Contacts of the helix formed by residues 188 - 200 (chain A) in PDB entry 5HNK
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 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A LEU* 4.6 10.1 - - + -
180A MET* 4.1 11.9 - - - -
186A VAL* 3.5 3.5 - - - +
187A ASP* 1.3 82.6 - - - +
189A VAL* 1.3 60.3 + - - +
190A GLU* 3.3 11.9 + - - +
191A GLN* 3.0 32.9 + - - +
192A PHE* 3.0 25.1 + - - +
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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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157A ASP 3.6 18.6 - - - +
158A THR* 3.2 24.0 - - - +
160A LEU* 3.3 27.8 - - + +
177A LEU* 4.0 14.3 - - + +
180A MET* 4.0 7.4 - - + -
188A ASP* 1.3 75.8 - - - +
190A GLU* 1.3 67.0 + - + +
192A PHE* 3.1 7.9 + - - +
193A ILE* 2.9 43.0 + - + +
263A PRO* 5.2 2.5 - - + -
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Residues in contact with GLU 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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188A ASP* 3.3 11.4 + - - +
189A VAL* 1.3 85.2 - - + +
191A GLN* 1.3 58.1 + - - +
193A ILE* 3.5 17.7 + - - +
194A SER* 3.1 30.7 + - - -
226A ASN* 3.5 22.1 - - - +
261A ASP* 5.3 4.0 - - - +
263A PRO* 5.9 1.6 - - - +
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Residues in contact with GLN 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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186A VAL* 4.0 10.4 - - + +
187A ASP* 3.1 45.8 + - - +
188A ASP* 3.0 24.9 + - - +
190A GLU* 1.3 75.0 - - + +
192A PHE* 1.3 59.2 + - - +
194A SER* 3.7 3.7 - - - -
195A LEU* 2.8 32.2 + - - +
218A TYR* 3.5 14.3 - - - -
221A ILE* 3.7 30.3 + - + +
222A ARG* 3.9 17.0 - - - +
226A ASN* 3.9 8.7 - - - +
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Residues in contact with PHE 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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154A GLY 3.7 24.7 - - - -
155A ASP* 4.4 0.9 - - - -
157A ASP* 4.0 3.6 - - + -
158A THR* 3.6 40.2 - - + -
180A MET* 3.5 27.1 - - + -
184A HIS* 3.5 44.9 - + + -
186A VAL* 3.8 11.8 - - + +
188A ASP 3.0 6.9 + - - +
189A VAL 3.1 8.0 + - - +
191A GLN* 1.3 75.7 - - - +
193A ILE* 1.3 55.7 + - - +
195A LEU* 3.3 7.4 + - + +
196A LYS* 2.9 54.6 + - + +
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Residues in contact with ILE 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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158A THR* 3.9 21.1 - - + +
189A VAL* 2.9 35.7 + - + +
190A GLU* 3.8 20.2 - - - +
192A PHE* 1.3 74.5 - - - +
194A SER* 1.3 59.4 + - - +
196A LYS* 3.4 6.9 + - - -
197A ALA* 3.0 24.6 + - - +
257A LEU* 3.7 23.6 - - + -
260A VAL* 3.5 13.8 - - + +
261A ASP* 3.6 37.7 - - + +
263A PRO* 4.3 13.5 - - + -
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Residues in contact with SER 194 (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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190A GLU 3.1 18.9 + - - -
191A GLN 3.7 4.3 - - - -
193A ILE* 1.3 78.5 - - - +
195A LEU* 1.3 56.5 + - - +
197A ALA* 3.3 1.9 + - - -
198A ILE* 3.0 32.4 + - - +
221A ILE* 3.9 16.2 - - - -
226A ASN* 3.4 14.2 - - - +
227A VAL* 3.1 41.8 + - - +
257A LEU* 5.2 2.9 - - - +
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Residues in contact with LEU 195 (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 HIS 4.4 9.9 - - - +
185A ASN 4.8 0.9 - - - +
186A VAL* 3.6 25.1 - - + -
191A GLN 2.8 22.1 + - - +
192A PHE* 3.3 9.2 + - + +
194A SER* 1.3 69.3 - - - +
196A LYS* 1.3 61.3 + - + +
198A ILE* 3.3 4.5 + - + -
199A MET* 2.9 63.0 + - + +
213A GLY 4.0 3.8 - - - +
214A ALA* 4.1 15.3 - - + +
217A GLY* 3.7 36.3 - - - -
218A TYR 4.0 1.3 - - - +
221A ILE* 3.7 8.5 - - + +
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Residues in contact with LYS 196 (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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155A ASP* 2.7 33.7 + - - +
158A THR* 4.1 16.4 - - + -
192A PHE* 2.9 54.6 + - + +
193A ILE* 3.7 4.9 - - - +
194A SER 3.4 0.2 - - - -
195A LEU* 1.3 75.2 - - + +
197A ALA* 1.3 55.8 + - - +
199A MET* 4.7 3.1 - - - -
200A GLY* 2.7 39.9 + - - +
201A ASP* 4.6 12.9 + - - +
256A ASN* 4.8 0.3 + - - +
260A VAL* 4.1 34.2 - - + +
262A LEU* 6.4 0.4 - - - -
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Residues in contact with ALA 197 (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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193A ILE 3.0 14.7 + - - +
194A SER* 3.5 9.4 - - - +
195A LEU 3.3 0.2 - - - -
196A LYS* 1.3 76.7 - - - +
198A ILE* 1.3 59.3 + - - +
208A GLY* 5.0 0.2 - - - -
227A VAL* 4.1 14.1 - - + -
252A LEU* 5.5 0.3 - - - +
253A LEU* 4.0 12.7 - - + +
256A ASN* 2.9 37.3 + - + +
257A LEU* 3.8 30.1 - - + +
260A VAL* 3.9 4.2 - - + +
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Residues in contact with ILE 198 (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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194A SER 3.0 18.2 + - - +
195A LEU* 3.8 5.2 - - + +
196A LYS 3.3 0.2 - - - -
197A ALA* 1.3 76.3 - - - +
199A MET* 1.3 61.1 + - + +
208A GLY* 3.4 0.9 - - - -
209A VAL* 2.9 39.8 + - + +
212A ILE* 3.6 36.5 - - + +
217A GLY* 4.7 7.6 - - - +
220A ILE* 5.3 5.6 - - + -
221A ILE* 4.0 28.3 - - + -
227A VAL* 4.0 10.1 - - + -
230A ILE* 4.2 12.1 - - + -
246A LEU* 4.8 6.5 - - + -
253A LEU* 3.8 21.1 - - + -
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Residues in contact with MET 199 (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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195A LEU* 2.9 46.0 + - + +
196A LYS* 4.2 2.2 - - - +
198A ILE* 1.3 78.6 - - + +
200A GLY* 1.3 69.4 + - - +
201A ASP 3.9 0.3 + - - -
208A GLY* 3.4 13.7 + - - -
212A ILE 3.7 20.6 - - - +
213A GLY* 4.0 6.5 - - - +
214A ALA* 3.6 31.0 - - + +
10Y C 6.1 0.2 - - - +
103Y K 3.5 11.0 - - - -
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Residues in contact with GLY 200 (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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196A LYS* 2.7 28.1 + - - +
197A ALA 4.0 0.6 + - - -
198A ILE 3.5 1.6 - - - -
199A MET* 1.3 83.2 - - - +
201A ASP* 1.3 64.6 + - - +
206A ILE* 3.6 23.6 - - - -
208A GLY* 4.0 5.5 - - - -
256A ASN* 4.2 3.8 - - - -
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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