Contacts of the strand formed by residues 152 - 163 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ASP 3.5 2.4 + - - -
151A THR* 1.3 79.3 - - - +
153A ILE* 1.3 63.6 + - - -
154A TYR* 3.4 13.4 - - - -
209A HIS* 3.5 8.6 - - - -
210A LEU 2.9 33.0 + - - +
240A LYS* 4.9 8.1 - - - -
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Residues in contact with ILE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A GLY* 1.3 71.2 - - - -
154A TYR* 1.3 60.5 + - - +
207A VAL* 3.4 31.6 - - + -
208A PHE 3.5 3.4 - - - +
209A HIS* 3.7 26.9 - - + -
240A LYS* 3.7 4.7 - - - +
241A LEU* 2.9 39.1 + - + +
108B VAL* 4.0 20.6 - - + -
133B LEU* 4.3 17.9 - - + -
134B ARG 5.6 0.2 - - - +
135B ARG* 3.8 46.8 - - + +
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Residues in contact with TYR 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A SER* 6.0 1.3 - - - -
138A GLY* 4.1 10.3 + - - -
139A LEU* 3.7 35.2 - - + -
148A VAL* 4.5 0.6 - - + +
150A ASP* 2.7 41.1 + - - +
152A GLY* 3.4 26.9 - - - -
153A ILE* 1.3 74.9 - - - +
155A LEU* 1.3 62.3 + - - +
156A LEU* 3.6 22.5 + - + +
206A GLY 3.7 0.2 - - - +
207A VAL* 3.3 6.7 - - - -
208A PHE 2.9 31.0 + - - +
210A LEU* 3.7 24.7 - - + -
238A PHE* 4.4 4.3 - - + -
239A VAL 3.2 6.3 - - - +
240A LYS* 3.8 37.6 - - + +
241A LEU* 4.4 0.2 - - - -
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A TYR* 1.3 70.3 - - - +
156A LEU* 1.3 61.2 + - - +
157A TYR* 4.6 12.0 - - + -
205A ALA* 4.3 9.4 - - + -
206A GLY* 3.4 24.5 - - - +
207A VAL* 4.0 19.1 - - + -
237A GLY 3.8 0.5 - - - +
238A PHE* 3.2 8.7 - - - +
239A VAL* 2.8 56.5 + - + +
241A LEU* 4.0 12.1 - - + +
155B LEU* 4.5 22.7 - - + -
157B TYR* 5.4 3.4 - - + -
203B TYR* 5.5 1.8 - - - +
239B VAL* 6.1 0.2 - - + -
155D LEU* 4.7 21.1 - - + -
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A TYR* 3.8 15.3 - - + +
155A LEU* 1.3 72.1 - - - +
157A TYR* 1.3 61.9 + - - +
173A VAL* 3.8 28.0 - - + -
184A LEU* 4.1 15.3 - - + -
185A PHE* 3.7 11.7 - - + -
205A ALA* 3.1 5.4 - - - +
206A GLY 2.8 34.9 + - - +
208A PHE* 4.4 7.4 - - + -
210A LEU* 3.6 21.8 - - + -
216A ILE* 4.1 10.8 - - + -
236A LEU* 5.5 3.4 - - + -
237A GLY 3.4 3.4 - - - +
238A PHE* 3.5 37.9 - - + -
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Residues in contact with TYR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU 4.3 1.4 + - - -
110A HIS* 2.6 41.6 + + - +
155A LEU* 4.6 16.4 - - + -
156A LEU* 1.3 76.9 - - - +
158A SER* 1.3 62.5 + - - +
185A PHE* 4.5 1.3 - - - -
203A TYR* 3.3 24.2 - + + +
204A SER 3.5 4.3 - - - -
205A ALA* 3.6 6.7 - - + -
235A PHE* 4.0 12.3 - + - -
236A LEU* 3.4 7.8 - - - +
237A GLY* 2.9 62.1 + - - -
238A PHE 3.9 2.2 - - - -
239A VAL* 4.7 4.3 - - + -
155D LEU* 5.4 4.0 - - + -
205D ALA 4.0 11.0 - - - -
206D GLY* 3.9 9.0 - - - -
207D VAL* 3.2 38.8 + - + +
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Residues in contact with SER 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TRP* 6.0 0.7 - - - -
157A TYR* 1.3 77.2 - - - +
159A GLN* 1.3 62.4 + - - +
160A VAL* 4.4 1.4 - - - +
171A GLN* 3.1 27.8 + - - +
173A VAL* 4.1 9.2 - - - -
185A PHE* 4.0 19.1 - - - -
203A TYR* 3.4 6.0 - - - -
204A SER 3.0 32.1 + - - -
218A VAL* 4.1 10.7 - - - +
235A PHE* 3.7 7.3 + - - -
236A LEU* 4.3 9.7 - - - +
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Residues in contact with GLN 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TRP* 5.1 0.3 - - - -
158A SER* 1.3 73.8 + - - +
160A VAL* 1.3 75.6 + - - +
201A SER* 3.9 15.2 + - - -
202A CYS 3.1 12.8 - - - +
203A TYR* 3.7 13.2 - - + +
233A GLY* 2.9 26.5 + - - +
234A THR* 3.3 2.3 - - - +
235A PHE* 3.0 61.0 + - + +
186D ARG 2.8 25.2 + - - +
203D TYR 4.5 0.3 - - - +
204D SER* 2.7 30.7 + - - -
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A VAL* 5.9 1.3 - - + -
129A TRP* 5.8 2.0 - - + -
158A SER* 4.4 2.7 - - - +
159A GLN* 1.3 80.0 - - - +
161A LEU* 1.3 62.4 + - - +
162A PHE* 3.6 35.4 - - + -
171A GLN* 3.5 32.5 - - + +
201A SER* 3.3 0.9 - - - -
202A CYS* 2.8 36.3 + - - -
218A VAL* 4.9 5.4 - - + -
220A ILE* 4.6 8.5 - - + -
227A LEU* 4.0 28.0 - - + -
233A GLY 3.8 3.1 - - - -
234A THR* 3.8 14.1 - - + +
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A VAL* 1.3 71.8 - - - +
162A PHE* 1.3 73.1 + - - +
163A HIS* 6.2 0.4 - - + -
199A TYR* 5.2 7.2 - - + -
200A ASN 3.7 17.9 - - - +
201A SER* 4.1 8.1 - - - +
227A LEU* 3.3 5.0 - - - +
228A SER* 2.9 51.1 + - - +
233A GLY* 3.4 24.3 + - - +
234A THR* 3.1 10.0 + - - +
186D ARG* 3.5 33.9 - - - +
188D ILE* 3.7 24.9 - - + -
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Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A VAL* 3.6 39.9 - - + -
161A LEU* 1.3 80.4 - - - +
163A HIS* 1.3 61.5 + - - +
164A ASP* 3.9 3.8 - - + -
169A MET* 3.6 40.6 - - + -
170A GLY* 3.4 40.2 - - - -
189A ARG* 5.5 1.8 - - + -
191A MET* 4.0 17.9 - - + -
198A ALA 4.2 0.4 - - - -
199A TYR* 3.4 5.2 - - - +
200A ASN 2.8 39.5 + - - +
202A CYS* 3.9 13.2 - - + -
220A ILE* 3.9 13.7 - - + -
226A LYS 3.8 9.9 - - - +
227A LEU* 4.3 5.4 - - + -
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Residues in contact with HIS 163 (chain A).
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* 4.2 1.1 + - + -
162A PHE* 1.3 73.4 - - - +
164A ASP* 1.3 58.6 + - - +
195A PRO* 3.0 28.9 + - + -
196A ASP* 4.8 2.2 - - - -
198A ALA 3.1 15.5 + - - +
199A TYR* 3.4 44.2 + + + -
226A LYS* 3.1 38.5 + - + +
227A LEU* 4.7 1.3 - - - +
228A SER* 6.1 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