Contacts of the strand formed by residues 181 - 190 (chain D) in PDB entry 1XU1
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 ARG 181 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D SER* 4.4 14.8 + - - +
175D ARG 3.6 4.7 - - - +
176D GLU* 3.0 40.1 + - + +
180D ARG* 1.3 76.6 - - - +
182D GLU* 1.3 66.3 + - - +
183D THR* 5.1 4.9 + - - +
217D THR* 3.9 8.5 + - - -
219D LYS* 3.1 40.7 - - - +
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Residues in contact with GLU 182 (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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174D SER* 3.3 4.1 - - - -
175D ARG* 2.8 76.3 + - - +
180D ARG* 4.2 1.5 - - + -
181D ARG* 1.3 76.7 - - - +
183D THR* 1.3 73.2 + - - +
184D LEU* 3.5 13.0 + - + +
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Residues in contact with THR 183 (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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232A HIS* 3.6 47.2 + - + +
172D VAL* 3.7 25.1 - - + +
173D VAL 3.8 3.6 - - - +
174D SER* 3.7 11.6 + - - -
181D ARG* 4.3 5.1 + - - +
182D GLU* 1.3 80.5 - - - +
184D LEU* 1.3 64.6 + - - +
185D PHE 4.1 5.8 - - - +
186D ARG* 4.1 2.2 - - + -
84T ARG* 3.1 23.0 + - - +
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Residues in contact with LEU 184 (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* 5.4 0.5 + - - -
231A PRO 4.3 3.5 - - - +
232A HIS* 3.5 13.9 - - - +
235A PHE* 4.8 1.7 - - - -
156D LEU* 3.7 29.2 - - + -
173D VAL* 2.8 16.8 + - + +
174D SER 4.4 3.8 - - - -
175D ARG* 4.2 34.8 - - + +
182D GLU* 3.9 23.1 - - + +
183D THR* 1.3 75.4 - - - +
185D PHE* 1.3 67.7 + - + +
208D PHE* 3.7 49.4 - - + -
209D HIS 6.1 0.2 - - - +
210D LEU* 4.3 8.5 - - + -
216D ILE* 4.6 1.8 - - + -
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Residues in contact with PHE 185 (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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232A HIS* 3.5 7.9 - - - -
235A PHE* 3.7 23.6 - - + -
156D LEU* 3.9 28.9 - - + -
158D SER* 4.0 13.9 - - - -
171D GLN* 4.2 2.9 - - + +
172D VAL* 3.8 0.9 - - - -
173D VAL* 2.9 64.1 + - + +
183D THR* 3.8 1.4 - - - +
184D LEU* 1.3 79.8 - - + +
186D ARG* 1.3 65.6 + - - +
187D CYS* 5.7 0.2 - - + -
204D SER* 3.4 46.2 - - - +
205D ALA* 4.2 2.0 - - - -
206D GLY 4.4 3.4 - - - -
208D PHE* 3.6 27.4 - + + -
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Residues in contact with ARG 186 (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* 2.8 27.9 + - - +
161A LEU* 3.7 21.4 - - + +
201A SER* 4.6 0.5 - - - -
228A SER* 4.3 1.2 + - - -
230A SER* 3.3 32.7 + - - -
232A HIS* 2.9 36.2 + - - +
233A GLY* 4.1 4.3 - - - +
171D GLN 3.3 7.9 - - - +
172D VAL* 4.1 18.8 - - + -
183D THR* 4.1 7.4 - - + -
185D PHE* 1.3 82.1 - - - +
187D CYS* 1.3 62.3 + - - +
188D ILE* 3.8 18.6 - - + +
204D SER* 4.0 1.4 + - - -
82T LEU* 2.9 37.3 + - + -
83T LEU 3.7 16.4 + - - -
84T ARG* 3.8 19.2 - - - +
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Residues in contact with CYS 187 (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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201A SER* 3.5 12.3 - - - -
170D GLY* 3.1 22.7 - - - -
171D GLN* 3.1 29.0 + - + +
185D PHE* 5.7 0.2 - - + -
186D ARG* 1.3 73.9 - - - +
188D ILE* 1.3 66.7 + - - +
189D ARG* 3.8 3.8 - - - -
202D CYS* 2.0 57.4 - - - -
203D TYR 3.4 15.5 - - - -
204D SER* 4.0 10.3 - - - -
82T LEU* 3.9 0.5 - - - +
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Residues in contact with ILE 188 (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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161A LEU* 3.8 24.7 - - + -
199A TYR* 3.8 23.8 - - + +
200A ASN* 3.4 1.6 - - - -
201A SER* 2.9 35.5 + - - +
168D THR* 4.4 6.5 - - - -
169D MET 3.6 6.5 - - - +
186D ARG* 3.8 28.5 - - + +
187D CYS* 1.3 82.4 - - - +
189D ARG* 1.3 75.3 + - - +
202D CYS* 3.4 0.2 - - - -
82T LEU* 3.8 22.9 - - + +
83T LEU* 3.8 28.0 - - + -
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Residues in contact with ARG 189 (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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189A ARG* 3.4 17.4 - - - +
199A TYR 4.0 2.2 - - - -
200A ASN* 3.3 9.5 + - - -
201A SER* 2.9 39.0 + - - -
202A CYS* 4.4 0.8 - - - +
203A TYR* 4.6 3.8 - - - +
189B ARG* 3.1 32.3 - - - +
162D PHE* 5.7 2.0 - - + -
168D THR* 3.3 3.2 - - - -
169D MET* 2.9 37.8 + - + +
187D CYS* 3.8 8.3 - - - -
188D ILE* 1.3 83.1 + - - +
190D SER* 1.3 67.6 + - - +
191D MET* 3.9 5.8 - - - +
200D ASN* 4.4 17.5 - - + -
201D SER 3.0 29.8 + - - +
202D CYS* 3.6 24.6 - - + +
203D TYR 4.2 9.3 + - - +
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Residues in contact with SER 190 (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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190A SER 4.9 0.3 + - - -
192A PRO* 3.7 17.0 - - - +
197A ARG* 3.3 26.5 - - - -
199A TYR 3.5 6.6 + - - -
200A ASN* 3.0 27.9 + - - +
167D PHE 3.4 9.2 - - - -
168D THR* 4.2 2.0 - - - -
189D ARG* 1.3 74.1 - - - +
191D MET* 1.3 61.3 + - - +
192D PRO* 4.4 0.9 - - - +
200D ASN* 3.3 18.0 + - - -
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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