 3.5 0.5 - - - -
196A LYS* 2.8 52.1 + - + +
198A THR* 5.3 7.0 - - - +
223A ILE* 4.5 11.0 - - + -
225A CYS* 5.9 3.4 - - + -
231A ALA* 3.9 22.0 - - + -
232A THR 3.8 4.9 - - - +
233A GLN* 4.3 24.2 - - + +
46B ALA* 6.1 1.6 - - + -
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Residues in contact with VAL 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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187A ASN* 3.3 27.6 - - - +
188A VAL* 1.3 78.0 - - - +
190A CYS* 1.3 64.3 + - - +
194A GLY 3.5 5.4 - - - +
195A GLN* 4.0 14.6 - - + +
231A ALA* 3.2 7.4 - - - +
232A THR* 3.1 45.9 + - + +
234A TYR* 4.8 10.1 - - + -
317A PRO* 5.0 10.3 - - + -
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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