Contacts of the strand formed by residues 179 - 192 (chain A) in PDB entry 5J0Z
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 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ARG* 4.0 24.6 + - - +
134A SER* 3.8 23.5 + - - +
135A VAL* 4.5 7.5 - - - +
136A ASP* 3.9 36.4 + - - +
175A ALA* 3.5 4.9 - - - -
176A LEU* 2.9 29.2 + - - +
177A GLU 2.9 10.1 + - - +
178A ASP* 1.3 80.2 - - + +
180A LEU* 1.3 64.6 + - - +
63E VAL* 5.2 1.2 - - - +
91E ASP* 3.5 20.4 + - - +
93E SER* 3.7 21.8 + - - -
101E GLN* 6.3 0.4 - - - +
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Residues in contact with LEU 180 (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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133A ARG* 4.0 3.8 - - - +
134A SER* 3.0 55.5 + - - +
139A ASN* 4.0 26.6 + - - +
140A ILE 3.6 14.6 - - - +
141A VAL* 5.0 4.3 - - + -
173A ASN* 4.2 22.0 - - + +
174A PHE* 3.4 16.2 - - - +
175A ALA* 4.5 1.1 - - - +
179A ARG* 1.3 77.7 - - - +
181A GLU* 1.3 74.7 + - - +
182A SER* 4.1 1.1 - - - +
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Residues in contact with GLU 181 (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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77A ARG* 3.6 3.6 + - - -
131A ILE* 3.5 19.1 - - + +
132A VAL 3.5 18.6 - - - +
133A ARG* 2.5 45.8 + - - +
173A ASN* 3.4 3.3 - - - +
174A PHE* 2.9 50.0 + - + +
176A LEU* 3.6 15.1 - - + +
180A LEU* 1.3 74.5 - - - +
182A SER* 1.3 57.9 + - - +
183A LYS 4.2 0.2 - - - -
407A ACT 2.6 40.4 - - - +
42E PHE* 3.7 1.9 - - - -
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Residues in contact with SER 182 (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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131A ILE* 4.2 1.3 - - - -
132A VAL* 3.1 34.8 + - - -
140A ILE 3.6 21.5 - - - -
141A VAL* 3.7 5.9 - - - -
142A LEU* 3.1 30.4 + - - +
171A PRO* 3.7 6.4 - - - +
173A ASN* 2.9 26.6 + - - -
180A LEU* 4.1 1.0 - - - +
181A GLU* 1.3 73.5 - - - +
183A LYS* 1.3 59.7 + - - +
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Residues in contact with LYS 183 (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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79A VAL* 4.5 9.2 - - - -
129A TYR* 3.5 35.2 - - + -
130A LEU 3.2 7.6 - - - +
131A ILE* 3.8 16.4 - - + -
171A PRO* 3.4 20.5 - - - +
172A ALA* 3.4 21.0 + - + +
174A PHE* 4.1 20.0 - - + -
181A GLU 4.2 0.2 - - - -
182A SER* 1.3 74.1 + - - +
184A LEU* 1.3 70.8 + - - +
152E ASN* 4.9 5.8 - - - +
154E ASP* 3.5 27.5 + - - -
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Residues in contact with LEU 184 (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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20A THR* 3.0 31.4 - - + +
129A TYR* 3.6 6.8 - - - +
130A LEU* 2.7 33.8 + - + +
142A LEU* 3.7 28.7 - - + +
143A ALA* 4.0 9.9 - - - -
144A VAL* 3.7 15.5 - - + -
168A VAL 3.2 27.4 - - - +
169A VAL 4.0 8.1 - - - +
171A PRO* 4.1 12.6 - - + -
183A LYS* 1.3 83.6 - - - +
185A ASP* 1.3 61.0 - - - +
186A TYR* 4.1 18.2 - - + -
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Residues in contact with ASP 185 (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 HIS* 3.2 13.9 + - - -
128A ILE 4.3 0.4 - - - -
129A TYR* 3.4 27.3 + - + -
167A ALA* 3.6 1.3 - - - +
168A VAL* 3.0 41.3 + - + +
184A LEU* 1.3 81.2 - - - +
186A TYR* 1.3 65.6 + - - +
187A GLN* 3.1 37.3 + - - +
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Residues in contact with TYR 186 (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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20A THR* 2.8 40.5 + - - -
21A GLY 3.5 0.3 + - - -
22A ILE* 3.7 34.5 - - + -
126A LEU 3.8 0.2 - - - +
127A HIS* 3.4 2.9 - - - -
128A ILE* 2.9 46.0 + - + +
130A LEU* 3.7 20.2 - - + -
144A VAL* 4.5 2.8 - - + +
149A VAL* 3.9 13.4 - - + +
165A PHE* 3.7 32.3 - + + -
166A THR 3.7 3.8 - - - -
167A ALA* 3.8 23.3 - - + -
184A LEU* 4.1 18.1 - - + +
185A ASP* 1.3 85.2 + - - +
187A GLN* 1.3 59.9 + - - +
188A LEU 4.2 0.2 + - - -
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Residues in contact with GLN 187 (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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125A THR* 4.3 4.4 - - + +
126A LEU 3.4 5.8 - - - +
127A HIS* 3.7 18.6 - - + +
164A SER 3.5 2.4 - - - +
165A PHE* 3.5 7.2 - - - -
166A THR* 2.9 38.3 + - - +
168A VAL* 3.4 22.9 - - - +
185A ASP* 3.1 39.4 + - - +
186A TYR* 1.3 71.5 - - - +
188A LEU* 1.3 60.3 + - - +
189A ARG* 3.1 39.5 + - - +
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Residues in contact with LEU 188 (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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24A LEU* 4.2 19.5 - - + -
27A CYS* 3.8 28.5 - - + -
37A PHE* 4.4 11.7 - - + -
125A THR* 4.5 0.2 - - - -
126A LEU* 2.6 70.9 + - + +
128A ILE* 5.8 3.6 - - + +
151A LYS* 5.1 0.2 - - + -
157A LEU* 5.6 1.1 - - + -
162A ILE* 3.5 32.3 - - + -
164A SER 3.5 10.1 - - - +
165A PHE* 3.7 16.2 - - + -
186A TYR 4.2 0.4 - - - -
187A GLN* 1.3 72.1 - - - +
189A ARG* 1.3 58.6 + - - +
190A ILE* 4.1 7.6 + - + -
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Residues in contact with ARG 189 (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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123A SER* 6.5 0.4 - - - -
124A GLN 3.2 7.0 - - - +
125A THR* 3.4 33.5 + - - +
162A ILE* 3.8 1.9 - - - +
163A GLU* 2.9 36.8 + - + +
164A SER* 3.1 28.7 + - - +
166A THR* 3.0 27.1 + - - +
187A GLN* 3.1 37.1 + - - +
188A LEU* 1.3 73.6 - - - +
190A ILE* 1.3 64.8 + - - +
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Residues in contact with ILE 190 (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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30A LEU* 3.3 33.9 - - + -
123A SER* 3.2 5.1 - - - -
124A GLN* 2.7 51.7 + - + +
126A LEU* 3.8 17.9 - - + -
157A LEU* 3.9 12.1 - - + -
160A TRP* 3.6 22.4 - - + -
161A ASP 3.2 14.4 - - - +
162A ILE* 3.9 20.6 - - + -
163A GLU* 3.8 4.7 - - - -
188A LEU* 4.5 10.1 - - + -
189A ARG* 1.3 80.5 - - - +
191A SER* 1.3 59.9 + - - +
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Residues in contact with SER 191 (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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122A ASP 3.9 0.9 - - - -
123A SER* 3.0 20.6 - - - -
160A TRP* 3.4 4.9 - - - -
161A ASP* 2.8 50.5 + - - +
163A GLU* 3.5 15.4 + - - -
190A ILE* 1.3 73.7 - - - +
192A ARG* 1.3 64.8 + - - +
409A PLC 6.2 5.6 - - - -
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Residues in contact with ARG 192 (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 ASP* 2.1 43.6 + - - -
116A PHE* 4.4 1.8 - - - -
119A TYR* 3.2 24.1 - - - -
120A PRO* 3.7 20.1 - - - +
121A PHE* 5.5 1.0 - - - -
122A ASP* 2.4 73.4 + - - +
159A GLY 3.6 9.4 + - - +
160A TRP* 3.1 36.1 - - + +
161A ASP* 4.8 1.3 - - - +
191A SER* 1.3 75.2 + - - +
193A GLN* 1.3 68.1 + - - +
194A TYR* 3.1 19.6 + - - +
197A TYR* 3.9 23.8 + - + -
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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