Contacts of the strand formed by residues 193 - 201 (chain A) in PDB entry 5JKC
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 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A VAL 5.4 0.4 - - - +
143A LEU* 5.1 3.6 - - + -
186A TRP* 5.0 0.2 - - + -
187A HIS* 3.9 16.4 - - + +
190A SER* 3.2 36.1 - - - +
191A GLU 3.1 18.6 - - - +
192A GLY* 1.3 82.5 - - - +
194A THR* 1.3 68.3 + - - +
214A LYS* 5.1 4.0 - - - -
235A LEU* 3.6 32.8 - - + -
236A GLY 3.5 6.5 - - - +
237A SER* 4.9 2.7 - - - +
238A VAL* 5.3 1.0 - - - +
243A ALA* 4.3 19.3 - - + -
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Residues in contact with THR 194 (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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193A LEU* 1.3 81.0 - - - +
195A ASP* 1.3 84.1 + - - +
196A TYR* 5.6 1.0 - - - -
212A LYS* 5.3 2.9 + - - -
214A LYS* 3.3 23.3 - - - +
235A LEU* 4.6 5.6 - - - +
236A GLY* 2.8 25.0 + - - -
237A SER 3.5 28.4 + - - +
238A VAL* 3.7 11.4 - - + +
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Residues in contact with ASP 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 THR* 1.3 88.6 + - - +
196A TYR* 1.3 59.8 + - - +
197A SER* 3.6 3.0 + - - -
212A LYS* 3.5 33.0 + - + +
213A GLY* 3.6 25.8 + - - +
214A LYS* 2.6 38.6 + - - +
234A GLU 3.3 3.8 - - - +
235A LEU* 3.5 5.6 - - - -
236A GLY* 2.8 25.5 + - - -
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Residues in contact with TYR 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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182A CYS* 3.7 45.3 - - + -
183A GLU* 4.1 5.5 + - - +
187A HIS* 2.8 31.0 + + - +
194A THR 5.6 0.9 - - - -
195A ASP* 1.3 71.4 - - - +
197A SER* 1.3 61.2 + - - +
198A PHE* 4.1 12.0 + - + -
211A SER* 3.9 1.4 + - - +
212A LYS* 3.3 3.9 + - - -
213A GLY 2.8 28.8 + - - +
214A LYS* 3.7 15.5 - - + -
215A GLU 3.3 27.1 - - - +
216A ALA* 3.5 24.3 - - + +
233A CYS* 3.8 2.7 - - - -
234A GLU 3.5 1.8 - - - -
235A LEU* 3.9 30.7 - - + +
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Residues in contact with SER 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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195A ASP 3.6 2.8 + - - -
196A TYR* 1.3 71.9 - - - +
198A PHE* 1.3 60.5 + - - +
199A TYR* 3.7 27.9 + - - -
209A LEU* 4.0 7.6 - - - -
211A SER 3.5 5.4 - - - -
212A LYS* 3.7 27.3 - - - +
232A ARG 3.6 0.9 - - - +
233A CYS* 3.3 5.4 - - - -
234A GLU* 2.8 44.7 + - - +
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Residues in contact with PHE 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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180A LEU* 3.9 20.2 - - + -
182A CYS* 3.8 11.4 - - + -
196A TYR* 4.2 12.3 - - + -
197A SER* 1.3 76.6 - - - +
199A TYR* 1.3 60.4 + - - +
209A LEU* 3.7 3.9 - - - +
210A VAL* 2.9 29.7 + - + +
211A SER* 2.9 33.6 + - - +
215A GLU 4.2 11.0 - - - -
216A ALA 3.5 23.1 - - - -
217A THR 3.8 15.5 - - - -
218A LEU* 3.6 39.5 - - + -
231A TYR* 5.8 3.8 - - + -
232A ARG 3.5 2.9 - - - -
233A CYS* 3.9 21.8 - - + -
248A PHE* 4.3 7.0 - + - -
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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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197A SER* 3.7 25.1 + - - -
198A PHE* 1.3 75.6 - - - +
200A ARG* 1.3 65.1 + - - +
201A VAL* 5.0 0.4 - - + -
207A GLU* 3.7 26.5 - - + +
208A THR 3.3 6.1 - - - +
209A LEU* 3.7 42.0 - - + +
210A VAL* 4.9 1.1 - - - -
212A LYS* 6.0 0.7 - - - +
231A TYR* 3.2 8.5 - - - +
232A ARG* 2.8 60.9 + - + +
234A GLU* 3.9 26.1 + - + -
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Residues in contact with ARG 200 (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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199A TYR* 1.3 71.4 - - - +
201A VAL* 1.3 61.2 + - - +
202A TRP* 3.4 48.5 + - + -
207A GLU* 3.2 8.5 - - - +
208A THR* 3.0 32.0 + - - +
210A VAL* 3.9 21.2 - - + +
220A LYS* 5.0 6.2 - - - +
226A GLU 3.2 22.8 + - - -
227A ASP* 3.6 18.6 + - - +
228A ALA 2.9 29.1 + - - -
229A GLY* 4.8 1.6 - - - -
230A SER 3.6 6.1 + - - +
231A TYR* 3.5 40.1 + - + -
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Residues in contact with VAL 201 (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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199A TYR* 4.8 3.1 - - + +
200A ARG* 1.3 73.6 - - - +
202A TRP* 1.3 73.7 + - - +
203A GLY 4.1 0.2 + - - -
205A ASN* 6.0 2.0 - - - +
206A THR 4.0 4.7 - - - +
207A GLU* 4.3 11.9 - - + +
230A SER* 2.9 43.8 + - - +
231A TYR 5.0 0.4 - - - -
232A ARG* 3.7 37.5 - - + +
247A ASN* 5.4 3.6 - - - +
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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