Contacts of the strand formed by residues 191 - 196 (chain B) in PDB entry 3C3P
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 PHE 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LEU* 4.3 10.5 - - + -
146B ASN* 3.9 17.7 - - - -
149B LEU* 4.3 12.3 - - + -
153B ALA 5.2 0.7 - - - -
155B LEU* 4.9 8.1 - - + -
185B LEU* 3.8 32.9 - - + +
186B SER 6.1 0.2 - - - -
188B ARG* 3.0 24.1 + - + +
189B ARG 3.3 0.9 - - - -
190B ASP* 1.3 105.1 - - - +
192B PHE* 1.3 59.0 + - - +
193B THR* 3.8 14.1 + - - +
205B GLY* 3.8 26.9 - - - -
206B TYR 3.4 14.8 - - - -
207B ARG* 4.0 27.1 - - + -
208B LEU* 3.8 9.3 - - - +
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Residues in contact with PHE 192 (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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45A ARG* 3.3 76.1 - - + +
48A TYR* 3.6 32.5 - + + -
49A LEU* 3.7 18.9 - - + +
219A PEG 3.6 34.1 - - - -
191B PHE* 1.3 72.5 - - - +
193B THR* 1.3 63.9 + - - +
194B THR* 5.0 1.3 - - - -
204B LEU 3.7 1.9 - - - +
206B TYR* 2.8 39.5 + - + +
208B LEU* 3.9 20.5 - - + +
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Residues in contact with THR 193 (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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45A ARG* 3.0 16.7 + - - +
214A EDO 2.8 21.4 - - - +
185B LEU* 2.9 39.8 + - + +
186B SER* 3.8 20.2 - - - +
191B PHE* 3.8 6.7 + - - +
192B PHE* 1.3 79.8 + - - +
194B THR* 1.3 67.5 + - - +
195B ILE* 5.0 0.2 - - + -
203B LEU* 3.9 30.5 - - + -
204B LEU 3.3 9.9 - - - +
205B GLY* 3.9 1.7 - - - -
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Residues in contact with THR 194 (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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42A GLN* 3.8 21.7 + - - -
45A ARG* 4.5 18.8 + - - +
46A LEU* 4.6 16.1 - - + +
49A LEU* 4.4 14.3 - - + +
214A EDO 3.9 5.6 - - - -
192B PHE* 5.0 1.6 - - - -
193B THR* 1.3 78.1 - - - +
195B ILE* 1.3 67.9 + - - +
196B VAL* 4.0 20.1 + - + +
202B VAL 3.8 0.3 - - - +
203B LEU* 3.6 1.2 - - - -
204B LEU* 2.8 44.2 + - + +
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Residues in contact with ILE 195 (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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13A LEU* 3.8 26.6 - - + +
16A LEU* 3.6 27.8 - - + -
42A GLN* 5.1 4.4 + - - +
214A EDO 4.3 10.0 + - - +
160B ALA* 4.4 3.6 - - + -
161B LEU* 4.0 29.4 - - + -
182B ASN* 3.7 32.3 - - + +
186B SER* 5.5 0.2 - - - +
193B THR* 5.0 0.2 - - + -
194B THR* 1.3 80.4 + - - +
196B VAL* 1.3 66.4 + - - +
197B PRO* 3.9 5.2 - - - +
202B VAL 3.4 20.2 - - - +
203B LEU* 3.9 20.4 - - + +
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Residues in contact with VAL 196 (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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46A LEU* 4.0 33.9 - - + -
196A VAL* 5.0 11.4 - - + -
198A VAL* 5.2 6.5 - - + -
46B LEU* 3.9 15.7 - - + -
161B LEU* 5.2 0.2 - - - -
194B THR* 4.0 14.3 - - + +
195B ILE* 1.3 76.5 - - - +
197B PRO* 1.3 66.7 - - + +
198B VAL* 2.8 31.0 + - + +
201B GLY* 3.5 1.7 - - - -
202B VAL* 2.8 42.8 + - + +
204B LEU* 4.4 9.2 - - + -
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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