Contacts of the strand formed by residues 194 - 200 (chain B) in PDB entry 1UDY
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 194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B VAL 4.5 0.4 - - - -
145B ALA* 3.5 28.0 - - - -
147B ILE* 3.7 25.6 - - + -
179B LEU* 3.4 23.6 - - + -
180B ALA 3.3 6.3 - - - -
181B ARG* 3.3 51.4 - - + -
190B ALA* 3.3 31.5 + - + -
193B ALA* 1.3 79.0 - - + +
195B THR* 1.3 63.7 + - - +
242B GLY* 3.0 16.7 + - - +
244B GLY* 3.0 18.7 + - - -
245B PHE* 3.7 28.9 - + - +
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Residues in contact with THR 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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158B TYR* 5.7 0.4 - - + -
178B LEU 3.5 0.2 - - - +
179B LEU* 3.9 1.5 - - - -
180B ALA 2.9 30.2 + - - +
182B SER* 2.8 32.1 + - - -
194B PHE* 1.3 74.0 + - - +
196B GLY* 1.3 61.3 + - - +
197B PHE* 3.3 28.7 - - + -
237B VAL* 3.6 22.0 - - + -
240B GLY 3.7 3.6 - - - +
241B GLU* 3.5 29.6 - - + +
242B GLY 3.5 4.3 + - - -
244B GLY* 3.9 6.1 - - - +
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Residues in contact with GLY 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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177B PHE* 4.1 20.0 - - - -
178B LEU 3.3 6.7 - - - -
179B LEU* 4.8 1.1 - - - -
195B THR* 1.3 75.5 - - - +
197B PHE* 1.3 69.6 + - - -
237B VAL* 3.7 3.6 - - - -
238B LEU* 3.2 30.9 + - - +
240B GLY 5.3 0.2 + - - -
244B GLY* 3.8 12.4 - - - +
247B ILE* 5.1 3.9 - - - +
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Residues in contact with PHE 197 (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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151B ALA* 4.3 9.4 - - + -
158B TYR* 3.5 51.6 - + + -
160B ILE* 4.1 11.7 - - + -
176B TYR 3.3 1.6 - - - +
177B PHE* 3.3 3.4 - - - -
178B LEU* 2.6 48.5 + - + +
180B ALA* 4.4 12.1 - - + -
182B SER* 6.0 0.4 - - - -
195B THR* 3.3 39.3 - - + -
196B GLY* 1.3 79.3 - - - -
198B ILE* 1.3 60.2 + - - +
199B VAL* 3.7 17.5 - - + -
232B VAL* 3.6 23.3 - - + -
236B ASN 3.9 2.2 - - - -
237B VAL* 3.8 11.7 - - + -
238B LEU* 3.4 8.1 - - - +
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Residues in contact with ILE 198 (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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108B LEU* 4.0 20.6 - - + -
116B GLN* 5.1 5.6 - - + +
120B TYR* 3.4 42.3 + - + -
175B TRP* 3.2 51.6 - - + -
176B TYR 3.1 6.5 - - - -
177B PHE* 4.5 1.8 - - + +
197B PHE* 1.3 73.4 - - - +
199B VAL* 1.3 59.2 + - - +
200B GLU 4.4 0.2 + - - -
232B VAL* 4.8 0.3 - - - +
236B ASN* 3.1 50.3 + - + +
238B LEU* 3.9 10.8 - - + -
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Residues in contact with VAL 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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160B ILE* 4.5 6.5 - - + -
175B TRP* 3.1 3.0 - - - -
176B TYR* 2.4 54.4 + - + +
178B LEU* 4.5 13.5 - - + -
197B PHE* 4.0 15.0 - - + -
198B ILE* 1.3 76.4 - - - +
200B GLU* 1.3 78.2 + - - +
203B THR* 4.7 2.5 - - - +
206B VAL* 4.7 1.3 - - + -
227B PHE* 4.5 18.8 - - + -
230B VAL* 4.5 16.2 - - + -
232B VAL* 3.7 27.6 - - + -
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Residues in contact with GLU 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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119B LYS* 3.3 12.8 + - - -
120B TYR* 3.1 39.1 + - + -
123B ARG* 3.9 15.9 + - - +
174B ASN* 3.6 9.9 - - - +
175B TRP* 4.1 1.8 - - + +
176B TYR* 4.9 0.4 - - - -
199B VAL* 1.3 84.6 - - - +
201B ALA* 1.3 62.9 + - - +
202B ASP* 4.0 19.7 - - - +
203B THR* 3.0 32.0 + - - +
206B VAL* 4.1 2.8 - - - +
236B ASN* 5.7 0.2 - - - -
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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