Contacts of the strand formed by residues 195 - 209 (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 GLU 195 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLN* 4.1 18.4 + - + +
157B GLY 2.8 18.1 + - - +
158B LYS* 3.3 6.2 - - + -
159B LEU* 2.8 26.8 + - - +
189B ALA* 4.1 0.7 - - - +
193B ASP 5.0 3.3 - - - +
194B LEU* 1.3 80.2 - - - +
196B VAL* 1.3 62.8 + - - +
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Residues in contact with VAL 196 (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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37B ASN* 4.7 0.3 - - - +
38B LEU* 3.5 30.3 - - + -
39B GLN* 3.2 38.7 + - + +
158B LYS* 4.2 1.5 - - - +
159B LEU 4.0 2.7 - - - -
185B VAL* 4.3 5.6 - - + -
186B HIS* 3.6 44.4 - - + +
189B ALA* 3.8 22.2 - - + -
195B GLU* 1.3 73.6 + - - +
197B GLY* 1.3 62.6 + - - +
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Residues in contact with GLY 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN* 3.8 3.3 - - - +
38B LEU* 3.0 29.3 + - - +
158B LYS* 3.9 16.4 - - - -
159B LEU 2.6 23.1 + - - +
160B SER* 3.8 5.6 - - - -
196B VAL* 1.3 76.3 - - - +
198B ASP* 1.3 66.0 + - - +
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Residues in contact with ASP 198 (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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35B ARG* 3.1 49.1 + - + +
36B PHE 3.2 4.3 - - - +
37B ASN* 3.4 29.3 + - - +
38B LEU* 4.7 3.4 - - - +
160B SER* 2.9 17.9 + - - +
161B CYS* 2.9 26.7 + - - +
185B VAL* 5.5 0.3 - - - +
197B GLY* 1.3 75.8 - - - -
199B PHE* 1.3 59.4 + - - +
200B VAL* 3.8 3.7 + - + +
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Residues in contact with PHE 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG* 3.6 1.0 - - - -
36B PHE* 2.7 54.0 + + + +
38B LEU* 4.0 25.0 - - + +
43B PRO* 5.4 0.2 - - + -
161B CYS* 3.3 20.6 - - + +
163B LEU* 3.7 37.9 - - + -
178B ILE* 4.1 34.5 - - + -
181B TYR* 3.7 28.7 - + + -
182B ALA* 4.9 5.4 - - + -
185B VAL* 4.7 5.4 - - + -
198B ASP* 1.3 72.4 - - - +
200B VAL* 1.3 65.7 + - - +
201B TRP* 4.0 21.1 - + + -
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 4.0 15.0 - - + +
31A GLY* 4.3 5.4 - - - -
33B GLN* 3.7 27.4 - - + +
34B MET 3.4 5.4 - - - +
35B ARG* 3.4 38.6 - - + +
161B CYS 2.7 14.9 + - - +
162B GLN* 3.2 31.5 - - + +
163B LEU 2.9 26.9 + - - -
198B ASP* 4.3 4.9 - - + +
199B PHE* 1.3 78.7 - - - +
201B TRP* 1.3 60.0 + - - +
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Residues in contact with TRP 201 (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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7B LEU* 4.3 4.3 - - + -
32B HIS* 4.2 22.0 - - + -
33B GLN* 3.1 6.1 - - - +
34B MET* 2.8 75.0 + - + +
36B PHE* 4.6 4.5 - - + -
163B LEU* 3.8 21.1 - - + -
165B GLN* 2.8 29.1 + - + +
168B CYS* 3.6 33.7 - - + -
174B LEU* 3.6 14.4 - - + +
177B ASN* 5.5 0.4 - - + -
178B ILE* 4.7 3.6 - - + -
199B PHE* 3.9 22.1 + + + -
200B VAL* 1.3 71.9 - - - +
202B THR* 1.3 64.8 + - - +
203B GLY* 3.5 28.9 - - - -
206B THR* 3.9 15.7 - - + -
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Residues in contact with THR 202 (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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33A GLN* 3.8 4.3 - - - +
162A GLN* 3.3 25.8 - - - +
164A TYR* 5.6 0.2 - - - -
202A THR* 3.9 7.4 - - + +
32B HIS 3.3 8.7 - - - +
33B GLN* 2.9 17.2 + - - +
162B GLN* 2.6 25.5 + - - -
163B LEU 3.0 16.1 + - - +
164B TYR* 3.5 20.3 - - + -
165B GLN* 2.8 29.3 + - - +
201B TRP* 1.3 75.9 - - - +
203B GLY* 1.3 61.6 + - - +
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Residues in contact with GLY 203 (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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162A GLN* 3.1 8.4 + - - -
31B GLY* 3.1 25.5 - - - -
32B HIS 2.9 11.8 + - - +
164B TYR* 4.7 1.1 - - - -
165B GLN 3.2 7.4 - - - -
168B CYS* 5.7 0.4 - - - -
201B TRP* 3.5 25.2 - - - -
202B THR* 1.3 75.5 - - - +
204B GLY* 1.3 62.3 + - - -
206B THR* 3.8 3.1 - - - -
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Residues in contact with GLY 204 (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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151A GLN* 3.7 16.8 - - - -
162A GLN* 3.8 5.8 - - - -
30B PHE* 3.3 17.3 - - - -
31B GLY 3.0 20.1 + - - -
164B TYR* 3.8 0.6 + - - -
165B GLN 2.8 12.7 + - - -
166B ARG 3.6 6.7 - - - -
168B CYS* 6.0 0.4 - - - +
203B GLY* 1.3 70.1 - - - -
205B ASP* 1.3 61.3 + - - +
206B THR* 3.0 12.5 + - - -
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Residues in contact with ASP 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASP 4.6 2.1 - - - +
125A SER 5.1 0.7 - - - +
126A ARG* 3.2 38.5 + - + +
151A GLN* 4.2 3.6 + - - +
153A TYR* 3.5 27.8 - - + -
18B LYS* 4.6 5.9 + - - +
28B SER* 3.5 14.7 + - - -
29B ILE 3.7 4.3 - - - -
30B PHE* 3.7 8.0 - - + -
166B ARG 2.9 15.1 + - - +
167B SER* 3.3 0.7 - - - -
168B CYS 2.8 25.5 + - - -
204B GLY* 1.3 67.0 - - - -
206B THR* 1.3 59.1 + - - +
207B HIS* 2.8 26.0 + - - -
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Residues in contact with THR 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 4.1 19.1 - - + -
11B VAL* 4.1 2.4 - - + +
28B SER* 3.4 0.9 - - - -
29B ILE* 2.9 48.5 + - + +
32B HIS* 4.5 4.8 - - + +
168B CYS* 3.8 6.3 - - + +
170B VAL* 3.5 25.6 - - + -
201B TRP* 3.9 24.5 - - + -
203B GLY* 3.8 11.1 - - - -
204B GLY 3.0 15.1 + - - -
205B ASP* 1.3 70.8 - - - +
207B HIS* 1.3 61.8 + - - +
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Residues in contact with HIS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 3.5 20.5 + - - -
11B VAL* 4.4 2.0 - - - -
26B THR* 4.0 12.1 - - + -
27B LEU 3.1 14.6 - - - +
28B SER* 3.6 10.1 - - - -
167B SER* 3.4 25.6 - - - -
168B CYS 2.9 24.3 + - - +
169B ASP* 3.7 1.8 - - - -
170B VAL* 2.9 37.3 + - - +
205B ASP* 2.8 22.4 + - - -
206B THR* 1.3 76.0 - - - +
208B LEU* 1.3 61.4 - - - +
209B TYR* 3.7 21.5 - + - -
305B UMP 2.6 24.9 + - - -
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Residues in contact with LEU 208 (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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8B MET* 3.8 19.7 - - + +
11B VAL* 3.6 31.4 - - + -
12B LEU* 4.3 13.5 - - + -
26B THR* 3.4 3.0 - - - -
27B LEU 2.9 28.2 + - - -
169B ASP* 5.4 1.3 - - - -
170B VAL* 3.7 26.0 - - + -
171B PHE* 3.9 18.2 - - + +
207B HIS* 1.3 74.1 - - - +
209B TYR* 1.3 65.3 + - - +
210B SER 3.7 0.2 + - - -
212B HIS* 5.2 1.1 - - + -
213B MET* 3.8 14.8 - - + +
216B THR* 3.7 32.5 - - + +
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Residues in contact with TYR 209 (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* 3.3 19.3 + - - -
20B ASP* 5.5 1.3 - - + -
24B THR* 3.2 30.3 - - + -
25B GLY 3.8 1.6 - - - -
26B THR* 3.3 19.3 - - + -
169B ASP* 3.5 29.1 + - - -
207B HIS* 3.7 13.5 - + - -
208B LEU* 1.3 75.0 - - - +
210B SER* 1.3 66.4 + - - +
211B ASN* 3.4 15.7 - - - +
212B HIS* 3.0 34.5 + + + +
213B MET* 3.6 6.6 - - - +
263B ALA* 3.5 27.4 - - + +
305B UMP 2.8 32.5 + - - -
306B DDT 4.1 2.8 - + - -
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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