Contacts of the strand formed by residues 191 - 196 (chain B) in PDB entry 3UXO
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 MET 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B ILE* 4.7 0.2 - - - +
155B MET* 3.8 14.1 - - + +
158B MET* 3.5 43.5 - - + -
159B GLN 4.3 4.9 - - - -
162B VAL* 4.0 9.9 - - + -
177B VAL* 3.9 34.8 - - + -
190B ASP* 1.3 79.2 - - - +
192B ASP* 1.3 66.6 + - - +
193B VAL* 4.6 4.0 - - + -
223B PHE* 3.6 17.3 - - + -
239B CYS* 4.3 0.2 - - - -
254B ARG 3.0 8.6 + - - +
255B ILE* 3.1 31.3 - - + -
256B ASP 2.8 27.9 + - - +
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Residues in contact with ASP 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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176B THR 3.7 0.2 - - - +
177B VAL* 3.3 5.4 - - - +
178B CYS* 2.7 38.9 + - + +
179B GLY* 4.9 7.4 - - - +
190B ASP* 4.2 10.3 + - - +
191B MET* 1.3 74.3 - - - +
193B VAL* 1.3 61.1 + - - +
194B LEU* 3.1 26.8 - - - +
256B ASP* 3.6 9.3 - - - +
258B ARG* 2.8 33.0 + - - +
272B PHE* 4.0 14.4 - - - +
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Residues in contact with VAL 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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162B VAL* 4.5 17.5 - - + -
163B LEU* 5.9 0.4 - - + -
175B ALA* 4.1 24.2 - - + -
176B THR 3.3 10.3 - - - +
177B VAL* 4.4 13.5 - - + +
191B MET* 4.6 5.4 - - + -
192B ASP* 1.3 76.4 + - - +
194B LEU* 1.3 68.5 + - - +
195B LEU* 3.9 1.7 + - + -
255B ILE* 4.5 11.0 - - + -
256B ASP 3.0 18.9 + - - +
257B ILE* 3.4 28.2 - - + +
258B ARG 2.8 25.6 + - - -
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Residues in contact with LEU 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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175B ALA* 3.2 0.9 - - - -
176B THR 2.8 26.7 + - - +
178B CYS* 3.5 18.6 - - - -
192B ASP* 3.1 27.4 - - - +
193B VAL* 1.3 75.3 - - - +
195B LEU* 1.3 60.4 + - - +
258B ARG* 3.4 22.4 - - + +
260B GLN* 5.2 6.5 - - + -
265B TYR* 2.8 36.9 + - + +
268B GLY* 3.3 32.3 - - - +
269B VAL* 3.4 20.0 - - + +
272B PHE* 3.8 16.6 - - + -
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Residues in contact with LEU 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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166B VAL* 4.3 12.6 - - + -
173B TYR* 3.4 35.4 - - + -
174B ILE 3.4 8.1 - - - +
175B ALA* 4.0 16.4 - - + +
193B VAL* 3.9 2.2 + - + -
194B LEU* 1.3 73.7 - - - +
196B THR* 1.3 65.5 + - - +
210B LEU 4.3 5.2 - - - +
211B LEU* 4.4 18.2 - - + -
214B VAL* 3.6 30.7 - - + -
257B ILE* 4.4 9.4 - - + -
258B ARG 2.7 17.9 + - - +
259B LEU* 3.5 11.9 - - + +
260B GLN* 3.0 26.0 + - - +
265B TYR* 4.2 1.4 - - - -
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Residues in contact with THR 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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172B GLU 5.3 0.9 - - - +
173B TYR* 3.5 10.0 - - - -
174B ILE* 2.7 58.0 + - + +
195B LEU* 1.3 75.3 - - - +
197B HIS* 1.3 66.3 + - - +
198B PRO* 5.8 0.2 - - + -
259B LEU* 4.5 3.8 - - - -
260B GLN 3.2 17.5 + - - -
261B PRO 3.7 0.2 + - - -
262B LYS* 3.2 39.7 - - + +
265B TYR* 3.5 23.9 - - + -
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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