Contacts of the strand formed by residues 152 - 162 (chain B) 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 GLY 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B ASP 3.6 2.0 + - - -
151B THR* 1.3 78.8 - - - +
153B ILE* 1.3 63.5 + - - -
154B TYR* 3.5 7.1 - - - -
209B HIS* 3.5 8.5 - - - -
210B LEU 2.8 35.6 + - - +
240B LYS* 3.4 11.4 - - - -
105D LYS* 6.5 1.3 - - - -
135D ARG* 5.9 1.8 - - - -
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Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLY* 1.3 75.2 - - - -
154B TYR* 1.3 60.6 + - - +
207B VAL* 3.3 32.5 - - + -
208B PHE 3.4 6.5 - - - +
209B HIS* 3.8 19.7 - - + -
240B LYS* 3.7 6.1 - - - +
241B LEU* 2.9 33.0 + - + +
108D VAL* 4.3 13.9 - - + -
133D LEU* 4.1 22.7 - - + -
135D ARG* 3.7 53.6 - - + +
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Residues in contact with TYR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B SER* 5.4 3.1 - - - -
137B ARG 5.4 0.4 + - - -
138B GLY* 4.0 10.2 + - - -
139B LEU* 3.8 33.9 - - + -
148B VAL* 4.3 0.6 - - + +
150B ASP* 2.7 39.3 + - - +
152B GLY* 3.5 24.9 - - - -
153B ILE* 1.3 75.1 - - - +
155B LEU* 1.3 61.5 + - - +
156B LEU* 3.5 21.8 + - + +
207B VAL* 3.3 3.7 - - - -
208B PHE 2.9 31.4 + - - +
210B LEU* 3.6 26.5 - - + -
238B PHE* 4.4 2.9 - - + -
239B VAL 3.1 6.1 - - - +
240B LYS* 3.6 41.6 - - + +
241B LEU* 4.5 3.1 - - - +
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Residues in contact with LEU 155 (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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155A LEU* 4.5 26.5 - - + -
154B TYR* 1.3 70.1 - - - +
156B LEU* 1.3 78.7 + - - +
157B TYR* 4.3 15.8 - - + +
203B TYR* 5.9 0.9 - - - +
205B ALA* 4.4 11.7 - - + -
206B GLY* 3.5 17.0 - - - +
207B VAL* 4.1 11.9 - - + -
237B GLY 3.8 0.2 - - - +
238B PHE* 3.1 7.6 - - - +
239B VAL* 2.7 57.4 + - + +
241B LEU* 4.0 16.8 - - + +
155D LEU* 4.8 15.0 - - + -
157D TYR* 5.8 2.2 - - + -
203D TYR* 5.8 1.1 - - - +
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B TYR* 3.5 13.2 + - + +
155B LEU* 1.3 71.9 - - - +
157B TYR* 1.3 60.8 + - - +
173B VAL* 3.9 21.5 - - + -
184B LEU* 3.9 25.8 - - + -
185B PHE* 3.8 10.9 - - + -
205B ALA* 3.1 3.9 - - - +
206B GLY 2.8 37.6 + - - +
208B PHE* 4.3 5.2 - - + -
210B LEU* 3.5 23.6 - - + -
216B ILE* 4.1 7.6 - - + -
236B LEU* 5.4 3.8 - - + -
237B GLY 3.5 3.1 - - - +
238B PHE* 3.3 40.4 - - + -
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Residues in contact with TYR 157 (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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155A LEU* 5.4 2.2 - - + -
205A ALA 4.1 4.9 - - - -
206A GLY* 3.8 9.2 - - - -
207A VAL* 3.1 40.8 + - + +
109B LEU 4.6 1.0 + - - -
110B HIS* 2.8 31.8 + - - +
155B LEU* 4.3 18.2 - - + -
156B LEU* 1.3 75.2 - - - +
158B SER* 1.3 60.3 + - - +
185B PHE* 4.4 1.8 - - - -
203B TYR* 3.3 24.7 - + + +
204B SER 3.5 5.2 - - - -
205B ALA* 3.6 7.4 - - + -
235B PHE* 3.8 26.0 - + - -
236B LEU* 3.4 9.0 - - - +
237B GLY* 2.9 62.6 + - - -
238B PHE* 4.0 3.6 - - - -
239B VAL* 4.9 1.1 - - + -
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Residues in contact with SER 158 (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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129B TRP* 6.0 0.5 - - - -
157B TYR* 1.3 76.9 - - - +
159B GLN* 1.3 61.1 + - - +
160B VAL* 4.4 1.0 - - - +
171B GLN* 2.9 30.4 + - - +
173B VAL* 4.0 20.0 - - - -
185B PHE* 4.1 5.8 - - - -
203B TYR* 3.4 4.7 - - - -
204B SER 3.0 31.0 + - - -
218B VAL* 4.1 9.3 - - - +
235B PHE* 3.4 9.4 + - - -
236B LEU* 4.3 10.7 - - - +
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Residues in contact with GLN 159 (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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186A ARG 2.8 24.6 + - - +
203A TYR 4.6 0.3 - - - +
204A SER* 2.8 28.4 + - - -
129B TRP* 5.0 0.2 - - - -
158B SER* 1.3 73.9 + - - +
160B VAL* 1.3 76.6 + - - +
201B SER* 3.9 16.9 + - - -
202B CYS 3.2 12.6 - - - +
203B TYR* 3.7 13.9 - - + +
232B HIS 4.0 1.0 + - - -
233B GLY* 2.8 25.1 + - - +
234B THR* 3.3 2.1 - - - +
235B PHE* 2.8 60.8 + - + +
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Residues in contact with VAL 160 (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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127B VAL* 6.0 1.3 - - + -
129B TRP* 5.8 1.3 - - + -
158B SER* 4.4 3.1 - - - +
159B GLN* 1.3 80.8 - - - +
161B LEU* 1.3 61.4 - - - +
162B PHE* 3.4 37.2 - - + -
171B GLN* 3.6 31.6 - - + +
201B SER* 3.4 1.2 - - - -
202B CYS* 2.8 33.3 + - - +
218B VAL* 4.9 4.3 - - + -
220B ILE* 4.5 8.7 - - + -
227B LEU* 3.8 27.6 - - + -
233B GLY 3.9 2.9 - - - -
234B THR* 3.6 14.4 - - + +
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Residues in contact with LEU 161 (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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186A ARG* 3.6 30.5 - - - +
188A ILE* 3.6 32.5 - - + -
160B VAL* 1.3 72.1 - - - +
162B PHE* 1.3 72.1 + - - +
199B TYR* 5.2 7.2 - - + -
200B ASN 3.8 19.3 - - - +
201B SER* 4.0 7.0 - - - +
227B LEU* 3.2 5.4 - - - +
228B SER* 2.9 48.6 + - - +
233B GLY* 3.5 21.0 + - - +
234B THR* 3.1 7.1 + - - -
18R LEU* 5.8 0.7 - - - +
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Residues in contact with PHE 162 (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 VAL* 3.4 40.4 - - + -
161B LEU* 1.3 79.4 - - - +
163B HIS* 1.3 60.6 + - - +
164B ASP* 3.8 2.0 - - + -
169B MET* 3.7 40.8 - - + -
170B GLY* 3.5 42.0 - - - -
189B ARG* 5.6 1.8 - - + -
191B MET* 3.9 17.3 - - + -
199B TYR* 3.3 6.9 - - - +
200B ASN* 2.9 40.0 + - + +
202B CYS* 4.0 10.5 - - + -
220B ILE* 3.9 13.5 - - + -
226B LYS 3.6 4.5 - - - +
227B LEU* 4.2 11.2 - - + -
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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