Contacts of the strand formed by residues 199 - 210 (chain D) in PDB entry 1XU2
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B PHE* 4.5 0.7 - + - -
168B THR* 4.0 6.3 - - + -
188B ILE* 3.9 18.8 - - + +
190B SER* 2.8 27.6 + - - -
161D LEU* 5.2 8.1 - - + -
162D PHE 3.4 7.6 - - - +
163D HIS* 3.3 48.1 + + + -
191D MET* 4.0 0.4 - - - +
196D ASP* 3.5 20.8 + - - -
197D ARG 3.0 14.9 + - - -
198D ALA* 1.3 76.3 - - - +
200D ASN* 1.3 66.8 + - - +
18S LEU* 3.8 44.6 - - + -
20S ALA* 4.0 19.5 - - + +
21S CYS 5.1 1.6 + - - -
22S ILE* 4.7 6.1 - - + +
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Residues in contact with ASN 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B ILE* 3.4 5.3 - - - +
189B ARG* 3.5 17.7 - - - +
190B SER* 3.0 26.0 + - - +
161D LEU* 3.7 5.5 - - - +
162D PHE* 2.9 34.9 + - + +
189D ARG* 3.6 23.9 - - + +
190D SER 3.1 24.9 + - - -
191D MET* 3.4 20.4 - - - +
192D PRO* 3.8 11.9 - - - +
199D TYR* 1.3 78.4 + - - +
201D SER* 1.3 60.7 + - - +
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Residues in contact with SER 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ARG 4.6 0.2 - - - -
187B CYS* 3.7 10.4 - - - -
188B ILE* 2.9 34.8 + - - -
189B ARG* 2.8 27.1 + - - -
159D GLN* 3.8 26.9 + - - -
160D VAL 3.4 7.2 - - - -
161D LEU* 3.9 13.7 - - - +
189D ARG* 3.0 6.9 + - - -
200D ASN* 1.3 77.0 - - - +
202D CYS* 1.3 61.0 + - - +
203D TYR* 4.2 0.9 + - - +
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Residues in contact with CYS 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D GLN* 3.2 1.9 - - - -
160D VAL 2.8 34.2 + - - +
162D PHE* 3.9 11.7 - - + -
170D GLY* 4.5 2.7 - - - -
171D GLN* 3.0 20.0 + - - +
187D CYS* 2.0 59.5 - - - -
188D ILE* 3.5 14.8 - - - -
189D ARG* 3.8 15.0 - - + +
201D SER* 1.3 74.4 - - - +
203D TYR* 1.3 58.1 + - - +
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Residues in contact with TYR 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLN* 4.5 0.3 - - - +
201A SER* 5.3 0.2 + - - -
203A TYR* 3.5 39.1 + + - +
155B LEU* 5.8 0.7 - - - +
189B ARG* 5.8 1.8 - - - +
203B TYR* 3.5 35.7 + + - +
204B SER* 4.0 0.7 - - - -
205B ALA* 3.2 48.1 - - + +
157D TYR* 3.3 32.8 - + + +
158D SER 3.4 6.1 - - - -
159D GLN* 3.7 32.5 - - + +
187D CYS* 3.4 9.5 - - - -
189D ARG* 4.8 3.9 + - - +
201D SER* 4.2 1.3 - - - +
202D CYS* 1.3 74.5 - - - +
204D SER* 1.3 74.5 + - - +
205D ALA* 3.8 5.5 - - + +
235D PHE* 4.3 3.4 - + - -
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Residues in contact with SER 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLN* 2.7 27.7 + - - -
203A TYR* 4.0 5.1 - - - -
235A PHE* 3.7 7.4 - - - -
157D TYR* 3.5 0.2 - - - -
158D SER 2.9 33.0 + - - +
171D GLN* 4.6 0.2 - - - +
185D PHE* 3.4 28.4 - - - -
186D ARG 4.3 0.9 - - - -
187D CYS* 4.0 15.5 - - - -
202D CYS 4.4 0.2 + - - -
203D TYR* 1.3 83.7 - - - +
205D ALA* 1.3 69.5 + - - +
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Residues in contact with ALA 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A TYR* 4.0 1.8 - - - -
203A TYR* 3.3 29.3 - - - +
235A PHE* 3.3 23.0 - - - -
155D LEU* 4.6 9.0 - - + -
156D LEU 3.1 15.5 - - - +
157D TYR* 3.6 15.5 - - + -
185D PHE* 3.9 9.2 - - - -
203D TYR* 3.8 7.9 - - + +
204D SER* 1.3 81.9 + - - +
206D GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A HIS* 4.5 1.6 - - - -
157A TYR* 3.9 15.3 - - - -
155D LEU* 3.5 5.7 - - - +
156D LEU 2.8 31.5 + - - +
185D PHE* 4.1 0.4 - - - -
205D ALA* 1.3 77.8 - - - +
207D VAL* 1.3 62.4 + - - -
208D PHE* 3.3 25.7 - - - -
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Residues in contact with VAL 207 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A VAL* 4.2 11.0 - - + -
109A LEU 5.9 0.7 - - - +
110A HIS* 3.8 13.9 + - + +
133A LEU* 3.5 18.6 - - + +
157A TYR* 3.2 25.2 + - + +
238A PHE 5.3 0.7 - - - +
239A VAL* 3.8 26.9 - - + -
153D ILE* 3.3 32.5 - - + -
154D TYR 3.3 6.3 - - - +
155D LEU* 4.2 10.1 - - + -
206D GLY* 1.3 74.4 - - - +
208D PHE* 1.3 72.0 + - - +
241D LEU* 4.1 12.8 - - + -
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Residues in contact with PHE 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A HIS* 3.9 24.2 - + - -
133A LEU* 4.0 7.0 - - - -
235A PHE* 5.8 0.4 - + - -
153D ILE* 3.4 0.8 - - - -
154D TYR* 2.9 32.5 + - - +
156D LEU* 4.4 10.3 - - + -
184D LEU* 3.5 57.0 - - + -
185D PHE* 3.5 24.9 - + + -
206D GLY* 3.3 34.5 - - - -
207D VAL* 1.3 80.0 - - - +
209D HIS* 1.3 63.2 + - - +
210D LEU* 3.4 21.3 + - + +
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Residues in contact with HIS 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 3.9 24.6 - - + +
151D THR* 4.0 16.9 - - + +
152D GLY* 3.3 26.1 + - - -
153D ILE* 4.0 15.2 - - + +
175D ARG* 3.7 18.7 + - - -
208D PHE* 1.3 71.4 - - - +
210D LEU* 1.3 70.3 + - - +
211D HIS* 4.2 6.7 + + + -
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Residues in contact with LEU 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LEU* 5.0 0.7 - - + -
148D VAL* 4.1 19.3 - - + -
151D THR* 3.4 6.2 - - - +
152D GLY 2.9 31.9 + - - +
154D TYR* 3.7 39.0 - - + -
156D LEU* 4.6 5.4 - - + -
175D ARG* 3.8 19.1 - - - +
184D LEU* 4.4 6.7 - - + -
208D PHE* 4.0 18.8 - - + +
209D HIS* 1.3 83.4 - - - +
211D HIS* 1.3 60.0 + - - +
214D ASP* 4.0 2.0 - - - +
216D ILE* 4.0 24.5 - - + -
238D PHE* 4.3 16.6 - - + -
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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