Contacts of the helix formed by residues 193 - 203 (chain B) in PDB entry 1JS6
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 SER 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A LEU* 4.2 10.6 - - - +
191B ALA 3.9 0.8 + - - -
192B HIS* 1.3 81.1 + - - +
194B SER* 1.3 64.1 + - - +
195B VAL 3.0 6.1 - - - -
196B GLU* 3.0 32.1 + - - +
197B ARG* 3.2 15.6 + - - +
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Residues in contact with SER 194 (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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353A LEU* 3.9 8.5 - - - -
149B SER* 3.1 44.4 - - - +
152B THR* 4.3 11.3 + - - +
192B HIS* 2.9 25.2 - - - +
193B SER* 1.3 77.2 + - - +
195B VAL* 1.3 62.6 + - - +
197B ARG* 3.6 6.8 + - - +
198B ALA* 3.0 26.7 + - - +
271B ASP* 4.5 1.4 + - - -
602B PLP 4.1 6.8 - - - -
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B THR* 4.4 8.1 - - + +
156B LEU* 5.1 2.1 - - + +
185B ALA* 6.3 0.7 - - + -
186B TYR 5.1 0.4 - - - +
187B ALA* 3.9 17.9 - - + -
191B ALA* 4.3 14.8 - - + -
192B HIS* 3.4 18.4 - - + +
193B SER 3.0 0.4 - - - -
194B SER* 1.3 82.9 - - - +
196B GLU* 1.3 65.6 + - + +
198B ALA* 3.2 7.6 + - + +
199B GLY* 2.9 18.9 + - - -
206B LEU* 3.7 24.6 - - + +
238B PHE* 5.6 2.9 - - + -
240B VAL* 4.1 32.5 - - + -
242B THR* 5.9 0.4 - - - +
271B ASP* 5.2 4.3 - - - +
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Residues in contact with GLU 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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192B HIS 5.5 0.7 - - - +
193B SER* 3.0 21.3 + - - +
195B VAL* 1.3 75.3 - - + +
197B ARG* 1.3 55.9 + - + +
199B GLY* 3.1 1.9 + - - -
200B LEU* 2.7 37.2 + - - +
206B LEU* 3.6 22.4 - - + +
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Residues in contact with ARG 197 (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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326A PHE* 3.8 37.4 + - + +
347A ARG* 2.9 22.6 + - - +
348A HIS* 4.1 7.5 + - - -
350A GLN 2.7 29.7 + - - -
351A LEU 3.0 20.2 + - - +
352A PRO 3.9 2.0 + - - -
353A LEU* 3.2 41.1 - - - +
149B SER* 5.8 1.5 - - - -
193B SER* 3.2 11.9 + - - +
194B SER* 3.8 7.2 - - - +
196B GLU* 1.3 78.1 - - + +
198B ALA* 1.3 58.5 + - - +
200B LEU* 3.1 11.0 + - + +
201B ILE* 2.8 43.8 + - + +
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Residues in contact with ALA 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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152B THR* 4.1 11.0 - - + -
153B LEU* 3.8 39.0 - - + +
156B LEU* 4.0 16.3 - - + +
194B SER 3.0 15.0 + - - +
195B VAL* 3.3 10.5 - - + +
197B ARG* 1.3 77.3 - - - +
199B GLY* 1.3 58.7 + - - +
201B ILE* 3.7 2.2 - - - +
202B GLY* 2.8 28.2 + - - -
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Residues in contact with GLY 199 (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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156B LEU* 3.9 14.9 - - - +
185B ALA* 6.1 0.4 - - - -
195B VAL 2.9 14.5 + - - -
196B GLU* 3.6 2.7 - - - -
198B ALA* 1.3 75.5 - - - +
200B LEU* 1.3 57.4 + - - +
202B GLY 3.7 0.2 - - - -
203B GLY* 2.9 23.6 + - - -
204B VAL* 3.1 29.9 + - - +
206B LEU* 5.2 9.4 - - - -
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Residues in contact with LEU 200 (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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160A ARG* 3.7 7.4 + - - -
324A GLY 5.6 0.2 - - - +
325A ALA 3.3 27.6 - - - +
326A PHE* 3.9 21.1 - - - +
327A LYS 4.3 8.7 - - - +
196B GLU 2.7 17.4 + - - +
197B ARG* 3.3 15.5 - - + +
199B GLY* 1.3 72.7 - - - +
201B ILE* 1.3 65.8 + - + +
203B GLY* 3.2 12.7 + - - -
204B VAL 5.2 0.4 - - - -
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Residues in contact with ILE 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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153A LEU* 6.0 0.4 - - + -
157A LEU* 3.5 30.8 - - + +
160A ARG* 2.9 29.6 + - - +
201A ILE* 5.1 13.4 - - + +
325A ALA 5.7 1.6 - - - +
326A PHE* 4.3 15.5 - - + -
351A LEU* 3.7 33.0 - - + +
153B LEU* 3.8 30.1 - - + -
157B LEU* 5.7 0.4 - - + -
160B ARG* 4.6 1.0 + - - -
197B ARG* 2.8 31.7 + - + +
198B ALA* 3.8 2.9 - - - +
200B LEU* 1.3 71.2 - - + +
202B GLY* 1.3 62.0 + - - +
203B GLY 3.0 4.7 - - - -
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Residues in contact with GLY 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ARG* 4.9 0.7 - - - -
153B LEU* 4.6 0.6 - - - +
156B LEU* 4.1 17.3 - - - -
157B LEU* 4.4 8.3 - - - -
160B ARG* 2.8 39.7 + - - -
180B LEU* 4.3 3.5 - - - +
198B ALA 2.8 19.9 + - - -
199B GLY 3.9 0.7 - - - -
201B ILE* 1.3 73.6 - - - +
203B GLY* 1.3 62.3 + - - +
204B VAL* 3.5 4.9 - - - +
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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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160A ARG* 4.8 5.6 - - - -
176A GLN* 3.6 28.9 + - - -
180A LEU* 6.2 0.2 - - - -
180B LEU* 4.1 19.6 - - - +
199B GLY 2.9 7.4 + - - -
200B LEU 3.2 8.2 + - - -
201B ILE 3.0 5.5 - - - -
202B GLY* 1.3 79.9 - - - +
204B VAL* 1.3 62.3 + - - +
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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