Contacts of the strand formed by residues 192 - 199 (chain A) in PDB entry 4OE5
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 THR 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ILE* 3.7 17.3 - - - +
187A SER* 3.5 4.3 - - - -
188A VAL* 3.5 25.6 - - + +
191A SER* 1.3 73.6 - - - +
193A ASN* 1.3 65.9 + - - +
547A ILE 4.5 0.4 - - - -
548A LYS* 3.3 5.6 - - - +
549A GLU* 2.9 37.4 + - - +
551A HIS* 3.0 28.5 + - + +
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Residues in contact with ASN 193 (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 GLN* 5.1 0.3 - - - +
184A GLN 4.8 5.4 - - - +
186A ILE* 3.3 23.8 - - + +
191A SER 4.9 2.5 - - - +
192A THR* 1.3 80.7 - - - +
194A SER* 1.3 70.6 + - - +
195A THR* 5.3 1.6 + - - -
546A VAL* 3.3 29.5 - - - +
547A ILE 3.4 4.3 - - - -
548A LYS* 3.6 19.9 - - + +
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Residues in contact with SER 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLN* 3.9 10.8 - - - -
193A ASN* 1.3 79.2 - - - +
195A THR* 1.3 66.3 + - - +
196A VAL* 4.1 6.4 - - - +
545A GLN 3.8 0.5 - - - +
546A VAL* 3.4 4.2 - - - +
547A ILE* 2.8 42.8 + - - +
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Residues in contact with THR 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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181A GLU* 5.7 0.5 - - - +
183A GLN* 2.9 39.0 + - - +
193A ASN* 5.3 1.2 + - - -
194A SER* 1.3 77.9 - - - +
196A VAL* 1.3 64.5 + - - +
197A TYR* 3.9 21.9 + - + +
544A PRO* 3.7 27.4 - - + -
545A GLN 3.2 11.4 - - - +
546A VAL* 4.2 11.9 - - + +
531B LYS* 4.5 8.8 - - + +
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Residues in contact with VAL 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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194A SER* 5.0 6.3 - - - +
195A THR* 1.3 75.4 - - - +
197A TYR* 1.3 61.3 + - - +
198A ARG* 3.2 11.4 + - + -
544A PRO* 3.4 0.9 - - - +
545A GLN* 2.7 48.6 + - + +
547A ILE* 3.8 28.3 - - + -
498B ARG* 3.5 39.7 - - - +
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Residues in contact with TYR 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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117A ASP* 4.6 1.0 - - - +
124A ARG* 4.7 11.8 + - - -
180A LEU* 3.5 59.4 + - + +
181A GLU* 4.8 4.5 - - + -
183A GLN* 3.7 15.1 + - - +
195A THR* 3.9 20.4 + - + +
196A VAL* 1.3 75.2 - - - +
198A ARG* 1.3 61.6 + - - +
199A GLY 3.8 1.0 + - - -
226A MET* 4.8 7.8 - - + +
542A THR* 3.3 24.6 + - + +
543A SER 4.4 0.7 - - - -
544A PRO* 3.9 12.8 - - + -
498B ARG* 4.3 4.9 + - - -
532B PRO* 3.0 48.5 - - + +
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Residues in contact with ARG 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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117A ASP* 3.9 5.4 - - - +
196A VAL* 4.0 15.5 - - + +
197A TYR* 1.3 71.9 - - - +
199A GLY* 1.3 68.6 + - - +
226A MET 4.3 0.7 - - - -
542A THR* 2.9 6.9 + - - -
543A SER* 2.8 68.2 + - - +
544A PRO 3.4 13.3 + - - -
545A GLN* 3.5 16.7 - - + +
498B ARG* 2.9 53.9 + - + +
499B ASN* 3.6 24.3 + - - +
501B ALA 3.4 19.2 + - - -
502B GLY* 4.1 10.7 - - - -
528B THR* 5.4 0.4 - - - -
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Residues in contact with GLY 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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113A ARG* 4.5 7.3 + - - -
117A ASP* 3.0 19.2 + - - +
197A TYR 3.8 0.4 + - - -
198A ARG* 1.3 85.9 - - - +
200A LEU* 1.3 67.1 + - - -
201A GLU 3.7 1.6 + - - -
226A MET 3.3 22.0 + - - -
227A GLY 4.0 8.7 - - - -
228A ASN* 3.7 5.6 - - - -
541A TRP 4.2 2.7 - - - -
543A SER* 5.1 1.6 + - - -
499B ASN* 4.5 5.7 + - - +
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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