Contacts of the helix formed by residues 171 - 190 (chain A) 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 TYR 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A SER* 1.3 73.5 - - - +
172A GLU* 1.3 65.2 + - + +
173A MET* 3.7 19.2 - - + +
174A THR* 3.0 47.7 - - - +
175A ALA* 3.3 19.9 + - - +
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A SER 3.4 8.2 + - - +
171A TYR* 1.3 74.8 - - + +
173A MET* 1.3 63.4 + - - +
175A ALA* 3.0 11.9 + - - +
176A GLU* 2.8 61.0 + - - +
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Residues in contact with MET 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TYR* 3.6 21.1 - - + +
172A GLU* 1.3 75.9 - - - +
174A THR* 1.3 67.7 + - - +
176A GLU* 3.4 26.2 - - + +
177A LEU* 3.0 59.9 + - + +
347A PRO* 5.2 12.8 - - + -
350A GLU* 6.0 1.6 - - + -
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Residues in contact with THR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TYR* 3.0 35.1 - - - +
172A GLU 3.2 0.2 - - - -
173A MET* 1.3 79.0 - - - +
175A ALA* 1.3 63.1 + - - +
177A LEU* 4.0 4.7 - - - +
178A ASP* 3.1 42.5 + - - +
354A ILE* 5.9 3.6 - - - -
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A SER* 5.5 7.9 - - - +
171A TYR 3.3 10.9 + - - +
172A GLU* 3.0 17.3 + - - +
174A THR* 1.3 81.0 - - - +
176A GLU* 1.3 62.6 + - + +
178A ASP* 3.3 9.9 + - - +
179A ASP* 3.1 20.7 + - - +
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Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLU* 2.8 49.4 + - - +
173A MET* 3.4 30.8 - - + +
175A ALA* 1.3 76.9 - - + +
177A LEU* 1.3 60.4 + - + +
179A ASP* 3.2 8.7 - - - +
180A LEU* 3.0 26.5 + - - +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A MET* 3.0 57.5 + - + +
174A THR* 4.0 3.1 - - - +
176A GLU* 1.3 76.7 - - + +
178A ASP* 1.3 62.6 + - - +
179A ASP 3.1 2.0 - - - -
180A LEU* 3.7 8.2 - - + +
181A THR* 2.8 36.2 + - - +
347A PRO* 4.2 26.0 - - + +
350A GLU* 3.4 22.4 - - + -
351A ALA* 4.5 8.4 - - + +
354A ILE* 3.4 34.3 - - + -
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Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A THR* 3.1 33.7 + - - +
175A ALA* 3.3 7.5 + - - +
177A LEU* 1.3 78.0 - - - +
179A ASP* 1.3 61.2 + - - +
181A THR* 3.9 7.8 + - - +
182A GLU* 3.2 23.4 + - - +
354A ILE* 5.4 8.5 - - - +
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Residues in contact with ASP 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ALA 3.1 12.0 + - - +
176A GLU* 3.2 13.7 - - - +
177A LEU 3.1 0.2 - - - -
178A ASP* 1.3 75.7 - - - +
180A LEU* 1.3 66.0 + - - +
182A GLU* 3.1 6.2 + - - +
183A LYS* 3.0 48.0 + - - +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLU 3.0 12.7 + - - +
177A LEU* 3.7 8.3 - - + +
179A ASP* 1.3 80.9 + - - +
181A THR* 1.3 62.6 + - - +
183A LYS* 3.3 6.2 + - - +
184A ILE* 3.1 46.7 + - + +
240A PRO* 3.4 35.0 - - + -
347A PRO* 3.7 44.0 - - + +
348A LEU* 3.8 17.3 - - + -
351A ALA* 4.1 9.2 - - + -
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LEU 2.8 27.8 + - - -
178A ASP* 3.9 9.0 + - - +
180A LEU* 1.3 73.8 - - - +
182A GLU* 1.3 58.0 + - - +
184A ILE* 4.0 1.9 - - - +
185A ARG* 3.1 26.3 + - + +
317A THR* 3.4 28.4 - - + +
321A LEU* 4.7 11.4 - - + +
351A ALA* 3.5 22.0 + - - +
355A TYR* 4.0 18.6 - - + +
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Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP 3.2 16.6 + - - +
179A ASP* 3.1 6.1 + - - +
181A THR* 1.3 79.3 - - - +
183A LYS* 1.3 68.0 + - + +
184A ILE 3.2 0.2 - - - -
185A ARG* 2.9 41.7 + - - +
186A LYS* 3.0 28.3 + - + +
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Residues in contact with LYS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASP* 3.0 38.7 + - - +
180A LEU* 3.9 5.4 - - - +
182A GLU* 1.3 78.5 - - + +
184A ILE* 1.3 58.8 + - - +
186A LYS* 3.8 5.4 - - - +
187A ALA* 2.9 29.9 + - - +
238A ARG* 5.0 9.4 + - - +
240A PRO* 3.4 41.4 - - + +
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 3.1 26.9 + - + +
181A THR 4.0 2.9 - - - +
183A LYS* 1.3 76.3 - - - +
185A ARG* 1.3 64.8 + - - +
187A ALA* 3.4 6.6 + - - +
188A HIS* 3.0 21.8 + - - +
235A PHE* 4.0 10.2 - - + -
239A LEU* 4.1 13.0 - - + -
240A PRO* 4.5 5.4 - - + -
317A THR 5.0 0.7 - - - +
320A GLY* 3.5 33.2 - - - +
321A LEU* 3.5 21.8 - - + +
324A ALA* 4.1 8.5 - - + -
348A LEU* 3.3 34.3 - - + -
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Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A THR* 3.1 19.2 + - + +
182A GLU* 2.9 39.9 + - - +
184A ILE* 1.3 75.8 - - - +
186A LYS* 1.3 64.0 + - - +
188A HIS* 3.0 4.0 + - - +
189A GLN* 2.7 74.5 + - - +
316A ASP* 3.8 25.8 - - + -
317A THR* 3.2 29.8 - - - +
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Residues in contact with LYS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLU* 3.0 27.2 + - + +
183A LYS* 3.8 5.2 - - - +
185A ARG* 1.3 77.4 - - - +
187A ALA* 1.3 57.6 + - - +
188A HIS 3.0 5.4 + - - -
189A GLN* 3.2 11.5 + - - +
190A GLU* 2.9 61.7 + - + +
238A ARG* 4.0 6.7 - - - +
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Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LYS 2.9 20.1 + - - +
184A ILE* 3.8 6.7 - - - +
185A ARG 3.3 0.2 - - - -
186A LYS* 1.3 75.2 - - - +
188A HIS* 1.3 51.1 + - - +
191A THR* 2.7 37.0 + - - +
235A PHE* 3.2 17.7 - - + +
238A ARG* 3.5 47.6 - - + +
239A LEU* 5.4 0.4 - - + -
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Residues in contact with HIS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ILE 3.0 12.3 + - - +
185A ARG 3.0 8.4 + - - +
186A LYS 3.0 0.8 - - - -
187A ALA* 1.3 77.4 - - - +
189A GLN* 1.3 68.0 + - - +
190A GLU 3.2 1.3 - - - -
191A THR* 3.1 4.0 + - - -
192A PHE* 2.9 57.3 + + - +
235A PHE* 4.2 8.7 - + + -
265A ARG* 4.5 17.6 + - - +
316A ASP* 3.6 33.2 + - - +
319A THR* 3.3 35.1 - - + +
320A GLY* 3.7 18.2 - - - -
323A SER* 4.6 6.0 + - - -
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Residues in contact with GLN 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ARG* 2.7 52.6 + - - +
186A LYS* 3.9 7.0 - - - +
188A HIS* 1.3 78.2 + - - +
190A GLU* 1.3 62.1 + - + +
191A THR 3.2 3.2 + - - -
192A PHE 3.4 19.1 + - - +
193A PRO* 4.2 4.0 - - - +
197A GLN* 5.2 2.3 - - - +
316A ASP* 3.1 41.4 - - - +
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Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LYS* 2.9 34.6 + - + +
189A GLN* 1.3 80.5 - - + +
191A THR* 1.3 61.8 + - + +
192A PHE 3.7 0.2 - - - -
231A LYS* 4.8 7.4 + - - -
234A GLU* 4.9 2.4 - - - +
238A ARG* 2.9 40.2 + - - +
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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