Contacts of the helix formed by residues 174 - 190 (chain B) in PDB entry 4JYH
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 THR 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B GLU* 3.6 10.8 + - + +
173B MET* 1.3 79.0 - - - +
175B ALA* 1.3 69.0 + - - +
176B GLU 3.7 0.9 - - - -
177B LEU* 2.9 19.6 + - - +
178B ASP* 2.7 35.6 + - - -
354B ILE* 3.8 36.5 - - + +
358B LYS* 4.2 10.0 + - - -
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Residues in contact with ALA 175 (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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173B MET* 3.6 7.3 - - + +
174B THR* 1.3 73.3 - - - +
176B GLU* 1.3 55.7 + - + +
177B LEU 2.5 13.9 + - - -
178B ASP* 2.6 23.2 + - - +
179B ASP* 3.2 9.4 + - - +
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Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B THR 3.4 0.8 + - - -
175B ALA* 1.3 75.5 - - + +
177B LEU* 1.3 57.6 + - + +
179B ASP* 4.2 14.6 - - + +
180B LEU* 3.9 14.3 + - - +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B THR* 3.1 13.0 - - - +
175B ALA 2.5 6.5 + - - -
176B GLU* 1.3 77.3 - - + +
178B ASP* 1.3 61.2 + - - +
179B ASP 3.3 0.9 - - - -
180B LEU* 3.7 10.2 - - + +
181B THR* 2.6 39.1 + - - +
347B PRO* 4.7 7.4 - - + +
350B GLU* 4.1 13.0 - - + -
351B ALA* 3.4 42.0 - - + +
354B ILE* 3.6 33.2 - - + -
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Residues in contact with ASP 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B THR* 2.7 38.8 + - - -
175B ALA* 2.6 14.9 + - - +
177B LEU* 1.3 77.1 - - - +
179B ASP* 1.3 58.4 + - - +
181B THR* 3.3 9.8 + - - -
182B GLU* 2.9 28.9 + - - +
354B ILE* 5.0 2.3 - - - +
358B LYS* 3.6 21.8 + - - -
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Residues in contact with ASP 179 (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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175B ALA 3.2 11.3 + - - +
176B GLU* 4.4 11.2 - - - +
178B ASP* 1.3 74.9 - - - +
180B LEU* 1.3 64.1 + - - +
182B GLU* 3.2 8.2 + - - +
183B LYS* 3.0 43.0 + - - +
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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
----------------------------------------------------------
176B GLU 3.9 13.4 + - - +
177B LEU* 3.7 11.1 + - + +
179B ASP* 1.3 77.0 - - - +
181B THR* 1.3 66.8 + - - +
183B LYS* 3.0 21.4 + - - +
184B ILE* 3.1 24.8 + - + +
240B PRO* 3.7 31.6 - - + -
321B LEU* 5.9 0.2 - - + -
347B PRO* 3.8 35.2 - - + +
348B LEU* 4.0 19.7 - - + -
351B ALA* 4.7 7.9 - - + -
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Residues in contact with THR 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 2.6 25.3 + - - +
178B ASP* 3.4 13.6 + - - -
180B LEU* 1.3 77.9 - - - +
182B GLU* 1.3 64.1 + - - +
184B ILE* 3.3 8.7 + - - +
185B ARG* 3.2 21.1 + - - +
317B THR* 3.5 27.5 - - + +
321B LEU* 4.2 12.3 - - + -
351B ALA* 3.8 18.0 + - - +
355B TYR* 4.0 17.3 - - + +
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Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ASP 2.9 13.9 + - - +
179B ASP* 3.5 13.5 - - - +
180B LEU 3.1 0.4 - - - -
181B THR* 1.3 75.8 - - - +
183B LYS* 1.3 66.8 + - - +
185B ARG* 2.9 44.3 + - - +
186B LYS* 3.1 30.1 + - + +
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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
----------------------------------------------------------
179B ASP* 3.0 40.8 + - - +
180B LEU* 3.3 14.4 - - - +
182B GLU* 1.3 77.2 - - - +
184B ILE* 1.3 62.3 + - + +
186B LYS* 4.1 3.9 - - - +
187B ALA* 3.0 29.8 + - - +
238B ARG* 5.0 7.6 + - - +
240B PRO* 3.9 26.1 - - + +
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Residues in contact with ILE 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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180B LEU* 3.1 35.0 + - + +
181B THR 3.7 7.6 - - - +
182B GLU 3.2 0.2 - - - -
183B LYS* 1.3 78.1 - - - +
185B ARG* 1.3 61.2 + - + +
187B ALA* 3.5 4.9 + - + +
188B HIS* 3.0 27.7 + - - +
235B PHE* 4.1 2.3 - - + -
238B ARG 5.7 0.2 - - - +
239B LEU* 3.8 29.2 - - + -
240B PRO* 4.2 9.0 - - + -
317B THR 4.0 4.9 - - - +
320B GLY* 3.6 5.2 - - - +
321B LEU* 3.4 53.2 - - + +
324B ALA* 4.4 4.9 - - + -
348B LEU* 4.1 11.0 - - + -
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Residues in contact with ARG 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B THR 3.2 12.9 + - - +
182B GLU* 2.9 37.3 + - - +
184B ILE* 1.3 81.0 - - - +
186B LYS* 1.3 81.8 + - - +
188B HIS* 3.3 4.8 + - - +
189B GLN* 2.9 43.6 + - - +
316B ASP* 4.4 8.8 - - + +
317B THR* 3.3 40.6 - - + +
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Residues in contact with LYS 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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182B GLU* 3.1 24.9 + - + +
183B LYS* 4.1 4.7 - - - +
185B ARG* 1.3 99.7 - - - +
187B ALA* 1.3 65.2 - - - +
189B GLN* 4.7 2.2 - - - -
190B GLU* 3.0 52.0 + - - +
238B ARG* 4.7 2.2 - - - +
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Residues in contact with ALA 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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183B LYS 3.0 20.4 + - - +
184B ILE* 3.7 6.5 - - + +
185B ARG 3.3 0.2 - - - -
186B LYS* 1.3 78.1 - - - +
188B HIS* 1.3 53.0 + - - +
190B GLU 4.3 0.2 - - - -
191B THR* 2.7 38.5 + - - +
235B PHE* 3.6 12.7 - - + +
238B ARG* 3.3 47.0 - - + +
239B LEU* 5.3 2.0 - - + -
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Residues in contact with HIS 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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184B ILE 3.0 19.0 + - - +
185B ARG 3.6 3.1 - - - +
186B LYS 3.2 0.2 - - - -
187B ALA* 1.3 74.8 - - - +
189B GLN* 1.3 56.0 + - - +
191B THR* 2.9 6.5 + - - -
192B PHE* 2.8 69.4 + + + +
235B PHE* 3.7 17.9 - - + -
265B ARG* 4.3 13.9 + - + -
316B ASP* 3.4 41.5 + - + +
319B THR* 3.3 31.2 - - + +
320B GLY* 3.8 15.0 - - - -
323B SER* 4.9 4.7 + - - -
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Residues in contact with GLN 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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185B ARG* 2.9 34.4 + - - +
186B LYS* 4.2 2.2 - - - +
188B HIS* 1.3 76.5 - - - +
190B GLU* 1.3 65.6 + - + +
192B PHE 3.1 27.5 + - - +
193B PRO* 3.8 4.5 - - - +
316B ASP* 4.8 13.2 - - + +
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LYS* 3.0 32.0 + - - +
187B ALA 4.5 0.7 - - - +
189B GLN* 1.3 78.8 - - + +
191B THR* 1.3 61.6 + - - +
193B PRO* 5.6 1.4 - - - +
231B LYS* 4.0 10.2 + - - -
234B GLU* 4.9 1.6 - - - +
238B ARG* 2.6 48.5 + - - +
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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