Contacts of the helix formed by residues 174 - 193 (chain A) in PDB entry 4UN0
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A GLY* 1.3 68.6 - - - -
175A LYS* 1.3 68.0 + - - +
176A ASN* 3.2 16.4 + - - +
177A LYS* 3.2 40.0 + - + +
178A ILE* 3.0 25.8 + - - +
225A TRP* 4.2 8.3 - - + +
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Residues in contact with LYS 175 (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 GLY 3.2 7.6 + - - +
174A ASP* 1.3 74.8 + - - +
176A ASN* 1.3 63.3 - - - +
178A ILE* 4.1 6.8 - - - +
179A GLN* 3.2 25.1 + - - +
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Residues in contact with ASN 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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174A ASP* 3.1 15.2 + - - +
175A LYS* 1.3 80.4 - - - +
177A LYS* 1.3 64.9 + - + +
179A GLN* 3.6 5.9 + - - +
180A LYS* 3.3 21.3 + - - +
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Residues in contact with LYS 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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174A ASP* 3.2 29.3 + - + +
176A ASN* 1.3 76.0 - - + +
178A ILE* 1.3 66.2 + - - +
180A LYS* 3.3 3.8 + - - +
181A LEU* 3.0 18.7 + - - +
220A PHE* 3.2 50.3 - - + -
225A TRP* 3.8 17.5 - - + -
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Residues in contact with ILE 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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168A ALA* 4.2 18.6 - - + +
171A LEU* 3.3 44.2 - - + +
173A GLY* 3.7 22.7 - - - +
174A ASP 3.0 17.6 + - - +
175A LYS* 4.3 5.2 - - - +
177A LYS* 1.3 73.2 - - - +
179A GLN* 1.3 67.0 + - - +
181A LEU* 3.1 13.0 + - + +
182A VAL* 3.2 21.6 + - + +
225A TRP* 3.6 28.9 - - + -
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Residues in contact with GLN 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 LYS 3.2 18.9 + - - +
176A ASN* 3.7 7.4 - - - +
178A ILE* 1.3 79.5 - - - +
180A LYS* 1.3 62.1 + - - +
182A VAL* 3.3 16.5 + - - +
183A GLN* 3.2 42.8 + - - +
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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 ASN 3.3 10.8 + - - +
177A LYS* 3.3 11.1 + - - +
178A ILE 3.2 0.4 - - - -
179A GLN* 1.3 77.4 - - - +
181A LEU* 1.3 64.8 + - - +
183A GLN* 3.3 14.1 + - + +
184A MET* 3.2 39.2 + - + +
218A CYS* 4.9 11.7 - - - -
220A PHE* 4.6 13.0 - - + -
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Residues in contact with LEU 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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168A ALA* 5.9 0.7 - - + -
171A LEU* 4.2 18.8 - - + -
177A LYS 3.0 12.6 + - - +
178A ILE* 3.1 11.9 + - + +
180A LYS* 1.3 78.3 - - - +
182A VAL* 1.3 59.1 + - + +
184A MET* 5.0 0.9 - - - -
185A ALA* 3.0 30.0 + - - +
211A MET* 3.6 30.7 - - + +
214A ALA* 3.7 14.5 - - + +
215A GLY* 3.5 35.7 - - - +
218A CYS* 5.9 0.4 - - - -
220A PHE* 4.3 12.9 - - + -
222A ILE* 4.6 9.2 - - + -
225A TRP* 3.9 20.6 - - + -
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Residues in contact with VAL 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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164A LEU* 4.0 13.6 - - + +
165A LEU* 3.9 28.5 - - + -
168A ALA* 3.6 29.6 - - + -
178A ILE* 3.2 19.7 + - + +
179A GLN* 3.6 17.7 - - - +
180A LYS 3.2 0.4 - - - -
181A LEU* 1.3 77.5 - - + +
183A GLN* 1.3 59.6 + - - +
185A ALA* 3.7 4.9 - - - +
186A TRP* 2.8 31.7 + - + +
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Residues in contact with GLN 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 GLN* 3.2 39.9 + - - +
180A LYS* 3.3 15.7 + - + +
182A VAL* 1.3 76.1 - - - +
184A MET* 1.3 63.7 + - + +
186A TRP* 3.3 8.2 + - - +
187A THR* 3.1 25.0 + - - -
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Residues in contact with MET 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* 3.2 26.9 + - + +
183A GLN* 1.3 73.7 - - + +
185A ALA* 1.3 65.0 + - - +
187A THR* 3.1 10.2 + - - -
188A PHE* 3.0 50.7 + - + -
214A ALA* 3.8 14.1 - - + -
217A LEU* 4.0 19.1 - - + -
218A CYS* 3.4 31.2 - - - -
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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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164A LEU* 3.6 29.6 - - + -
181A LEU 3.0 20.4 + - - +
182A VAL 3.7 1.8 - - - +
184A MET* 1.3 75.8 - - - +
186A TRP* 1.3 63.3 + - - +
188A PHE* 3.2 4.3 + - - +
189A VAL* 3.0 26.5 + - - +
210A VAL* 3.6 32.7 - - + +
211A MET* 4.2 3.6 - - + +
214A ALA* 4.1 0.6 - - - +
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Residues in contact with TRP 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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68A TYR* 3.6 51.6 - + + +
161A TYR* 3.5 33.1 - + + -
164A LEU* 3.5 20.8 - - + +
165A LEU* 3.8 33.9 - - + -
182A VAL* 2.8 22.5 + - + +
183A GLN* 3.4 8.7 - - - +
185A ALA* 1.3 76.3 - - - +
187A THR* 1.3 62.8 + - - +
189A VAL* 3.3 5.3 + - - +
190A ASN* 3.2 42.8 + - - +
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Residues in contact with THR 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 GLN 3.1 12.2 + - - -
184A MET* 3.1 12.5 + - - -
186A TRP* 1.3 79.4 - - - +
188A PHE* 1.3 65.9 + - + +
190A ASN* 3.2 11.7 + - + +
191A ASP* 3.0 37.9 + - - +
258A TYR* 4.2 7.9 - - - +
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Residues in contact with PHE 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 MET* 3.0 35.2 + - + -
185A ALA 3.5 5.8 - - - +
187A THR* 1.3 78.7 - - + +
189A VAL* 1.3 60.2 + - - +
191A ASP* 3.3 16.2 + - - +
192A SER* 2.9 27.9 + - - -
210A VAL* 3.6 31.4 - - + -
213A LEU* 3.6 32.8 - - + -
214A ALA* 3.9 19.7 - - + -
217A LEU* 3.6 21.8 - - + -
254A ILE* 4.1 14.6 - - + +
255A LEU* 5.8 2.0 - - + -
258A TYR* 4.0 18.8 - + - -
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Residues in contact with VAL 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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160A PRO* 3.8 36.6 - - + -
161A TYR* 3.5 34.1 - - + -
164A LEU* 4.3 11.2 - - + -
185A ALA 3.0 17.3 + - - +
186A TRP 3.5 7.0 - - - +
187A THR 3.2 0.2 - - - -
188A PHE* 1.3 75.1 - - - +
190A ASN* 1.3 63.9 + - - +
192A SER* 2.7 24.9 + - - +
193A LEU* 3.3 11.7 + - + +
206A ILE* 5.1 0.2 - - + -
210A VAL* 3.8 22.4 - - + -
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Residues in contact with ASN 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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58A PHE* 3.4 35.7 - - + -
161A TYR* 2.3 43.4 + - - -
186A TRP* 3.2 21.0 + - - +
187A THR* 3.2 13.5 + - + +
189A VAL* 1.3 76.2 - - - +
191A ASP* 1.3 64.1 + - - +
193A LEU* 3.6 17.9 + - - +
194A CYS* 4.1 9.7 + - - -
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Residues in contact with ASP 191 (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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187A THR* 3.0 24.3 + - - +
188A PHE* 3.5 12.9 - - - +
189A VAL 3.1 0.2 - - - -
190A ASN* 1.3 77.6 - - - +
192A SER* 1.3 59.4 + - - +
193A LEU 3.1 2.5 - - - -
194A CYS* 3.0 23.4 + - - +
195A THR 3.8 0.3 + - - -
254A ILE* 4.3 7.6 - - + -
257A LEU* 3.2 34.0 - - + +
258A TYR* 2.4 36.3 + - - -
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Residues in contact with SER 192 (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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160A PRO* 5.3 1.2 - - - +
188A PHE 2.9 14.5 + - - -
189A VAL* 2.7 24.6 + - - +
191A ASP* 1.3 76.6 - - - +
193A LEU* 1.3 62.9 + - - +
195A THR* 2.5 34.5 + - - +
197A LEU* 3.8 27.6 + - - +
198A SER* 4.8 2.9 + - - -
206A ILE* 4.0 17.4 - - - +
254A ILE* 4.3 9.2 - - - +
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Residues in contact with LEU 193 (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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54A ALA* 3.3 4.2 - - - +
58A PHE* 5.2 7.0 - - + -
68A TYR 5.6 0.2 - - - +
71A LEU* 5.9 0.2 - - + -
72A ALA* 3.7 33.4 - - + +
75A ILE* 3.2 41.1 - - + +
76A ILE* 5.1 10.3 - - + -
79A HIS* 2.7 28.9 + - - -
159A HIS* 5.5 2.0 - - - +
160A PRO* 5.6 6.3 - - + -
161A TYR* 3.5 24.5 - - + +
189A VAL* 3.4 15.7 - - + +
190A ASN* 3.6 11.2 - - - +
191A ASP 3.1 0.6 - - - -
192A SER* 1.3 81.0 + - - +
194A CYS* 1.3 52.8 + - - +
195A THR 3.1 2.9 - - - -
198A SER* 5.1 9.0 - - - -
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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