Contacts of the strand formed by residues 158 - 169 (chain B) in PDB entry 1JG0
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 LYS 158 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B GLN* 3.7 30.5 - - - +
153B TYR* 3.8 0.7 - - - +
154B VAL* 3.4 7.9 - - - +
155B ALA 3.0 28.7 + - - +
156B ASP* 3.5 32.8 + - - +
157B GLY* 1.3 81.1 - - - +
159B LEU* 1.3 61.2 + - - +
160B SER* 3.8 2.9 + - - +
194B LEU* 5.0 0.4 - - - -
195B GLU* 3.3 8.3 - - + +
196B VAL 4.2 2.7 - - - +
197B GLY* 3.9 17.7 - - - +
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Residues in contact with LEU 159 (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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119B LEU* 3.7 32.3 - - + -
152B PHE* 3.8 17.0 - - + -
153B TYR 3.6 14.8 - - - +
154B VAL* 3.9 4.0 - - + -
158B LYS* 1.3 70.9 - - - +
160B SER* 1.3 67.1 + - - +
185B VAL* 3.8 19.6 - - + +
188B MET* 3.6 17.5 - - + -
189B ALA* 3.4 34.5 - - + +
194B LEU* 4.0 15.0 - - + +
195B GLU 2.8 15.8 + - - +
196B VAL 3.7 0.2 - - - -
197B GLY* 2.6 24.9 + - - +
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Residues in contact with SER 160 (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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30A PHE* 3.9 21.9 - - - +
152B PHE* 3.3 10.8 - - - -
153B TYR* 2.8 44.3 + - - +
158B LYS* 3.8 2.8 + - - +
159B LEU* 1.3 75.3 - - - +
161B CYS* 1.3 63.8 + - - +
185B VAL* 5.3 0.2 - - - -
197B GLY* 3.8 2.9 - - - -
198B ASP* 2.9 35.5 + - - +
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Residues in contact with CYS 161 (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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30A PHE* 3.8 3.4 - - - -
150B PHE* 4.1 21.5 - - - -
151B GLN 3.2 12.6 - - - -
152B PHE* 3.7 25.4 - - + -
160B SER* 1.3 77.8 - - - +
162B GLN* 1.3 57.7 + - - +
181B TYR* 5.0 5.8 - - - -
184B LEU* 6.1 0.4 - - - -
185B VAL* 3.4 29.6 - - + -
198B ASP 2.9 6.9 + - - +
199B PHE* 3.3 14.1 - - + -
200B VAL* 2.7 31.5 + - - +
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Residues in contact with GLN 162 (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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30A PHE* 3.5 16.9 - - + -
31A GLY* 3.7 9.3 - - - +
164A TYR* 3.2 31.2 + - + +
202A THR* 3.4 6.6 - - - +
203A GLY 3.1 23.6 + - - -
204A GLY* 3.8 4.2 - - - -
33B GLN* 3.0 11.7 + - - -
149B PHE* 5.5 0.2 - - - -
150B PHE* 3.1 6.3 - - - -
151B GLN* 2.8 33.9 + - - +
161B CYS* 1.3 74.8 - - - +
163B LEU* 1.3 68.4 + - - +
200B VAL* 3.2 22.7 - - + +
202B THR* 2.6 25.3 + - - -
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Residues in contact with LEU 163 (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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164A TYR* 5.7 0.2 - - - -
147B HIS* 3.5 28.5 - - + -
149B PHE 3.6 11.9 - - - +
150B PHE* 4.1 6.5 - - + -
162B GLN* 1.3 76.9 - - - +
164B TYR* 1.3 73.1 + - - +
165B GLN* 4.1 10.8 - - + +
177B ASN* 5.0 4.3 - - + +
181B TYR* 3.9 38.8 - - + +
199B PHE* 3.7 21.2 - - + -
200B VAL 2.9 6.4 + - - +
201B TRP* 3.8 26.7 - - + +
202B THR* 3.0 31.5 + - - +
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Residues in contact with TYR 164 (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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149A PHE* 3.5 33.7 - + + -
151A GLN* 2.7 41.5 + - - +
162A GLN* 3.1 47.1 + - + +
164A TYR* 4.0 33.4 - + + -
202A THR* 5.3 0.4 - - - -
148B ALA* 3.2 24.2 + - + -
149B PHE* 2.9 28.0 + - + +
162B GLN 4.3 0.2 + - - -
163B LEU* 1.3 77.2 - - - +
165B GLN* 1.3 61.9 + - - +
166B ARG* 3.8 11.7 - - + -
202B THR* 3.5 16.8 - - + -
204B GLY* 3.8 3.5 - - - -
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Residues in contact with GLN 165 (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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146B CYS* 3.4 16.2 - - - +
147B HIS* 4.3 4.5 - - - +
163B LEU* 3.9 8.9 - - + +
164B TYR* 1.3 74.7 - - - +
166B ARG* 1.3 61.1 + - - +
167B SER* 3.0 27.0 + - - +
168B CYS* 3.4 15.4 - - + +
174B LEU* 4.3 0.9 - - - +
177B ASN* 2.9 37.5 + - - +
201B TRP* 2.8 39.7 + - + +
202B THR 2.8 10.5 + - - +
203B GLY* 3.2 2.4 - - - -
204B GLY 2.8 24.9 + - - -
305B UMP 3.4 14.5 + - - -
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Residues in contact with ARG 166 (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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126A ARG* 3.0 27.9 + - - +
127A ARG* 3.9 11.2 - - - +
129A ILE* 3.7 25.8 - - + -
149A PHE* 5.2 1.1 - - + -
151A GLN* 3.1 32.7 - - - +
133B TRP* 3.7 11.2 - - - -
144B ALA* 3.0 29.4 + - - +
145B PRO 2.8 17.6 + - - +
146B CYS* 3.0 30.8 + - - +
148B ALA* 5.0 2.4 - - + +
164B TYR* 3.8 9.2 + - + -
165B GLN* 1.3 73.6 - - - +
167B SER* 1.3 63.9 + - - +
205B ASP* 2.9 23.8 + - - +
305B UMP 2.9 40.8 + - - -
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Residues in contact with SER 167 (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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126A ARG* 3.1 21.3 + - - -
146B CYS* 3.9 11.7 + - - -
165B GLN* 3.0 20.0 + - - +
166B ARG* 1.3 95.6 - - - +
168B CYS* 1.3 61.9 + - - +
205B ASP 3.3 5.4 - - - -
207B HIS* 3.4 0.7 - - - -
305B UMP 2.6 45.1 + - - +
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Residues in contact with CYS 168 (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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165B GLN* 3.4 15.9 - - + +
167B SER* 1.3 77.2 + - - +
169B ASP* 1.3 65.3 + - - +
170B VAL* 3.2 6.8 + - - -
174B LEU* 3.6 37.0 - - - -
201B TRP* 3.6 33.2 - - + -
205B ASP 2.8 13.4 + - - +
206B THR* 4.2 4.5 - - + +
207B HIS* 2.9 37.7 + - - +
305B UMP 3.5 2.2 - - - -
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Residues in contact with ASP 169 (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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168B CYS* 1.3 68.1 - - - +
170B VAL* 1.3 58.6 + - - +
171B PHE 3.2 5.0 + - - -
172B LEU* 3.0 31.7 + - - +
173B GLY 3.0 20.1 + - - -
174B LEU 3.0 8.3 + - - -
207B HIS* 3.7 10.2 - - - +
208B LEU* 5.4 0.2 - - - -
209B TYR* 3.5 21.9 + - + -
212B HIS* 3.6 12.7 + - - -
305B UMP 2.8 32.8 + - - +
306B DDT 3.2 27.1 - - - +
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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