Contacts of the strand formed by residues 179 - 192 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A VAL* 5.1 4.6 - - - +
91A ASP* 3.1 14.3 + - - +
93A SER* 3.4 17.2 + - - -
101A GLN* 6.2 0.2 - - - +
133B ARG* 3.6 28.7 + - - +
134B SER* 3.8 22.7 + - - +
135B VAL* 4.5 7.6 - - - +
136B ASP* 3.0 42.2 + - - +
175B ALA* 3.4 4.4 - - - -
176B LEU 2.9 28.8 + - - +
177B GLU 2.9 10.0 + - - +
178B ASP* 1.3 80.4 - - + +
180B LEU* 1.3 63.9 + - - +
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Residues in contact with LEU 180 (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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133B ARG* 4.0 4.2 - - - +
134B SER* 2.9 54.5 + - - +
139B ASN* 3.9 27.8 + - - +
140B ILE 3.6 14.4 - - - +
141B VAL* 5.0 4.3 - - + -
173B ASN* 4.2 20.9 - - + +
174B PHE* 3.4 16.2 - - - +
175B ALA* 4.4 1.1 - - + +
179B ARG* 1.3 77.6 - - - +
181B GLU* 1.3 76.3 + - - +
182B SER* 4.1 0.9 - - - +
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Residues in contact with GLU 181 (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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42A PHE* 3.7 10.6 - - - -
77B ARG* 3.6 18.5 + - - -
131B ILE* 3.5 30.2 - - + +
132B VAL 3.5 18.6 - - - +
133B ARG* 2.8 43.7 + - - +
173B ASN* 3.4 3.5 - - - +
174B PHE* 2.8 50.3 + - + +
176B LEU* 3.6 18.8 - - + +
180B LEU* 1.3 74.6 - - - +
182B SER* 1.3 58.7 + - - +
183B LYS 4.2 0.2 - - - -
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Residues in contact with SER 182 (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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131B ILE* 3.4 2.4 - - - -
132B VAL* 3.1 34.7 + - - -
140B ILE 3.6 21.3 - - - -
141B VAL* 3.8 6.0 - - - -
142B LEU* 3.1 30.7 + - - +
171B PRO* 3.7 6.2 - - - +
173B ASN* 2.9 27.3 + - - -
180B LEU* 4.1 1.0 - - - +
181B GLU* 1.3 71.7 - - - +
183B LYS* 1.3 58.9 + - - +
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Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ASN* 4.9 5.2 - - - +
154A ASP* 3.5 27.4 + - - -
79B VAL* 4.5 9.6 - - + -
129B TYR* 3.5 34.1 - - + -
130B LEU 3.3 7.9 - - - +
131B ILE* 3.8 16.4 - - + -
171B PRO* 3.4 21.5 - - - +
172B ALA* 3.4 22.0 + - + +
173B ASN* 3.6 0.2 + - - -
174B PHE* 4.0 21.6 - - + -
181B GLU 4.2 0.2 + - - -
182B SER* 1.3 73.7 + - - +
184B LEU* 1.3 70.0 + - - +
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Residues in contact with LEU 184 (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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20B THR* 3.0 31.2 - - + +
129B TYR* 3.6 6.6 - - - +
130B LEU* 2.7 33.3 + - + +
142B LEU* 3.7 28.5 - - + +
143B ALA* 4.0 9.6 - - - -
144B VAL* 3.7 15.3 - - + -
167B ALA* 5.6 0.2 - - + -
168B VAL 3.2 26.0 - - - +
169B VAL 3.9 9.2 - - - +
171B PRO* 4.1 13.7 - - + -
183B LYS* 1.3 82.6 - - - +
185B ASP* 1.3 62.1 + - - +
186B TYR* 4.1 17.3 - - + -
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Residues in contact with ASP 185 (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 HIS* 3.2 13.2 + - - -
129B TYR* 3.4 27.3 + - + -
167B ALA* 3.6 1.7 - - - +
168B VAL* 3.0 40.7 + - + +
184B LEU* 1.3 81.6 - - - +
186B TYR* 1.3 66.6 + - - +
187B GLN* 3.1 38.2 + - - +
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Residues in contact with TYR 186 (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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20B THR* 2.8 40.2 + - - -
21B GLY 3.5 0.3 + - - -
22B ILE* 3.7 39.3 - - + -
126B LEU 3.8 0.2 - - - +
127B HIS* 3.4 4.0 - - - -
128B ILE* 2.9 45.7 + - + +
130B LEU* 3.6 19.5 - - + -
144B VAL* 4.5 3.2 - - + +
149B VAL* 3.9 13.9 - - + +
165B PHE* 3.8 30.5 - + + -
166B THR 3.7 3.8 - - - -
167B ALA* 3.8 23.8 - - + +
184B LEU* 4.1 17.4 - - + +
185B ASP* 1.3 84.3 - - - +
187B GLN* 1.3 60.1 + - - +
188B LEU 4.2 0.2 + - - -
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Residues in contact with GLN 187 (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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125B THR* 4.3 4.7 - - + +
126B LEU 3.5 5.4 - - - +
127B HIS* 3.7 17.1 - - + +
164B SER 3.5 2.4 - - - +
165B PHE* 3.5 7.2 - - - -
166B THR* 2.9 37.7 + - - +
168B VAL* 3.3 25.0 - - + +
185B ASP* 3.1 39.4 + - - +
186B TYR* 1.3 71.3 - - - +
188B LEU* 1.3 59.8 + - - +
189B ARG* 3.1 39.6 + - - +
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Residues in contact with LEU 188 (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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24B LEU* 4.2 18.6 - - + -
27B CYS* 3.8 28.0 - - + -
37B PHE* 4.4 12.3 - - + -
124B GLN 4.1 0.3 - - - +
125B THR* 4.5 0.7 - - - -
126B LEU* 2.6 69.7 + - + +
128B ILE* 5.8 4.0 - - + +
157B LEU* 5.6 1.1 - - + -
162B ILE* 3.5 32.1 - - + -
164B SER 3.5 11.0 - - - +
165B PHE* 3.8 17.8 - - + -
186B TYR 4.2 0.4 + - - -
187B GLN* 1.3 70.4 - - - +
189B ARG* 1.3 57.3 + - - +
190B ILE* 4.5 7.6 - - + -
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Residues in contact with ARG 189 (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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124B GLN 3.2 7.2 - - - +
125B THR* 3.3 33.5 + - - +
162B ILE* 3.8 2.1 - - - +
163B GLU* 2.9 36.5 + - + +
164B SER* 3.1 28.5 + - - +
166B THR* 3.0 27.7 + - - -
187B GLN* 3.1 37.2 + - - +
188B LEU* 1.3 72.3 - - - +
190B ILE* 1.3 65.5 - - - +
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Residues in contact with ILE 190 (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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30B LEU* 3.3 34.5 - - + -
123B SER* 3.2 5.3 - - - -
124B GLN* 2.7 55.1 + - + +
126B LEU* 3.8 18.8 - - + -
157B LEU* 3.9 11.9 - - + -
160B TRP* 3.6 22.0 - - + -
161B ASP 3.2 13.9 - - - +
162B ILE* 3.9 20.9 - - + -
163B GLU* 3.8 4.7 + - - -
188B LEU* 4.5 9.9 - - + -
189B ARG* 1.3 81.1 - - - +
191B SER* 1.3 58.7 + - - +
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Residues in contact with SER 191 (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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122B ASP 3.9 0.4 - - - -
123B SER* 3.0 21.1 - - - +
160B TRP* 3.4 4.9 - - - -
161B ASP* 2.8 50.9 + - - +
163B GLU* 3.5 16.3 + - - -
190B ILE* 1.3 72.9 - - - +
192B ARG* 1.3 64.7 + - - +
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Residues in contact with ARG 192 (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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32B ASP* 2.1 43.6 + - - -
116B PHE* 4.1 2.2 - - - -
119B TYR* 3.2 23.9 - - - -
120B PRO* 3.7 21.3 - - - +
121B PHE* 5.5 1.0 - - - -
122B ASP* 2.3 74.4 + - - +
159B GLY 3.6 10.0 + - - +
160B TRP* 3.1 35.9 - - + +
161B ASP* 4.8 1.7 - - - +
191B SER* 1.3 75.4 + - - +
193B GLN* 1.3 68.2 + - - +
194B TYR* 3.1 19.2 + - - +
197B TYR* 3.9 24.2 + - + -
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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