Contacts of the strand formed by residues 154 - 164 (chain A) in PDB entry 2YTZ
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 ALA 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ARG* 2.9 24.5 + - - -
132A PHE 3.3 10.3 - - - +
135A ILE* 3.7 15.6 - - + +
150A ALA 3.1 15.2 + - - +
151A LEU 5.1 0.4 - - - +
152A ARG 3.5 0.2 - - - -
153A SER* 1.3 81.8 - - - +
155A LYS* 1.3 70.9 + - - +
158A GLY* 4.6 5.4 - - - -
159A ILE 4.8 8.5 - - - +
160A LEU* 5.1 5.2 - - + -
233A LEU* 4.1 16.2 - - + -
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Residues in contact with LYS 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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50A ILE* 5.1 4.1 - - - +
130A ARG* 3.5 25.5 + - + +
131A TYR* 3.4 23.5 + - - +
132A PHE 2.7 25.9 + - - +
133A HIS* 3.7 31.4 - - + +
153A SER 3.8 0.4 + - - -
154A ALA* 1.3 77.9 - - - +
156A ARG* 1.3 59.0 + - - +
157A ARG* 2.9 7.9 - - + +
158A GLY* 2.7 29.9 + - - +
233A LEU* 3.6 8.8 - - - +
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Residues in contact with ARG 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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130A ARG* 3.6 33.4 - - + +
155A LYS* 1.3 70.5 - - - +
157A ARG* 1.3 59.8 + - + +
158A GLY 3.5 0.2 - - - -
211A TYR 2.8 27.2 + - - -
212A ASP* 3.1 21.8 + - - +
213A LEU* 3.4 25.0 - - + +
233A LEU* 3.3 16.9 - - - +
235A ASP* 2.9 45.8 + - + +
1004A SO4 2.9 37.2 + - - -
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Residues in contact with ARG 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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155A LYS* 2.9 6.0 - - + +
156A ARG* 1.3 81.9 - - + +
158A GLY* 1.3 64.3 + - - +
159A ILE* 4.9 0.2 - - - +
232A LYS* 2.8 38.0 + - - +
233A LEU 3.4 12.1 - - - +
234A LYS* 5.5 0.7 - - - +
235A ASP* 3.7 37.2 + - + +
239A LYS* 5.5 5.3 - - - +
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Residues in contact with GLY 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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132A PHE 4.2 0.4 - - - -
133A HIS* 3.4 13.0 - - - -
154A ALA* 4.6 2.2 - - - -
155A LYS* 2.7 31.4 + - - +
156A ARG 3.5 0.2 - - - -
157A ARG* 1.3 79.9 - - - +
159A ILE* 1.3 61.8 + - - -
232A LYS* 3.8 1.6 - - - -
233A LEU* 3.0 33.6 + - - +
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Residues in contact with ILE 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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42A LEU* 5.3 0.2 - - + -
43A LEU* 6.2 0.2 - - + -
46A LEU* 3.3 45.1 - - + +
48A PRO* 4.8 13.7 - - + -
133A HIS 2.7 18.3 + - - +
134A PHE* 3.2 23.3 - - + -
135A ILE* 3.1 23.4 + - - +
154A ALA* 4.8 4.3 - - - +
158A GLY* 1.3 77.8 - - - +
160A LEU* 1.3 66.8 + - - +
218A ILE* 3.9 13.0 - - + -
230A PHE* 5.2 5.4 - - + -
231A VAL 3.3 13.0 - - - +
232A LYS* 4.0 23.6 - - + +
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Residues in contact with LEU 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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135A ILE* 3.7 36.3 - - + +
137A LEU* 4.9 1.3 - - + -
147A LEU* 4.1 21.1 - - + -
150A ALA* 4.0 19.3 - - + +
151A LEU* 3.5 33.7 - - + +
154A ALA* 5.1 2.5 - - + -
158A GLY 4.2 0.6 + - - -
159A ILE* 1.3 77.8 - - - +
161A GLY* 1.3 59.2 + - - +
162A VAL* 4.0 15.4 - - + +
204A ILE* 4.4 7.6 - - + +
229A ALA 3.4 2.6 - - - +
230A PHE* 3.4 3.3 - - - -
231A VAL* 2.8 50.6 + - + +
233A LEU* 5.2 8.5 - - + -
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Residues in contact with GLY 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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134A PHE* 3.8 6.0 - - - -
135A ILE 2.8 16.1 + - - +
136A ASP* 3.3 2.2 - - - +
137A LEU* 2.6 33.1 + - - +
160A LEU* 1.3 72.8 - - - +
162A VAL* 1.3 58.3 + - - +
228A ARG* 3.3 17.7 - - - -
229A ALA 3.4 5.2 - - - -
230A PHE* 4.0 11.2 - - - -
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Residues in contact with VAL 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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137A LEU* 3.6 17.9 - - + +
143A PRO* 3.4 38.1 - - + -
147A LEU* 4.3 10.1 - - + -
160A LEU* 4.0 24.9 - - + +
161A GLY* 1.3 78.9 - - - +
163A THR* 1.3 67.6 + - - +
200A LEU* 4.4 11.6 - - + +
204A ILE* 4.4 15.9 - - + -
227A PHE 3.6 2.4 - - - +
228A ARG* 3.4 3.5 - - - +
229A ALA* 2.8 39.7 + - + +
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Residues in contact with THR 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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32A MET* 4.2 6.5 - - + -
35A ASN* 3.6 21.0 + - - +
136A ASP* 4.4 0.3 + - - -
137A LEU 2.9 12.7 + - - -
138A ASP* 3.7 23.1 + - - +
139A PRO* 3.7 18.9 - - - +
141A GLY 4.0 0.2 - - - +
143A PRO* 4.0 3.6 - - - +
162A VAL* 1.3 83.2 - - - +
164A ALA* 1.3 66.1 + - - +
165A THR* 4.2 4.7 - - - +
226A TYR* 4.0 18.8 - - + -
227A PHE 3.2 8.3 - - - +
228A ARG* 3.2 27.6 + - + +
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Residues in contact with ALA 164 (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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141A GLY 3.3 9.4 - - - +
143A PRO* 4.1 6.7 - - + -
163A THR* 1.3 76.4 - - - +
165A THR* 1.3 58.8 + - - +
166A ASP 3.1 5.4 + - - +
170A LEU* 3.9 24.0 - - + -
182A TYR* 4.1 10.3 - - - +
200A LEU* 4.2 11.2 - - + -
226A TYR* 3.4 1.7 - - - -
227A PHE* 2.8 47.8 + - + +
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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