Contacts of the strand formed by residues 199 - 210 (chain B) in PDB entry 1UXU
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 TYR 199 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B TYR* 6.0 0.2 - - - +
154B ASN* 4.2 20.0 - - + -
188B ASN 4.0 0.5 - - - +
189B VAL* 3.6 2.1 - - - +
190B ILE* 2.9 45.3 + - + +
192B TYR* 4.2 24.0 - + - -
196B SER* 4.1 9.0 + - - -
197B GLU* 3.3 37.9 + - + -
198B PRO* 1.3 77.3 - - - +
200B PRO* 1.3 66.7 - - - +
201B ASP* 5.1 0.5 - - - +
1213B MLK 3.8 79.4 - - + +
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Residues in contact with PRO 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TYR* 3.9 17.7 + - - +
149B GLY* 4.3 4.9 - - - -
150B SER 5.1 0.7 + - - -
153B TYR 5.4 1.8 - - - +
154B ASN* 4.4 2.2 - - - -
155B GLY* 3.5 33.7 - - - +
158B VAL 4.1 9.2 - - - +
159B ASP* 4.2 11.0 - - - +
160B ILE* 3.9 21.2 - - + +
187B LYS* 4.3 2.7 - - - -
188B ASN 3.1 10.1 - - - +
189B VAL* 4.0 17.0 - - + -
198B PRO 3.6 1.3 - - - +
199B TYR* 1.3 88.0 - - - +
201B ASP* 1.3 62.4 + - - +
1213B MLK 5.2 0.4 - - - -
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Residues in contact with ASP 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TYR* 4.0 9.6 - - + -
147B THR* 3.5 21.5 - - + +
148B PHE 3.2 15.7 - - - +
160B ILE* 4.2 5.4 - - - -
187B LYS* 3.4 9.2 - - - +
188B ASN* 2.7 58.8 + - - +
199B TYR 5.1 0.3 - - - +
200B PRO* 1.3 75.0 - - - +
202B VAL* 1.3 65.6 + - - +
203B THR* 2.9 21.0 + - - -
1213B MLK 3.6 20.0 - - + -
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Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.6 31.4 - - + -
146B LEU 3.7 1.4 - - - +
147B THR* 3.5 1.2 - - - -
148B PHE* 2.8 37.9 + - + +
160B ILE* 3.9 24.4 - - + +
161B PHE 4.2 1.6 - - - -
162B ASN* 3.7 37.9 - - - +
186B VAL 3.3 7.9 - - - +
187B LYS* 4.4 5.8 - - + -
201B ASP* 1.3 81.5 - - - +
203B THR* 1.3 57.9 + - - +
204B PHE* 3.9 16.2 - - + -
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Residues in contact with THR 203 (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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145B ASN* 3.9 14.6 - - - +
146B LEU 3.3 3.8 - - - +
147B THR* 2.7 27.6 + - - +
184B PRO 3.8 1.0 - - - +
185B ALA* 3.4 2.3 - - - -
186B VAL* 2.9 35.7 + - - +
188B ASN* 3.6 6.6 + - - -
201B ASP* 2.9 19.1 + - - -
202B VAL* 1.3 72.5 - - - +
204B PHE* 1.3 67.5 + - - +
205B THR* 4.0 1.5 + - - +
2215B NAG 3.5 38.2 + - - +
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Residues in contact with PHE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 4.6 7.2 - - + -
36B GLN* 5.8 0.2 - - - -
37B ILE* 3.4 37.5 - - + -
144B CYS 3.6 0.5 - - - +
145B ASN* 3.4 2.9 - - - -
146B LEU* 2.8 45.5 + - + +
148B PHE* 3.9 12.3 - + - -
162B ASN* 3.5 16.4 - - - -
164B LEU* 5.7 0.4 - - + -
166B SER 4.1 4.0 - - - -
167B GLY* 3.7 34.3 - - - -
183B MET* 3.9 24.9 - - + -
184B PRO 3.5 2.9 - - - -
185B ALA* 3.6 20.2 - - + -
202B VAL* 3.9 23.3 - - + -
203B THR* 1.3 75.0 - - - +
205B THR* 1.3 61.0 + - - +
206B LEU 3.4 2.8 + - - -
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Residues in contact with THR 205 (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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143B GLN* 3.6 35.7 - - + +
144B CYS 5.2 0.2 - - - +
145B ASN* 2.9 22.7 + - - +
183B MET* 4.1 3.1 - - - -
184B PRO* 3.0 43.6 + - + +
186B VAL* 5.8 0.7 - - - +
203B THR* 4.0 1.6 + - - +
204B PHE* 1.3 70.5 - - - +
206B LEU* 1.3 61.1 - - - +
207B LEU* 3.2 8.3 + - + +
2215B NAG 3.6 22.9 + - - -
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Residues in contact with LEU 206 (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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39B LEU* 4.2 25.4 - - + -
42B ILE* 5.1 2.0 - - + -
52B LEU* 3.8 28.9 - - + -
142B GLN 3.6 2.8 - - - +
143B GLN* 3.8 0.3 - - - -
144B CYS* 2.8 46.3 + - + +
146B LEU* 5.0 5.6 - - + -
180B VAL* 3.7 30.1 - - + -
182B GLY 3.6 6.3 - - - +
183B MET* 4.0 29.4 - - + +
204B PHE 3.4 2.2 + - - +
205B THR* 1.3 70.4 - - - +
207B LEU* 1.3 58.2 + - - +
208B LEU* 3.7 24.9 + - + -
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Residues in contact with LEU 207 (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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133B ASP* 4.3 9.0 - - - +
136B TYR* 6.1 0.7 - - + -
137B PHE 3.9 17.9 - - - +
138B PRO* 4.2 5.6 - - + -
141B ASN* 3.8 22.2 - - + +
142B GLN 3.8 13.0 - - - +
143B GLN* 4.0 24.0 - - + +
180B VAL* 3.8 2.3 - - - -
181B HIS* 2.9 51.3 + - + +
182B GLY 2.9 20.2 + - - +
205B THR* 3.2 8.0 + - + +
206B LEU* 1.3 71.7 - - - +
208B LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 208 (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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42B ILE* 3.8 30.1 - - + -
45B MET* 4.2 22.4 - - + -
52B LEU* 4.4 10.8 - - + -
141B ASN* 3.1 8.9 - - - +
142B GLN* 2.9 38.3 + - + +
144B CYS* 4.2 19.1 - - - -
178B TRP* 3.9 19.5 - - + -
179B GLU 3.3 5.4 - - - +
180B VAL* 3.9 10.8 - - + -
181B HIS* 5.1 0.2 - - - -
206B LEU* 3.7 33.7 - - + +
207B LEU* 1.3 74.3 - - - +
209B LYS* 1.3 59.4 + - - +
210B ARG 4.1 0.2 + - - -
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Residues in contact with LYS 209 (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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138B PRO* 3.6 46.9 + - + +
140B ASP* 3.6 16.3 - - - +
141B ASN* 4.2 1.1 - - - +
178B TRP* 3.5 4.3 - - - -
179B GLU* 2.7 71.4 + - + +
181B HIS* 4.7 7.4 - - + +
207B LEU 4.1 1.0 + - - -
208B LEU* 1.3 73.7 - - - +
210B ARG* 1.3 80.4 + - - +
211B ARG 3.2 0.3 + - - -
212B SER* 4.9 11.1 - - - +
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Residues in contact with ARG 210 (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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47B GLU* 2.8 42.8 + - - -
132B VAL* 5.6 6.3 - - - +
140B ASP* 2.9 49.3 + - - +
141B ASN 5.5 2.4 + - - -
142B GLN* 4.8 3.2 - - - +
177B GLU* 3.9 12.0 + - - +
178B TRP* 3.4 33.0 - - + -
209B LYS* 1.3 95.1 + - - +
211B ARG* 1.3 73.0 + - - +
212B SER* 4.8 0.7 - - - -
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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