Contacts of the strand formed by residues 222 - 233 (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 THR 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B TRP* 3.8 34.1 + - - -
167B ILE 3.2 9.0 - - - -
168B THR* 4.4 3.6 - - - -
211B LYS* 3.8 9.8 - - - +
212B GLU* 2.9 27.5 + - - +
214B ASN* 3.9 22.1 + - - +
217B GLN 5.4 2.5 - - - +
220B SER* 3.8 17.0 + - - +
221B ASP* 1.3 78.9 + - - +
223B ARG* 1.3 65.1 + - - +
1399B FAD 4.4 16.6 - - + -
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Residues in contact with ARG 223 (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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165B MET* 4.6 0.7 - - - -
166B TRP 4.0 6.5 - - - +
167B ILE* 3.0 32.6 + - - +
170B GLY* 4.4 6.1 - - - -
171B GLY* 3.5 26.3 + - - +
172B LYS* 4.6 6.5 - - - +
208B ILE* 3.9 8.3 - - + +
209B GLY 2.9 29.1 + - - +
210B ARG* 3.0 25.6 - - - +
211B LYS* 3.7 20.2 - - - +
212B GLU* 3.9 9.9 - - - -
221B ASP* 2.6 51.1 + - - -
222B THR* 1.3 74.5 + - - +
224B GLY* 1.3 66.7 + - - +
225B ILE* 4.2 1.5 - - + +
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Residues in contact with GLY 224 (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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163B GLN* 4.3 2.9 - - - -
164B LYS 3.6 12.6 - - - -
165B MET* 3.8 23.6 - - - -
207B GLN 4.3 0.3 - - - +
209B GLY* 2.9 30.1 + - - -
210B ARG 4.6 1.6 + - - -
212B GLU* 4.7 3.2 + - - +
223B ARG* 1.3 75.3 - - - +
225B ILE* 1.3 64.3 + - - +
226B VAL* 4.3 1.6 - - - -
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Residues in contact with ILE 225 (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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134B CYS* 4.2 5.8 - - - -
163B GLN* 3.1 5.1 - - - +
164B LYS* 2.9 32.2 + - + -
167B ILE* 3.7 34.3 - - + -
170B GLY* 3.9 11.2 - - - +
176B TYR* 3.8 33.2 - - + +
206B VAL* 4.2 19.3 - - + -
207B GLN 3.7 9.9 - - - +
208B ILE* 4.7 6.1 - - - -
223B ARG* 4.2 3.6 - - + +
224B GLY* 1.3 80.5 - - - +
226B VAL* 1.3 62.9 + - - +
227B PHE* 3.5 30.0 - - + -
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Residues in contact with VAL 226 (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 GLY 3.7 9.2 - - - +
163B GLN* 4.0 25.6 - - + +
205B GLY 3.4 2.3 - - - +
206B VAL* 3.9 1.6 - - - -
207B GLN* 3.0 59.0 + - + +
224B GLY 5.5 1.1 - - - -
225B ILE* 1.3 75.9 - - - +
227B PHE* 1.3 69.3 + - - +
228B GLU* 5.1 2.5 - - + -
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Residues in contact with PHE 227 (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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134B CYS* 4.9 4.5 - - - -
149B THR* 5.6 2.2 - - + -
160B ILE* 4.2 19.1 - - + -
161B ASN* 3.4 2.6 + - - -
162B GLY 2.6 48.7 + - - +
163B GLN* 4.6 0.9 - - - -
164B LYS* 4.0 20.6 - - + -
176B TYR* 4.3 16.2 - + - -
178B LEU* 4.3 21.3 - - + -
199B VAL* 4.5 16.2 - - + -
205B GLY 3.8 2.2 - - - -
206B VAL* 4.4 15.5 - - + -
225B ILE* 3.5 41.1 - - + -
226B VAL* 1.3 76.2 - - - +
228B GLU* 1.3 61.8 + - - +
229B ASP 4.1 0.9 - - - -
230B VAL* 3.5 26.5 - - + -
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Residues in contact with GLU 228 (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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161B ASN* 3.2 6.7 - - - +
205B GLY* 3.1 24.1 + - - -
207B GLN* 2.6 39.0 + - - +
226B VAL* 5.1 2.9 - - + -
227B PHE* 1.3 73.3 - - - +
229B ASP* 1.3 79.3 + - + +
230B VAL* 3.1 2.1 + - - +
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Residues in contact with ASP 229 (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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159B ILE* 3.8 16.2 - - + +
160B ILE 3.1 2.4 + - - -
161B ASN* 2.4 45.9 + - - +
204B PRO* 4.6 2.8 - - - +
205B GLY* 5.3 0.2 - - - -
228B GLU* 1.3 77.3 - - + +
230B VAL* 1.3 67.5 + - - +
231B ARG* 3.4 13.5 + - - +
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Residues in contact with VAL 230 (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 3.5 0.4 - - - +
159B ILE* 3.3 3.6 - - - -
160B ILE* 2.8 38.4 + - + +
199B VAL* 4.5 9.0 - - + -
203B THR* 4.0 15.0 - - + -
204B PRO 3.6 15.0 - - - +
205B GLY 3.9 15.0 - - - -
206B VAL* 4.1 10.1 - - + -
227B PHE* 3.5 39.5 - - + -
228B GLU 3.1 8.7 - - - +
229B ASP* 1.3 78.9 - - - +
231B ARG* 1.3 67.3 + - - +
232B VAL* 4.5 10.1 - - + -
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Residues in contact with ARG 231 (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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154B LYS* 4.3 10.6 - - - +
157B GLU* 3.3 38.4 + - - +
158B TYR 3.5 3.1 - - - -
159B ILE* 3.4 24.5 - - + -
203B THR* 4.0 19.7 - - + +
204B PRO 4.6 0.6 + - - -
229B ASP 3.4 13.4 + - - +
230B VAL* 1.3 74.0 - - - +
232B VAL* 1.3 65.8 + - - +
233B PRO* 4.1 4.7 - - - +
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Residues in contact with VAL 232 (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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157B GLU* 3.0 6.1 - - - +
158B TYR* 2.6 42.6 + - - +
160B ILE* 3.8 16.8 - - + -
197B PHE* 3.6 30.1 - - + -
198B ILE 4.8 0.2 - - - +
199B VAL* 3.7 29.4 - - + -
230B VAL* 4.5 8.7 - - + -
231B ARG* 1.3 79.8 - - - +
233B PRO* 1.3 70.1 - - + +
234B LYS 3.5 0.2 + - - -
236B ASN* 3.6 25.4 - - + -
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Residues in contact with PRO 233 (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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156B ASP 3.4 11.2 - - - +
157B GLU* 4.2 6.5 - - + +
231B ARG 4.1 4.9 - - - +
232B VAL* 1.3 86.2 - - + +
234B LYS* 1.3 52.4 + - - +
235B GLU* 2.6 42.7 + - + +
236B ASN* 2.7 49.6 + - - +
237B VAL 4.2 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