Contacts of the helix formed by residues 176 - 193 (chain A) in PDB entry 5UAK
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 SER 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A LEU* 6.2 0.2 - - - +
171A VAL* 4.7 11.1 + - - +
174A LYS* 2.8 17.4 + - - +
175A ILE* 1.3 72.4 - - - +
177A ILE* 1.3 59.3 + - - +
178A GLY 3.5 1.8 - - - -
179A GLN* 3.6 31.0 - - - +
180A LEU* 2.9 31.4 + - - +
374A PHE* 5.2 10.6 - - - -
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Residues in contact with ILE 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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172A LEU* 5.9 5.4 - - + +
175A ILE* 3.5 23.0 - - + +
176A SER* 1.3 78.6 - - - +
178A GLY* 1.3 65.2 + - - +
180A LEU* 3.5 5.7 + - - +
181A VAL* 3.2 31.6 + - + +
1059A LEU* 4.0 31.6 - - + -
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Residues in contact with GLY 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ILE* 5.5 2.6 + - - +
177A ILE* 1.3 77.0 - - - +
179A GLN* 1.3 53.8 + - - +
181A VAL* 3.3 12.2 - - - +
182A SER* 2.7 38.3 + - - -
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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
----------------------------------------------------------
175A ILE 5.1 1.1 - - - +
176A SER* 3.6 30.4 - - - +
177A ILE 3.3 0.6 - - - -
178A GLY* 1.3 76.4 - - - +
180A LEU* 1.3 56.1 + - - +
182A SER* 3.9 5.9 - - - -
183A LEU* 2.9 30.3 + - + +
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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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160A ILE* 4.9 15.9 - - + -
164A THR* 3.9 21.1 - - - +
167A LEU* 5.9 2.9 - - + -
176A SER* 2.9 18.5 + - - +
177A ILE* 3.8 6.1 - - - +
178A GLY 3.2 0.2 - - - -
179A GLN* 1.3 73.9 - - - +
181A VAL* 1.3 63.0 + - + +
183A LEU* 2.8 36.2 + - + +
184A LEU* 2.8 19.9 + - + +
374A PHE* 3.9 33.7 - - + -
1055A LEU* 5.0 18.2 - - + -
1059A LEU* 6.1 6.1 - - + -
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE* 3.2 20.8 + - + +
178A GLY* 3.3 20.4 - - - +
180A LEU* 1.3 75.7 - - + +
182A SER* 1.3 59.6 + - - +
184A LEU* 4.0 6.3 - - - +
185A SER* 3.2 25.8 + - - -
1052A PHE* 4.1 21.0 - - + -
1055A LEU* 4.5 20.9 - - + -
1056A VAL* 5.1 11.7 - - + -
1059A LEU* 6.6 0.2 - - + -
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Residues in contact with SER 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 GLY 2.7 24.1 + - - -
179A GLN* 3.9 6.5 - - - -
181A VAL* 1.3 73.3 - - - +
183A LEU* 1.3 57.5 + - - +
185A SER* 4.0 3.3 - - - -
186A ASN* 2.7 43.5 + - - +
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Residues in contact with LEU 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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157A PHE* 6.2 1.3 - - + -
160A ILE* 5.5 10.8 - - + -
179A GLN* 2.9 21.7 + - + +
180A LEU* 2.8 28.5 + - + +
182A SER* 1.3 72.4 - - - +
184A LEU* 1.3 63.4 + - + +
186A ASN* 3.1 24.8 - - - +
187A ASN* 3.7 8.1 - - - +
370A LYS* 4.3 29.6 - - + -
371A ILE* 4.0 27.8 - - + +
374A PHE* 4.7 28.5 - - + -
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Residues in contact with LEU 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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157A PHE* 3.5 45.0 - - + -
160A ILE* 4.8 11.2 - - + -
180A LEU* 2.8 20.9 + - + +
181A VAL* 4.1 7.0 - - + +
183A LEU* 1.3 77.5 - - + +
185A SER* 1.3 66.7 + - - +
187A ASN* 3.1 18.2 + - - +
188A LEU* 3.9 6.3 + - + +
1051A ILE* 5.3 10.3 - - + -
1052A PHE* 3.9 30.1 - - + -
1055A LEU* 3.8 33.4 - - + -
1078A PHE* 6.2 1.1 - - + -
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Residues in contact with SER 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 VAL 3.2 17.6 + - - -
182A SER* 3.4 4.5 + - - -
184A LEU* 1.3 80.6 - - - +
186A ASN* 1.3 61.5 + - - +
188A LEU* 3.7 22.1 - - - +
189A ASN* 5.0 1.6 + - - +
1048A ARG* 5.4 4.9 + - - -
1052A PHE* 4.1 20.2 - - - -
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Residues in contact with ASN 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 SER* 2.7 31.8 + - - +
183A LEU* 3.1 14.9 - - - +
185A SER* 1.3 79.0 - - - +
187A ASN* 1.3 83.7 + - - +
188A LEU 3.5 0.5 + - - -
189A ASN* 4.0 4.7 + - - +
190A LYS* 3.5 42.8 + - - +
367A ALA* 5.9 1.7 - - - +
370A LYS* 4.9 15.1 + - - +
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Residues in contact with ASN 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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153A ARG* 4.8 2.4 - - - +
156A MET* 4.0 26.5 - - - +
157A PHE* 3.7 25.1 - - + -
183A LEU 3.7 11.2 - - - +
184A LEU 3.1 12.1 + - - +
186A ASN* 1.3 84.8 + - - +
188A LEU* 1.3 63.3 + - - +
190A LYS* 3.3 7.3 - - - +
191A PHE* 3.1 50.4 + - - +
367A ALA* 4.1 19.9 - - + +
371A ILE* 5.6 7.7 - - + +
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Residues in contact with LEU 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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153A ARG* 3.7 38.3 + - - +
157A PHE* 4.1 12.7 - - + -
184A LEU* 3.9 13.5 + - + +
185A SER* 3.7 23.6 - - - +
187A ASN* 1.3 77.4 - - - +
189A ASN* 1.3 82.7 + - + +
192A ASP* 3.3 29.1 + - - +
1048A ARG* 3.4 35.7 - - + +
1052A PHE* 5.4 5.4 - - + -
1085A HIS* 5.8 5.4 - - + -
1089A TRP* 4.9 12.8 - - + -
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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 SER 5.6 1.3 - - - +
186A ASN 4.0 4.8 + - - +
187A ASN 3.4 0.6 - - - -
188A LEU* 1.3 91.4 - - + +
190A LYS* 1.3 64.3 + - - +
191A PHE 3.6 0.2 + - - -
193A GLU* 3.0 46.5 + - - +
194A GLY 4.9 0.2 + - - -
1089A TRP* 5.7 3.3 - - - -
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Residues in contact with LYS 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 ASN* 3.5 36.0 + - - +
187A ASN* 3.3 15.5 - - - +
189A ASN* 1.3 78.7 - - - +
191A PHE* 1.3 67.6 + - + +
194A GLY* 4.0 16.3 + - - -
360A THR* 4.8 4.7 + - - -
363A ASP* 3.5 40.8 + - - +
364A SER* 5.7 4.5 - - - -
367A ALA* 4.4 21.9 - - + +
370A LYS* 5.7 4.8 - - - +
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Residues in contact with PHE 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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73A LEU* 4.6 2.5 - - + -
149A GLY* 5.0 1.8 - - - -
152A MET* 3.5 43.0 - - + +
153A ARG* 4.3 15.7 - - + -
156A MET* 3.5 29.6 - - + -
187A ASN* 3.1 37.7 + - - +
188A LEU* 4.6 1.1 - - - +
190A LYS* 1.3 80.7 - - + +
192A ASP* 1.3 64.0 + - - +
194A GLY 4.5 0.6 - - - -
195A LEU* 4.1 24.1 + - + +
364A SER* 3.2 33.0 - - - -
367A ALA* 5.9 1.6 - - + -
368A ILE* 3.9 20.9 - - + -
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Residues in contact with ASP 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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146A HIS* 3.4 12.6 - - - +
149A GLY* 3.2 39.3 - - - +
150A MET* 3.3 34.6 + - - +
153A ARG* 3.2 33.2 + - - +
188A LEU 3.3 18.6 + - - +
191A PHE* 1.3 80.0 - - - +
193A GLU* 1.3 70.4 + - + +
195A LEU* 3.9 6.8 + - - +
1089A TRP* 5.4 2.2 - - + +
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Residues in contact with GLU 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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146A HIS* 3.7 34.5 + - + +
189A ASN* 3.0 34.6 + - - +
192A ASP* 1.3 83.6 - - + +
194A GLY* 1.3 59.2 + - - +
195A LEU 3.2 5.4 + - - -
196A ALA* 3.4 14.0 + - - +
197A LEU* 5.3 1.6 - - - +
1089A TRP* 4.3 20.4 - - + +
1093A LEU* 5.8 3.4 - - + -
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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