Contacts of the strand formed by residues 194 - 199 (chain A) in PDB entry 4BU2
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 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A TYR* 4.9 2.6 + - - +
169A THR* 2.8 37.0 + - - +
175A GLY* 5.4 1.2 - - - -
189A GLN* 4.0 11.4 - - - +
193A GLU* 1.3 73.8 - - - +
195A HIS* 1.3 63.7 + - - +
196A TRP* 3.5 26.6 + - + +
225A MSE 3.4 6.5 - - - -
226A LEU* 2.9 30.9 + - + -
242A ALA* 3.7 14.1 - - + -
243A ASP* 3.8 10.1 - - - +
244A THR* 3.8 8.1 - - - +
251A SER* 3.1 26.7 + - - +
253A HIS* 4.3 9.6 + - - +
701A AKG 3.1 34.6 + - - -
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Residues in contact with HIS 195 (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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194A LYS* 1.3 69.6 - - - +
196A TRP* 1.3 67.0 + - - +
197A ARG* 4.1 21.4 + - - +
223A GLU* 3.1 34.4 + - + +
224A PHE 3.7 12.6 - - - -
225A MSE 3.8 22.0 - - + -
241A GLN 3.9 0.3 - - - +
242A ALA* 3.0 5.5 - - - -
243A ASP* 2.7 51.5 + - - +
245A PRO* 4.7 1.8 - - + -
602A NI 2.4 36.8 - - + +
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Residues in contact with TRP 196 (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 ILE* 3.4 28.9 - - + +
189A GLN* 4.8 1.0 + - - -
194A LYS* 3.6 31.0 - - + +
195A HIS* 1.3 71.6 - - - +
197A ARG* 1.3 69.6 + - - +
198A LEU* 4.1 11.9 - - + -
222A HIS 4.8 0.2 - - - -
223A GLU* 3.3 3.2 - - - +
224A PHE* 2.8 57.7 + + + +
226A LEU* 3.3 30.8 - - + +
232A LEU* 3.8 10.8 - - + -
234A PHE* 4.0 8.5 - + - -
240A HIS* 3.4 36.8 - + + -
241A GLN 3.7 10.8 - - - -
242A ALA* 3.7 13.0 - - + -
253A HIS* 4.0 19.8 - + - -
701A AKG 4.0 15.0 - - + -
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Residues in contact with ARG 197 (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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174A GLN* 5.4 1.6 + - - -
195A HIS* 4.1 18.3 + - - +
196A TRP* 1.3 79.9 - - - +
198A LEU* 1.3 62.4 + - - +
199A TYR* 3.3 33.0 + - + +
214A GLU* 4.9 5.1 + - - -
220A PRO* 4.1 12.4 - - + +
222A HIS 3.6 5.6 - - - -
223A GLU* 3.8 29.4 - - + +
240A HIS* 3.4 1.0 - - - -
241A GLN* 3.1 61.5 + - + +
243A ASP* 4.0 16.7 + - - -
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Residues in contact with LEU 198 (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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63A PRO* 3.6 35.7 - - + -
196A TRP* 4.1 15.0 - - + -
197A ARG* 1.3 76.1 - - - +
199A TYR* 1.3 61.1 + - - +
220A PRO* 3.4 4.5 - - - +
221A VAL* 2.9 27.6 + - + -
222A HIS* 2.9 25.7 + - + +
224A PHE* 4.0 27.1 - - + -
232A LEU* 4.4 4.9 - - + -
234A PHE* 4.2 14.6 - - + -
238A THR* 4.5 7.4 - - + -
239A ILE 3.4 4.5 - - - +
240A HIS* 3.7 23.6 - - + -
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Residues in contact with TYR 199 (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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178A PRO* 5.4 0.2 - - + -
197A ARG* 3.3 39.3 + - + -
198A LEU* 1.3 75.6 - - - +
200A HIS* 1.3 66.4 + - - +
201A PRO* 3.5 4.2 - - - +
214A GLU* 4.4 1.0 + - - -
217A ILE* 3.4 43.5 - - + +
218A GLY 3.6 6.7 - - - -
219A ARG 3.8 0.7 - - - -
220A PRO* 3.4 41.9 - - + +
221A VAL* 4.2 8.5 - - - -
238A THR* 4.2 6.1 - - - +
239A ILE* 2.8 47.4 + - + +
240A HIS* 4.4 0.4 - - - -
241A GLN* 2.7 37.1 + - + -
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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