Contacts of the strand formed by residues 193 - 200 (chain A) in PDB entry 6PSI
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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127A LEU* 6.2 0.4 - - + -
186A PHE* 3.8 47.6 - - + -
187A ARG 4.2 1.8 - - - -
188A LEU* 3.6 26.5 - - + -
192A ASP* 1.3 73.3 - - - +
194A TYR* 1.3 64.5 + - - +
214A THR* 6.2 0.2 - - + -
215A LEU* 4.8 5.4 - - + -
238A LYS* 3.3 40.4 - - + +
239A GLY* 4.1 4.5 - - - -
240A PHE* 3.7 18.2 - - + -
248A ASP 3.0 7.7 + - - +
249A LEU* 3.5 15.3 - - + -
250A TYR* 2.9 26.3 + - - -
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Residues in contact with TYR 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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185A VAL 3.6 0.7 - - - +
186A PHE* 3.2 4.5 - - - -
187A ARG* 3.0 72.9 + - + +
189A GLU* 3.6 38.9 + - + +
192A ASP* 3.0 29.3 + - - -
193A LEU* 1.3 76.3 - - - +
195A ALA* 1.3 60.0 - - - +
232A LYS* 5.5 3.8 - - + -
250A TYR* 3.7 26.8 - + + +
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Residues in contact with ALA 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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185A VAL* 3.1 22.9 - - + +
186A PHE* 3.4 22.2 - - + -
194A TYR* 1.3 72.7 - - - +
196A THR* 1.3 66.6 + - - +
249A LEU* 3.7 3.2 - - + +
250A TYR 3.0 11.4 + - - +
251A LEU* 3.6 21.5 - - + -
252A GLU* 3.0 22.2 + - - +
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Residues in contact with THR 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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184A PRO 5.9 1.5 + - - -
185A VAL 4.1 2.6 + - - -
195A ALA* 1.3 77.7 + - - +
197A LEU* 1.3 67.1 + - - +
198A ASP* 4.2 2.2 + - + +
213A MET* 6.0 0.9 - - - +
251A LEU* 3.8 8.9 - - - +
252A GLU* 3.3 29.8 - - + +
254A ARG* 4.8 11.2 - - + -
416B ASP* 5.9 0.7 - - - +
418B ALA* 3.8 28.8 - - + +
419B VAL* 4.5 10.4 - - - +
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Residues in contact with LEU 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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196A THR* 1.3 76.4 - - - +
198A ASP* 1.3 66.4 + - - +
199A VAL* 3.6 16.7 + - + +
210A VAL* 3.7 22.9 - - + -
212A ALA* 4.6 13.5 - - + -
221A VAL* 6.3 1.6 - - + -
223A VAL* 3.8 26.9 - - + -
233A LEU* 3.6 28.5 - - + -
251A LEU* 3.7 30.3 - - + -
252A GLU 2.9 12.8 + - - +
253A VAL* 3.4 5.8 - - - -
254A ARG 3.1 21.4 + - - -
419B VAL* 4.8 11.0 - - + -
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Residues in contact with ASP 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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196A THR* 4.2 2.3 - - + +
197A LEU* 1.3 75.7 - - - +
199A VAL* 1.3 57.9 + - - +
200A PRO* 4.6 2.1 - - - +
210A VAL* 5.2 4.5 - - - +
254A ARG* 3.2 19.5 - - + +
256A THR* 5.0 9.0 - - + -
416B ASP 4.4 14.4 - - - +
417B GLY* 4.0 6.4 - - - -
418B ALA* 3.0 22.0 + - - +
419B VAL* 2.9 29.1 + - - +
420B MET* 3.2 25.6 + - - +
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Residues in contact with VAL 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 LEU* 4.0 18.2 - - + +
198A ASP* 1.3 74.4 - - - +
200A PRO* 1.4 82.3 - - + +
203A ILE* 3.8 20.0 - - + -
204A ALA* 3.9 18.8 - - + +
210A VAL* 4.3 3.4 - - + -
223A VAL* 4.0 15.7 - - + -
227A THR* 4.2 6.5 - - + -
253A VAL* 3.8 28.7 - - + -
254A ARG 3.1 3.8 + - - +
255A ILE* 3.0 11.6 - - + +
256A THR* 3.0 19.7 + - - -
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Residues in contact with PRO 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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198A ASP 4.6 2.5 - - - +
199A VAL* 1.4 90.4 - - + +
201A ALA* 1.3 61.2 + - - +
202A PRO* 3.5 1.1 - - + -
203A ILE* 3.1 27.9 + - + -
204A ALA* 2.9 25.3 + - - +
210A VAL* 4.7 5.6 - - + -
255A ILE* 4.1 0.2 - - - -
256A THR* 3.2 20.6 - - - +
257A ILE* 5.3 0.2 - - - -
276C TYR* 3.4 40.8 - - + +
279C ARG* 5.0 3.1 - - - +
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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