Contacts of the helix formed by residues 210 - 229 (chain A) in PDB entry 4HKC
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 210 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PRO* 4.0 26.8 - - - +
207A SER* 2.7 22.7 + - - -
209A GLU* 1.3 81.7 - - - +
211A TYR* 1.4 64.9 + - - +
212A LYS 3.2 3.6 - - - -
213A ASP* 3.0 16.9 + - - -
214A SER* 2.9 23.5 + - - -
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Residues in contact with TYR 211 (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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206A LEU* 3.9 32.5 - - + -
207A SER 2.8 24.9 + - - +
208A GLU* 3.2 44.5 + - - -
209A GLU 3.9 0.2 - - - -
210A SER* 1.4 71.1 - - - +
212A LYS* 1.3 84.9 + - + +
214A SER* 3.4 1.0 + - - -
215A THR* 2.9 44.0 + - + +
301A GOL 4.1 15.5 - - - +
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Residues in contact with LYS 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A SER* 3.2 0.8 - - - +
211A TYR* 1.3 104.7 - - + +
213A ASP* 1.4 61.0 + - - +
215A THR* 3.5 8.0 + - - +
216A LEU* 3.0 30.1 + - - +
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Residues in contact with ASP 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PRO* 4.0 17.2 - - + +
209A GLU 4.4 4.1 - - - +
210A SER* 3.0 24.7 + - - +
212A LYS* 1.4 77.6 - - - +
214A SER* 1.4 62.9 + - - +
216A LEU* 3.7 5.7 - - - +
217A ILE* 3.3 31.9 + - + +
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Residues in contact with SER 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A THR 2.6 28.4 + - - -
165A PRO* 3.5 13.6 - - - +
168A LEU* 3.7 15.4 - - - +
206A LEU* 3.5 25.3 - - - +
210A SER* 2.9 15.6 + - - -
211A TYR 3.6 2.2 - - - -
213A ASP* 1.4 75.9 - - - +
215A THR* 1.3 58.9 + - - +
217A ILE* 3.2 3.4 + - - -
218A MET* 3.0 31.2 + - - +
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Residues in contact with THR 215 (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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203A LEU* 5.1 2.5 - - + -
206A LEU* 4.2 21.3 - - + -
211A TYR* 2.9 34.9 + - + +
212A LYS* 3.5 10.6 + - - +
214A SER* 1.3 72.5 - - - +
216A LEU* 1.3 63.7 + - - +
218A MET* 3.3 18.5 + - - +
219A GLN* 3.0 35.8 + - - +
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Residues in contact with LEU 216 (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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212A LYS 3.0 20.4 + - - +
213A ASP* 3.7 7.2 - - - +
214A SER 3.2 0.2 - - - -
215A THR* 1.3 75.9 + - - +
217A ILE* 1.3 64.6 + - + +
219A GLN* 3.2 24.9 + - + +
220A LEU* 3.2 37.6 + - + +
1013B LEU* 6.5 0.7 - - + -
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Residues in contact with ILE 217 (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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165A PRO* 3.3 37.7 - - + +
168A LEU* 3.6 33.0 - - + +
169A GLY* 3.8 1.8 - - - +
172A LEU* 4.2 8.7 - - + -
213A ASP* 3.3 15.9 + - + +
214A SER 3.2 7.4 + - - +
216A LEU* 1.3 76.2 - - + +
218A MET* 1.3 60.3 + - - +
220A LEU* 3.1 10.9 + - + +
221A LEU* 2.9 29.0 + - + +
1012B ILE* 3.6 32.3 - - + -
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Residues in contact with MET 218 (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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163A THR* 5.5 0.7 - - - -
168A LEU* 4.0 20.4 - - + -
196A PHE* 3.3 32.9 - - + +
199A ALA* 3.7 26.5 - - + -
200A ILE* 3.6 36.1 - - + +
203A LEU* 4.0 17.5 - - + -
206A LEU* 5.4 0.9 - - - -
214A SER* 3.0 21.7 + - - +
215A THR* 3.5 20.4 - - - +
216A LEU 3.3 0.2 - - - -
217A ILE* 1.3 77.2 - - - +
219A GLN* 1.3 61.7 + - + +
221A LEU* 3.2 6.4 + - + +
222A ARG 3.0 18.5 + - - -
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Residues in contact with GLN 219 (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 PHE* 5.2 0.7 - - - -
215A THR* 3.0 32.6 + - - +
216A LEU* 3.3 25.0 - - + +
218A MET* 1.3 75.3 - - + +
220A LEU* 1.3 59.7 + - + +
222A ARG* 3.4 5.9 + - - +
223A ASP* 2.9 41.4 + - - +
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Residues in contact with LEU 220 (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* 3.9 30.5 - - + -
216A LEU* 3.5 30.5 - - + +
217A ILE* 3.1 14.6 + - + +
219A GLN* 1.3 76.6 - - + +
221A LEU* 1.4 66.3 + - - +
223A ASP* 3.3 8.9 + - + +
224A ASN* 3.0 29.3 + - - +
1010B LYS* 3.8 33.2 - - + -
1011B SEP 4.4 9.2 - - - +
1012B ILE* 4.7 9.4 - - + -
1013B LEU 4.9 4.5 - - - +
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 3.8 34.8 - - + +
171A ALA 4.2 2.2 - - - -
172A LEU* 3.7 41.7 - - + +
175A SER* 4.6 0.4 - - - +
192A ALA* 4.0 38.1 - - + +
195A ALA* 4.0 13.5 - - + -
196A PHE* 4.3 13.0 - - + +
217A ILE 2.9 18.9 + - - +
218A MET* 3.2 11.4 + - - +
220A LEU* 1.4 77.7 - - - +
222A ARG* 1.3 56.7 - - - +
224A ASN* 3.3 3.4 + - - +
225A LEU* 3.0 28.1 + - - +
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Residues in contact with ARG 222 (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 PHE* 3.6 37.5 - - + -
218A MET 3.0 16.1 + - - +
219A GLN* 4.0 4.8 - - - +
221A LEU* 1.3 76.5 - - - +
223A ASP* 1.3 67.0 + - - +
225A LEU* 3.3 13.4 + - + +
226A THR* 2.8 43.6 + - - +
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Residues in contact with ASP 223 (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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219A GLN* 2.9 29.4 + - - +
220A LEU* 3.8 10.8 - - + +
222A ARG* 1.3 83.2 + - - +
224A ASN* 1.3 62.6 + - - +
226A THR* 3.3 8.6 + - - -
227A LEU* 3.0 28.6 + - - +
1010B LYS* 5.5 10.2 - - + -
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Residues in contact with ASN 224 (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* 3.4 16.7 - - + +
176A VAL* 3.6 13.5 - - - +
192A ALA* 5.7 0.4 - - + -
220A LEU 3.0 15.9 + - - +
221A LEU* 3.6 4.7 - - - +
223A ASP* 1.3 77.8 - - - +
225A LEU* 1.3 57.8 + - - +
227A LEU* 3.1 8.5 + - - +
228A TRP* 2.8 55.0 + - + -
1008B GLN 4.8 0.2 - - - +
1009B TYR* 3.2 12.7 - - - +
1010B LYS* 2.7 51.3 + - - +
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Residues in contact with LEU 225 (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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189A CYS* 3.4 47.8 - - + +
192A ALA* 4.3 9.0 - - + +
193A LYS* 3.8 34.1 - - + +
196A PHE* 5.6 4.7 - - + -
221A LEU 3.0 14.0 + - - +
222A ARG* 3.4 20.2 - - + +
224A ASN* 1.3 76.0 - - - +
226A THR* 1.3 55.9 + - - +
228A TRP* 3.3 5.5 + - + -
229A THR* 2.6 45.9 + - + +
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Residues in contact with THR 226 (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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222A ARG* 2.8 37.8 + - - +
223A ASP* 3.5 9.9 + - - -
224A ASN 3.2 0.2 - - - -
225A LEU* 1.3 75.0 - - - +
227A LEU* 1.3 60.8 + - - +
229A THR* 3.4 5.8 + - - -
230A SER* 3.2 28.7 + - - -
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Residues in contact with LEU 227 (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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223A ASP 3.0 13.6 + - - +
224A ASN* 3.1 8.7 + - - +
226A THR* 1.3 76.0 - - - +
228A TRP* 1.3 65.0 + - + +
230A SER* 3.0 24.1 + - - +
1008B GLN* 3.2 45.8 - - + +
1009B TYR* 3.4 35.4 - - + +
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Residues in contact with TRP 228 (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 SER* 3.6 33.4 - - - -
176A VAL* 4.0 3.6 - - + -
179A TYR* 3.3 52.9 + + + -
185A PRO* 5.6 2.4 - - - +
188A ALA* 3.8 27.6 - - + -
189A CYS* 3.8 28.9 - - - -
192A ALA* 4.4 5.4 - - + -
224A ASN* 2.8 45.7 + - + +
225A LEU* 4.1 3.6 - - + +
226A THR 3.3 0.2 - - - -
227A LEU* 1.3 87.3 - - + +
229A THR* 1.3 58.8 + - - +
230A SER 3.4 2.5 + - - +
1009B TYR* 3.3 42.1 - + + +
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Residues in contact with THR 229 (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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189A CYS* 4.0 19.5 - - + -
225A LEU* 2.6 34.8 + - + +
226A THR* 3.4 8.5 + - - -
228A TRP* 1.3 76.3 - - - +
230A SER* 1.3 60.9 + - - +
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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
------------------------------------------------------------
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