Contacts of the helix formed by residues 172 - 190 (chain A) 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 VAL 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A GLN* 1.3 73.9 - - - +
173A ALA* 1.3 71.9 + - + +
174A ASP* 3.3 3.0 + - - -
175A LEU* 3.8 7.0 + - - +
176A LYS* 3.6 29.8 + - - +
383A PHE* 3.3 35.1 - - + -
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Residues in contact with ALA 173 (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 VAL* 1.3 85.5 - - + +
174A ASP* 1.3 59.6 + - - +
176A LYS* 3.8 22.2 - - - +
177A ALA* 3.4 18.4 + - - +
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Residues in contact with ASP 174 (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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171A GLN* 2.8 56.5 - - - +
173A ALA* 1.3 71.7 - - - +
175A LEU* 1.3 61.0 + - - +
176A LYS 3.2 0.9 - - - -
177A ALA* 3.2 7.2 + - - +
178A PHE* 2.7 35.6 + - - +
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLN* 4.1 18.6 - - + +
172A VAL* 3.8 7.6 + - - +
173A ALA 3.6 0.2 - - - -
174A ASP* 1.3 83.8 + - - +
176A LYS* 1.3 56.0 + - - +
178A PHE* 3.5 6.1 - - + +
179A SER* 2.6 39.1 + - - -
376A THR* 4.0 22.4 - - + +
379A ARG* 4.4 26.7 - - + +
380A ALA* 3.9 29.1 - - + +
383A PHE* 4.5 21.3 - - + -
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Residues in contact with LYS 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 VAL* 3.6 22.8 + - - +
173A ALA* 3.8 20.7 - - - +
174A ASP 3.2 0.2 - - - -
175A LEU* 1.3 77.9 - - - +
177A ALA* 1.3 51.7 + - - +
179A SER* 3.3 6.4 + - - -
180A LYS* 2.7 36.2 + - - +
383A PHE* 3.3 35.1 - - + -
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Residues in contact with ALA 177 (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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173A ALA 3.4 12.0 + - - +
174A ASP* 3.2 10.1 + - - +
176A LYS* 1.3 74.7 - - - +
178A PHE* 1.3 60.2 + - - +
180A LYS* 3.6 8.6 - - - +
181A HIS* 2.9 41.1 + - + +
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Residues in contact with PHE 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 ASP 2.7 21.8 + - - +
175A LEU* 3.5 8.3 - - + +
177A ALA* 1.3 73.8 - - - +
179A SER* 1.3 61.6 + - - +
181A HIS* 3.6 6.6 + - + +
182A ILE* 3.4 48.1 + - + +
267A ILE* 5.4 3.6 - - + -
269A SER* 4.3 20.2 - - - -
373A ILE* 5.0 1.8 - - + -
376A THR* 4.2 25.4 - - + -
377A ILE* 3.6 37.5 - - + -
380A ALA* 4.0 16.2 - - + -
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Residues in contact with SER 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 LEU 2.6 22.3 + - - -
176A LYS* 3.6 7.2 - - - -
178A PHE* 1.3 73.2 - - - +
180A LYS* 1.3 58.3 + - - +
182A ILE* 3.2 3.3 + - - +
183A TYR* 2.9 29.2 + - - +
350A LEU* 3.6 31.5 - - - +
380A ALA* 3.5 23.6 + - - +
383A PHE* 5.6 2.4 - - - -
384A HIS* 4.6 10.6 - - - +
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Residues in contact with LYS 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 LYS 2.7 21.7 + - - +
177A ALA* 3.2 9.8 + - - +
179A SER* 1.3 71.5 - - - +
181A HIS* 1.3 68.7 + - + +
183A TYR* 3.3 7.4 + - + +
184A ASN* 3.0 47.4 + - - +
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Residues in contact with HIS 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 ALA* 2.9 26.1 + - + +
178A PHE* 3.8 7.9 - - + +
179A SER 3.3 0.2 - - - -
180A LYS* 1.3 78.6 - - + +
182A ILE* 1.3 60.1 + - + +
184A ASN* 3.3 12.8 + - - +
185A ALA* 2.9 28.2 + - - +
266A SER 4.9 3.4 - - - +
267A ILE* 6.5 0.2 - - - -
268A PRO* 4.4 27.9 - - + +
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Residues in contact with ILE 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 PHE* 3.4 45.5 + - + +
179A SER 3.2 8.1 + - - +
181A HIS* 1.3 77.6 - - + +
183A TYR* 1.3 62.9 + - - +
185A ALA* 3.2 8.2 + - - +
186A TYR* 2.9 20.8 + - - +
263A PHE* 3.7 12.8 - - + -
267A ILE* 4.4 21.3 - - + -
349A ALA* 3.5 32.8 - - + +
350A LEU* 3.9 17.7 - - + +
353A ALA* 4.1 15.5 - - + -
377A ILE* 4.4 3.1 - - + -
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Residues in contact with TYR 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 SER 2.9 16.1 + - - +
180A LYS* 3.8 8.1 - - + +
182A ILE* 1.3 76.4 - - - +
184A ASN* 1.3 61.7 + - - +
186A TYR* 3.0 6.9 + + - +
187A LEU* 2.8 66.7 + - + +
345A ASP* 3.8 19.8 + - + +
346A SER* 3.8 44.8 + - - +
349A ALA* 3.9 8.7 - - + +
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Residues in contact with ASN 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 LYS* 3.0 46.2 + - - +
181A HIS* 3.6 11.3 - - - +
183A TYR* 1.3 80.4 - - - +
185A ALA* 1.3 57.2 + - - +
187A LEU* 3.4 14.1 + - - +
188A LYS* 2.9 33.3 + - - +
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Residues in contact with ALA 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 HIS 2.9 14.2 + - - +
182A ILE* 3.2 11.9 + - - +
184A ASN* 1.3 75.0 - - - +
186A TYR* 1.3 60.8 + - - +
188A LYS* 4.3 3.6 - - - -
189A ASN* 2.7 35.6 + - - +
263A PHE* 3.7 18.6 - - + +
266A SER* 3.6 33.7 - - - +
267A ILE* 4.5 1.8 - - + -
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Residues in contact with TYR 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 ILE 2.9 12.6 + - - +
183A TYR* 3.0 20.4 + + - +
185A ALA* 1.3 72.5 - - - +
187A LEU* 1.3 70.4 + - + +
188A LYS 3.1 1.6 + - - -
189A ASN 3.3 0.3 + - - -
190A PHE* 3.2 58.6 + + + +
192A MET 4.8 1.8 + - - -
193A THR* 4.3 14.9 - - + -
194A LYS 4.2 3.8 + - - -
263A PHE* 3.7 12.1 - + + -
293A MET* 4.9 12.1 - - + +
296A SER* 5.2 0.9 + - - -
345A ASP* 2.5 45.3 + - + -
348A LEU* 4.1 18.7 - - + +
349A ALA* 3.7 34.1 - - + -
352A ILE* 5.2 2.7 - - + -
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Residues in contact with LEU 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 TYR* 2.8 67.2 + - + +
184A ASN* 4.0 13.2 - - - +
186A TYR* 1.3 81.2 - - + +
188A LYS* 1.3 60.5 + - - +
189A ASN 3.6 0.3 + - - -
190A PHE 4.4 8.6 - - - +
193A THR* 4.3 18.8 - - + -
345A ASP* 5.1 1.6 - - + -
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Residues in contact with LYS 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 ASN 2.9 19.0 + - - +
185A ALA* 3.8 7.6 - - - +
186A TYR 3.1 0.2 - - - -
187A LEU* 1.3 79.5 - - - +
189A ASN* 1.3 74.3 + - - +
190A PHE 5.4 0.2 - - - -
266A SER* 4.3 11.8 + - - +
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Residues in contact with ASN 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 ALA 2.7 27.0 + - - +
186A TYR 3.3 2.0 + - - -
188A LYS* 1.3 96.2 + - - +
190A PHE* 1.3 64.0 + - + +
191A ASN 3.8 0.2 + - - -
259A GLU* 3.6 27.4 - - - +
262A GLU* 3.2 24.9 + - + +
263A PHE* 3.7 23.5 - - + +
266A SER* 3.3 23.2 + - - -
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Residues in contact with PHE 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 TYR* 3.2 60.7 + + + +
187A LEU 4.4 8.5 - - - +
189A ASN* 1.3 78.6 - - - +
191A ASN* 1.3 64.6 + - - +
192A MET* 3.4 17.3 + - - +
193A THR* 4.9 6.4 - - + +
259A GLU* 3.5 32.3 - - + +
260A LEU* 3.6 27.4 - - + -
263A PHE* 3.7 33.4 - + + -
293A MET* 3.7 31.9 - - + -
352A ILE* 4.9 1.8 - - + -
504A PGO 5.6 2.5 - - - +
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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