Contacts of the strand formed by residues 194 - 203 (chain B) in PDB entry 5O67
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 GLU 194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A LYS* 2.6 41.3 + - - -
358A VAL* 3.6 30.0 - - + +
359A SER 3.8 5.2 + - - -
361A ASP* 5.3 1.6 - - - +
146B LYS* 6.2 1.6 - - - -
178B THR* 3.5 29.2 + - + +
179B TYR 3.5 7.6 - - - +
180B GLN* 4.4 7.4 - - + -
193B SER* 1.3 81.3 + - - +
195B GLU* 1.3 68.0 + - - +
196B SER* 5.4 2.9 + - - -
248B ALA* 5.9 2.6 - - - +
252B LEU* 4.3 4.1 - - - +
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Residues in contact with GLU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B SER 4.0 0.2 - - - +
178B THR* 3.6 2.8 - - - -
179B TYR* 2.8 39.8 + - - +
194B GLU* 1.3 79.4 - - - +
196B SER* 1.3 66.3 - - - +
197B VAL* 5.2 0.7 - - - -
246B SER* 3.0 36.3 + - - -
247B THR* 4.8 3.1 - - - +
248B ALA* 4.8 6.2 - - - +
252B LEU* 4.6 3.6 - - + +
254B VAL* 4.2 26.9 - - + +
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Residues in contact with SER 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLU* 5.7 5.6 - - - -
177B SER 3.2 18.6 - - - -
178B THR* 4.0 12.3 - - - -
194B GLU* 5.4 2.4 + - - -
195B GLU* 1.3 83.3 - - - +
197B VAL* 1.3 67.7 + - - +
198B SER* 5.4 0.2 - - - -
254B VAL* 5.3 0.9 - - - +
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLU* 3.7 1.9 - - - +
177B SER 3.0 36.1 + - - +
179B TYR* 3.6 25.8 - - + -
196B SER* 1.3 81.2 - - - +
198B SER* 1.3 68.2 + - - +
254B VAL* 3.8 15.3 - - + -
255B PRO* 3.3 22.2 - - + +
256B GLU 4.1 15.0 - - - +
257B SER* 4.5 7.6 - - - +
258B LEU* 3.7 14.9 - - + +
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Residues in contact with SER 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TYR* 5.4 7.2 - - - -
175B ARG 3.4 9.4 - - - -
176B GLU* 4.9 8.7 - - - +
196B SER* 5.4 0.3 - - - -
197B VAL* 1.3 83.2 + - - +
199B ARG* 1.3 67.8 + - - +
200B ASP* 4.2 12.3 - - - -
257B SER* 5.1 2.6 - - - -
258B LEU* 4.2 14.9 + - - +
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Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B VAL* 4.2 10.8 - - + +
174B TYR* 3.4 9.2 - - - -
175B ARG* 2.9 34.9 + - + +
198B SER* 1.3 79.6 + - - +
200B ASP* 1.3 64.8 + - - +
202B THR* 3.1 27.6 + - - +
236B LYS* 4.0 29.6 - - - +
241B ILE* 5.8 0.4 - - - +
257B SER* 3.8 22.2 + - - -
258B LEU* 2.9 36.7 + - + +
259B PRO 5.2 0.7 - - - +
260B THR* 3.8 18.6 + - - +
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Residues in contact with ASP 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B TYR* 4.0 12.8 + - - -
198B SER* 5.0 9.5 - - - -
199B ARG* 1.3 76.4 - - - +
201B PRO* 1.3 81.3 - - + +
202B THR* 2.8 15.6 + - - -
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Residues in contact with PRO 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B VAL* 4.0 17.9 - - + -
173B VAL 3.4 13.0 - - - +
174B TYR* 3.8 21.7 - - + -
199B ARG 3.8 1.2 - - - -
200B ASP* 1.3 86.1 - - + +
202B THR* 1.3 58.5 + - - +
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Residues in contact with THR 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B VAL* 3.6 5.6 - - - -
173B VAL* 2.8 30.6 + - - +
199B ARG* 3.1 25.8 + - - +
200B ASP 2.8 13.7 + - - -
201B PRO* 1.3 71.6 + - - +
203B ILE* 1.3 76.7 + - + +
236B LYS* 3.8 29.8 - - + -
260B THR* 4.7 5.4 - - - -
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B VAL* 4.2 19.1 - - + -
171B PRO 3.4 7.6 - - - +
172B VAL* 4.4 8.7 - - + +
202B THR* 1.3 84.7 - - + +
204B GLY* 1.3 60.3 + - - +
206B VAL* 4.4 9.6 - - + -
234B THR* 4.0 31.9 - - + +
235B GLY* 3.7 4.3 - - - -
260B THR* 2.8 25.4 - - - +
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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