Contacts of the helix formed by residues 177 - 191 (chain A) in PDB entry 5NKS
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 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A GLN* 4.3 0.8 + - - +
176A CYS* 1.3 74.6 - - - +
178A ASP* 1.3 60.5 + - - +
179A SER* 3.6 8.2 + - - -
180A GLN* 3.1 34.1 + - - +
181A MET* 2.8 30.1 + - - +
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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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177A SER* 1.3 73.8 - - - +
179A SER* 1.3 58.3 + - - +
181A MET* 3.2 5.5 + - - +
182A TYR* 2.9 29.9 + - - +
238A ARG* 2.9 47.0 + - - -
242A ILE* 3.8 22.1 - - + +
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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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177A SER* 3.3 7.5 + - - -
178A ASP* 1.3 76.0 - - - +
180A GLN* 1.3 62.0 + - - +
182A TYR* 3.3 7.7 + - - +
183A GLU* 3.0 26.9 + - - +
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Residues in contact with GLN 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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144A TRP* 3.5 58.3 - - + +
175A GLN 4.4 2.3 - - - +
176A CYS* 3.4 16.0 - - + +
177A SER* 3.1 35.3 + - - +
179A SER* 1.3 78.1 - - - +
181A MET* 1.3 61.7 + - - +
183A GLU* 3.3 7.1 + - - +
184A ILE* 2.8 38.0 + - + +
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Residues in contact with MET 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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166A VAL* 4.6 12.1 - - + -
168A MET* 3.6 44.4 - - + +
176A CYS* 4.5 12.5 - - + +
177A SER 2.8 18.7 + - - +
178A ASP* 3.5 12.1 - - - +
180A GLN* 1.3 77.6 - - - +
182A TYR* 1.3 62.1 + - - +
184A ILE* 3.3 6.7 + - - -
185A PHE* 2.9 66.1 + - + -
197A VAL* 4.7 2.2 - - - -
238A ARG* 4.8 1.3 - - - +
239A ALA* 4.3 7.6 - - - -
242A ILE* 3.8 21.5 - - + -
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Residues in contact with TYR 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 2.9 16.3 + - - +
179A SER* 3.6 8.5 - - - +
180A GLN 3.2 0.2 - - - -
181A MET* 1.3 77.6 - - - +
183A GLU* 1.3 59.4 - - - +
185A PHE* 3.8 2.3 - - - +
186A SER* 2.9 48.0 + - - -
242A ILE* 3.7 26.2 - - + +
245A GLN* 3.8 36.6 + - + +
246A ALA* 4.2 11.5 - - + +
495A PRO* 5.6 5.4 - - - +
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Residues in contact with GLU 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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144A TRP* 2.6 44.0 + - - +
146A GLU* 5.3 4.7 - - - +
179A SER 3.0 16.1 + - - +
180A GLN* 3.7 5.1 - - - +
182A TYR* 1.3 81.3 - - - +
184A ILE* 1.3 62.5 + - - +
186A SER* 3.3 6.4 + - - -
187A ILE* 3.1 39.2 + - + +
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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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141A ILE* 4.1 23.6 - - + -
144A TRP* 4.1 26.7 - - + -
148A ILE* 5.8 6.3 - - + -
152A LEU* 5.0 5.4 - - + -
166A VAL* 3.8 22.7 - - + -
176A CYS* 4.1 25.6 - - - -
180A GLN 2.8 25.0 + - - +
181A MET* 3.8 3.8 - - - +
183A GLU* 1.3 69.9 - - + +
185A PHE* 1.3 61.1 + - + +
187A ILE* 3.4 11.5 + - + +
188A ILE* 2.8 49.6 + - + +
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Residues in contact with PHE 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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166A VAL* 4.4 16.6 - - + -
181A MET* 2.9 49.6 + - + +
182A TYR 3.8 4.3 - - - +
184A ILE* 1.3 80.3 - - + +
186A SER* 1.3 57.5 + - - +
188A ILE* 4.3 4.0 - - + -
189A ARG* 3.0 24.8 + - - +
195A ALA* 3.7 22.0 - - + -
196A GLN 5.0 0.2 - - - -
197A VAL* 3.9 19.1 - - + -
239A ALA 3.9 8.1 - - - -
242A ILE* 3.7 12.8 - - + -
243A ALA* 3.7 36.3 - - + -
246A ALA* 4.1 5.6 - - + -
248A CYS* 3.1 29.5 - - + +
250A LEU* 4.0 7.2 - - + -
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Residues in contact with SER 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 TYR* 2.9 38.1 + - - -
183A GLU* 3.7 6.7 - - - -
184A ILE 3.3 0.2 - - - -
185A PHE* 1.3 76.6 - - - +
187A ILE* 1.3 62.2 + - - +
189A ARG* 3.5 31.5 + - - +
190A ASP* 3.1 30.1 + - - -
246A ALA* 3.9 4.1 - - - +
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Residues in contact with ILE 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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144A TRP* 6.5 0.2 - - + -
148A ILE* 5.6 4.9 - - + -
149A LYS* 3.8 48.9 - - + +
152A LEU* 3.9 24.0 - - + -
183A GLU* 3.1 39.1 + - + +
184A ILE* 3.6 11.4 - - + +
186A SER* 1.3 73.5 - - - +
188A ILE* 1.3 65.0 + - - +
190A ASP* 3.3 9.7 + - - +
191A LEU* 3.0 30.5 + - + +
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Residues in contact with ILE 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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141A ILE* 4.9 0.9 - - + -
152A LEU* 4.7 7.9 - - + -
164A PHE* 4.1 32.3 - - + +
166A VAL* 5.0 2.9 - - + -
184A ILE* 2.8 44.5 + - + +
185A PHE* 3.8 4.9 - - + +
187A ILE* 1.3 72.0 - - - +
189A ARG* 1.3 62.3 + - - +
191A LEU* 3.2 6.6 + - - +
192A GLY 3.1 4.2 + - - -
193A ALA* 3.0 60.5 + - + +
194A LEU 3.7 1.1 - - - -
195A ALA* 3.6 34.1 - - + +
248A CYS* 3.9 7.4 - - - -
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Residues in contact with ARG 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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182A TYR* 6.1 0.2 - - - -
185A PHE 3.0 17.5 + - - +
186A SER* 3.5 35.0 + - - +
188A ILE* 1.3 76.9 - - - +
190A ASP* 1.3 92.8 + - - +
192A GLY* 3.1 10.4 + - - -
246A ALA* 2.8 29.9 + - - +
247A ASN* 3.2 29.6 - - - +
248A CYS* 4.0 8.0 - - + -
474A PHE* 4.2 4.3 - - - -
479A TYR* 3.3 19.2 + - - -
482A ILE* 4.1 12.1 - - + -
486A ASN* 3.8 28.5 + - - +
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Residues in contact with ASP 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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149A LYS* 4.6 17.2 + - - +
186A SER* 3.1 14.5 + - - +
187A ILE* 3.3 11.6 + - - +
189A ARG* 1.3 105.0 + - - +
191A LEU* 1.3 63.0 + - - +
192A GLY 3.6 0.2 + - - -
474A PHE* 3.7 11.6 - - - -
486A ASN* 5.9 0.3 + - - -
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Residues in contact with LEU 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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149A LYS* 4.7 9.9 - - + +
152A LEU* 3.7 34.8 - - + +
153A GLU* 3.7 43.7 - - + +
156A VAL* 4.2 16.6 - - + +
157A LYS* 4.8 8.6 - - - +
164A PHE* 5.1 2.0 - - + -
187A ILE* 3.0 32.2 + - + +
188A ILE* 3.2 7.8 + - - +
190A ASP* 1.3 77.3 - - + +
192A GLY* 1.3 61.7 + - - +
193A ALA* 3.6 6.7 + - + +
473A THR* 3.2 23.0 - - - +
474A PHE* 3.8 6.7 - - - -
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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