Contacts of the helix formed by residues 174 - 190 (chain B) in PDB entry 5U3Y
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 ASP 174 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173B ALA* 1.3 78.9 - - - +
175B LEU* 1.3 63.5 + - - +
176B LYS 3.4 1.1 - - - -
177B ALA* 3.8 3.6 - - - +
178B PHE* 2.8 27.5 + - - +
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Residues in contact with LEU 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 ALA* 4.5 1.0 - - + +
174B ASP* 1.3 76.5 - - - +
176B LYS* 1.3 63.2 + - + +
178B PHE* 3.3 8.5 + - + +
179B SER* 2.9 31.5 + - - -
376B THR* 3.8 37.5 - - + +
379B ARG* 4.5 10.3 - - + -
380B ALA* 4.0 26.7 - - + +
383B PHE* 4.4 22.7 - - + -
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Residues in contact with LYS 176 (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 ALA* 3.7 25.2 - - + +
174B ASP 3.4 0.2 - - - -
175B LEU* 1.3 78.9 - - + +
177B ALA* 1.3 57.4 + - - +
179B SER* 3.4 6.0 + - - +
180B LYS* 2.8 31.4 + - - +
383B PHE* 3.6 39.9 - - + -
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Residues in contact with ALA 177 (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 ALA* 3.3 23.7 + - - +
174B ASP* 3.6 6.7 + - - +
175B LEU 3.3 0.2 - - - -
176B LYS* 1.3 75.2 - - - +
178B PHE* 1.3 65.4 + - - +
180B LYS* 3.9 8.4 - - - +
181B HIS* 3.0 25.6 + - - +
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Residues in contact with PHE 178 (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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174B ASP 2.8 19.1 + - - +
175B LEU* 3.3 9.9 - - + +
177B ALA* 1.3 78.2 - - - +
179B SER* 1.3 62.6 + - - +
181B HIS* 3.5 4.3 + - - +
182B ILE* 3.3 47.9 + - + +
267B ILE* 5.2 4.0 - - + -
268B PRO* 6.5 0.7 - - + -
269B SER* 4.1 22.9 - - - -
373B ILE* 5.0 2.0 - - + -
376B THR* 4.2 24.9 - - + -
377B ILE* 3.7 37.7 - - + -
380B ALA* 4.3 15.0 - - + -
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 2.9 13.1 + - - +
176B LYS* 3.7 6.7 - - - -
178B PHE* 1.3 73.7 - - - +
180B LYS* 1.3 67.5 + - - +
182B ILE* 3.0 4.6 + - - +
183B TYR* 2.9 22.9 + - - +
350B LEU* 3.8 28.0 - - - +
380B ALA* 3.2 30.7 + - - +
383B PHE* 5.4 5.6 - - - -
384B HIS* 5.3 5.1 - - - +
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Residues in contact with LYS 180 (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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176B LYS 2.8 21.3 + - - +
177B ALA* 3.9 9.0 - - - +
178B PHE 3.4 0.2 - - - -
179B SER* 1.3 72.7 - - - +
181B HIS* 1.3 62.0 + - - +
183B TYR* 3.3 10.6 + - + +
184B ASN* 3.0 44.0 + - - +
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Residues in contact with HIS 181 (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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177B ALA 3.0 18.6 + - - +
178B PHE* 3.8 5.4 - - - +
180B LYS* 1.3 76.4 - - - +
182B ILE* 1.3 61.2 + - + +
184B ASN* 3.2 11.7 + - + +
185B ALA* 2.9 25.3 + - + +
266B SER* 2.9 29.3 + - - -
267B ILE* 4.7 1.8 - - - -
268B PRO* 3.6 27.9 - - + +
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Residues in contact with ILE 182 (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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178B PHE* 3.3 47.9 + - + +
179B SER 3.0 7.9 + - - +
181B HIS* 1.3 78.7 - - + +
183B TYR* 1.3 58.0 + - - +
185B ALA* 3.3 6.1 + - - -
186B TYR* 3.0 26.9 + - - +
263B PHE* 3.6 14.4 - - + -
267B ILE* 4.4 21.5 - - + -
349B ALA 3.7 30.3 - - - +
350B LEU* 4.0 17.3 - - + -
353B ALA* 4.1 15.5 - - + -
377B ILE* 4.6 3.4 - - + -
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Residues in contact with TYR 183 (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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179B SER 2.9 12.7 + - - +
180B LYS* 3.3 12.8 + - + +
182B ILE* 1.3 76.7 - - - +
184B ASN* 1.3 62.6 + - - +
186B TYR* 3.3 3.1 + + - +
187B LEU* 3.0 57.1 + - + +
345B ASP* 3.8 19.0 - - + +
346B SER* 3.5 47.2 + - - +
349B ALA* 4.0 11.4 - - + +
350B LEU* 6.4 0.7 - - + -
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Residues in contact with ASN 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 LYS* 3.0 40.0 + - - +
181B HIS* 3.2 12.0 + - + +
183B TYR* 1.3 79.0 - - - +
185B ALA* 1.3 60.5 + - - +
186B TYR 3.1 1.6 - - - -
187B LEU* 3.2 14.3 + - - +
188B LYS* 2.8 34.3 + - - +
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Residues in contact with ALA 185 (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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181B HIS* 2.9 13.4 + - + +
182B ILE* 3.6 11.4 - - - +
184B ASN* 1.3 75.8 - - - +
186B TYR* 1.3 60.4 + - - +
188B LYS* 4.4 3.8 - - - +
189B ASN* 2.8 36.3 + - - +
263B PHE* 3.4 16.5 - - + +
266B SER* 3.5 35.2 - - - +
267B ILE* 4.9 2.0 - - + -
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Residues in contact with TYR 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 ILE 3.0 12.4 + - - +
183B TYR* 3.4 10.5 - + - +
184B ASN 3.1 0.2 - - - -
185B ALA* 1.3 77.6 - - - +
187B LEU* 1.3 73.6 + - + +
190B PHE* 3.1 57.5 + + + +
193B THR* 4.6 11.8 - - + -
194B LYS 4.4 1.0 + - - -
263B PHE* 3.6 11.8 - + + -
293B MET* 5.0 8.0 - - - +
296B SER* 5.0 0.3 + - - -
345B ASP* 2.8 47.8 + - + -
348B LEU* 3.8 20.2 - - + +
349B ALA* 3.6 34.5 - - + -
352B ILE* 4.9 7.4 - - + -
503B PEG 4.3 13.2 + - - -
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Residues in contact with LEU 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 TYR* 3.0 58.0 + - + +
184B ASN* 3.9 13.5 - - - +
186B TYR* 1.3 81.9 - - + +
188B LYS* 1.3 62.4 + - - +
189B ASN 3.5 0.3 + - - -
190B PHE 3.9 11.9 - - - +
193B THR* 4.2 22.4 - - + -
196B LYS* 5.8 1.2 + - - -
345B ASP* 5.1 3.1 - - + -
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Residues in contact with LYS 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 ASN 2.8 18.0 + - - +
185B ALA* 5.0 2.5 - - - +
186B TYR 3.3 0.4 - - - -
187B LEU* 1.3 78.5 - - - +
189B ASN* 1.3 80.8 + - - +
190B PHE 5.3 0.2 - - - -
266B SER* 3.5 18.2 + - - -
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Residues in contact with ASN 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 ALA 2.8 26.8 + - - +
186B TYR 4.7 0.2 - - - +
188B LYS* 1.3 98.1 - - - +
190B PHE* 1.3 59.8 + - + +
259B GLU* 3.3 32.3 - - - +
262B GLU* 3.1 25.0 + - + +
263B PHE* 3.8 24.4 - - + +
266B SER* 3.3 22.4 + - - -
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Residues in contact with PHE 190 (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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186B TYR* 3.1 61.4 + + + +
187B LEU 3.9 11.3 - - - +
188B LYS 3.8 0.4 - - - -
189B ASN* 1.3 75.9 - - - +
191B ASN* 1.3 67.5 + - - +
192B MET 4.4 12.3 - - - +
193B THR* 4.3 9.7 - - + +
196B LYS* 4.8 1.9 + - - -
256B THR* 4.9 1.6 - - + -
259B GLU* 3.7 33.9 - - + -
260B LEU* 3.7 31.6 - - + -
263B PHE* 3.7 34.1 - + + -
293B MET* 3.8 23.3 - - + -
352B ILE* 5.0 1.1 - - + -
503B PEG 5.2 5.6 - - - +
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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