Contacts of the strand formed by residues 152 - 163 (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 GLY 152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A ARG* 5.6 2.2 - - - -
150D ASP 3.5 1.6 + - - -
151D THR* 1.3 78.6 - - - +
153D ILE* 1.3 60.2 + - - -
154D TYR* 3.4 13.7 - - - -
209D HIS* 3.3 11.4 - - - -
210D LEU 2.9 32.1 + - - +
240D LYS* 4.0 10.3 - - - -
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Residues in contact with ILE 153 (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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108A VAL* 4.2 17.3 - - + -
133A LEU* 4.2 16.6 - - + -
134A ARG 5.3 0.9 - - - +
135A ARG* 3.4 56.9 - - + +
152D GLY* 1.3 74.2 - - - -
154D TYR* 1.3 59.6 + - - +
207D VAL* 3.3 31.2 - - + -
208D PHE 3.4 5.6 - - - +
209D HIS* 4.0 24.2 - - + +
240D LYS* 3.7 3.8 - - - +
241D LEU* 2.9 31.3 + - + +
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Residues in contact with TYR 154 (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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107D SER* 5.1 3.5 + - - -
137D ARG 5.3 0.2 + - - -
138D GLY* 3.9 10.0 + - - -
139D LEU* 3.6 34.8 - - + -
148D VAL* 4.7 1.6 - - + -
150D ASP* 2.6 35.2 + - - +
152D GLY* 3.4 24.9 - - - -
153D ILE* 1.3 73.9 - - - +
155D LEU* 1.3 65.9 + - - +
156D LEU* 3.6 3.1 + - + +
206D GLY 3.7 0.2 - - - +
207D VAL* 3.3 7.6 - - - -
208D PHE* 2.9 33.4 + - - +
210D LEU* 3.7 34.8 - - + -
238D PHE* 4.3 7.6 - + + -
239D VAL 3.3 5.8 - - - +
240D LYS* 3.6 45.5 - - + +
241D LEU* 4.4 0.4 - - - -
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Residues in contact with LEU 155 (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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155A LEU* 4.7 23.1 - - + -
157A TYR* 5.4 4.0 - - + -
203A TYR* 5.7 1.1 - - - +
239A VAL* 5.8 0.2 - - + -
155B LEU* 4.8 18.6 - - + -
241B LEU* 6.4 0.4 - - + -
154D TYR* 1.3 71.5 - - - +
156D LEU* 1.3 66.6 + - - +
157D TYR* 4.6 13.4 - - + -
205D ALA* 4.6 8.3 - - + -
206D GLY* 3.5 23.1 - - - +
207D VAL* 4.2 10.8 - - + -
237D GLY 3.8 0.5 - - - +
238D PHE* 3.2 6.6 - - - -
239D VAL* 2.8 55.0 + - + +
241D LEU* 3.9 19.0 - - + +
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Residues in contact with LEU 156 (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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154D TYR* 3.6 3.3 + - + +
155D LEU* 1.3 73.9 - - - +
157D TYR* 1.3 64.6 + - - +
173D VAL* 4.0 20.2 - - + -
184D LEU* 3.7 30.1 - - + -
185D PHE* 3.8 13.8 - - + -
205D ALA* 3.1 4.2 - - - +
206D GLY 2.8 36.2 + - - +
208D PHE* 4.4 7.6 - - + -
210D LEU* 4.6 10.3 - - + -
216D ILE* 4.2 5.2 - - + -
236D LEU* 3.8 26.9 - - + -
237D GLY 3.4 4.5 - - - +
238D PHE* 3.7 28.5 - - + -
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Residues in contact with TYR 157 (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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155B LEU* 5.8 2.9 - - + -
205B ALA 3.9 11.0 - - - -
206B GLY* 3.9 9.4 - - - -
207B VAL* 3.1 41.6 + - + +
109D LEU 4.6 0.7 + - - -
110D HIS* 2.7 31.6 + - - +
155D LEU* 4.6 16.2 - - + -
156D LEU* 1.3 77.9 - - - +
158D SER* 1.3 61.4 + - - +
203D TYR* 3.3 25.1 - + + +
204D SER 3.5 4.3 - - - -
205D ALA* 3.6 7.6 - - + -
235D PHE* 3.8 20.2 - + - -
236D LEU* 3.5 7.6 - - - +
237D GLY* 2.9 61.7 + - - -
238D PHE 4.1 2.2 - - - -
239D VAL* 4.8 3.8 - - + -
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Residues in contact with SER 158 (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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129D TRP* 5.9 0.9 - - - -
157D TYR* 1.3 76.3 - - - +
159D GLN* 1.3 62.0 + - - +
160D VAL* 4.6 0.9 - - - +
171D GLN* 3.2 26.5 + - - +
173D VAL* 3.9 12.4 - - - +
185D PHE* 3.9 21.3 - - - -
203D TYR* 3.4 3.7 - - - -
204D SER 2.9 30.5 + - - -
218D VAL* 4.1 9.9 - - - +
235D PHE 3.6 8.2 + - - -
236D LEU* 4.2 8.2 - - - +
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Residues in contact with GLN 159 (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 2.7 26.0 + - - +
203B TYR 4.5 0.3 - - - +
204B SER* 2.7 29.0 + - - -
129D TRP* 5.1 0.2 - - - -
158D SER* 1.3 73.1 - - - +
160D VAL* 1.3 76.3 + - - +
201D SER* 3.8 18.6 + - - -
202D CYS 3.2 11.2 - - - +
203D TYR* 3.7 13.9 - - + +
232D HIS 4.0 0.4 + - - -
233D GLY* 3.0 24.5 + - - +
234D THR* 3.3 2.6 - - - +
235D PHE* 2.9 62.4 + - + +
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Residues in contact with VAL 160 (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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127D VAL* 6.0 1.6 - - + -
129D TRP* 5.7 2.0 - - + -
158D SER* 4.6 3.6 - - - +
159D GLN* 1.3 81.5 - - - +
161D LEU* 1.3 63.5 + - - +
162D PHE* 3.6 30.5 - - + -
171D GLN* 3.6 35.9 - - + +
201D SER* 3.4 0.9 - - - -
202D CYS* 2.8 33.9 + - - +
218D VAL* 4.7 5.4 - - + -
220D ILE* 4.5 8.5 - - + -
227D LEU* 3.8 26.9 - - + -
233D GLY 3.8 2.9 - - - -
234D THR* 3.8 14.1 - - + +
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Residues in contact with LEU 161 (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* 3.7 32.8 - - - +
188B ILE* 3.5 26.5 - - + -
160D VAL* 1.3 74.0 - - - +
162D PHE* 1.3 70.0 + - - +
163D HIS* 6.4 0.4 - - + -
199D TYR* 5.1 7.9 - - + -
200D ASN 3.6 22.4 - - - +
201D SER* 3.9 6.5 - - - +
227D LEU* 3.2 5.2 - - - +
228D SER* 2.8 50.5 + - - -
233D GLY* 3.5 24.4 + - - +
234D THR* 3.2 5.1 + - - -
18S LEU* 5.6 1.8 - - - +
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Residues in contact with PHE 162 (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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160D VAL* 3.6 37.2 - - + -
161D LEU* 1.3 79.2 - - - +
163D HIS* 1.3 61.1 + - - +
164D ASP* 3.9 1.6 - - + -
169D MET* 3.7 42.2 - - + -
170D GLY* 3.5 40.6 - - - -
171D GLN* 4.0 0.2 - - - -
189D ARG* 5.6 1.3 - - + -
191D MET* 4.0 17.3 - - + -
198D ALA 4.3 0.2 - - - -
199D TYR* 3.4 5.7 - - - +
200D ASN* 2.9 39.0 + - + +
202D CYS* 3.9 15.7 - - + -
220D ILE* 3.9 13.5 - - + -
226D LYS 3.5 10.1 - - - +
227D LEU* 4.3 5.8 - - + -
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Residues in contact with HIS 163 (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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161D LEU 4.2 0.2 + - - -
162D PHE* 1.3 72.2 - - - +
164D ASP* 1.3 58.8 + - - +
195D PRO* 2.9 30.6 - - + +
196D ASP* 4.9 1.6 - - - -
198D ALA 3.1 14.1 + - - -
199D TYR* 3.3 45.3 + + + -
226D LYS* 3.0 34.5 + - + +
227D LEU* 4.8 0.9 - - - +
228D SER 5.6 0.9 - - - +
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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