Contacts of the helix formed by residues 220 - 233 (chain A) in PDB entry 6DWY
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 THR 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A ARG* 3.1 13.6 + - + -
219A SER* 1.3 83.1 - - - +
221A ALA* 1.3 67.7 + - - +
222A GLU* 3.4 29.7 + - - +
223A ASN* 3.0 43.4 + - - +
224A ILE* 3.2 11.8 + - - +
21C C 3.7 7.6 - - - -
22C A 2.3 35.2 + - - -
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Residues in contact with ALA 221 (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 SER 3.9 0.4 + - - -
220A THR* 1.3 76.7 + - - +
222A GLU* 1.3 62.0 + - + +
224A ILE* 3.3 3.5 + - - +
225A TYR* 3.2 8.3 + - - +
252A ASN* 3.2 30.0 + - - +
255A LYS* 3.9 20.0 - - + -
256A SER* 2.8 41.5 + - - +
21C C 4.3 0.6 + - - -
22C A 2.9 12.1 + - - +
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Residues in contact with GLU 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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220A THR* 3.0 23.1 + - + +
221A ALA* 1.3 80.4 - - + +
223A ASN* 1.3 61.0 + - - +
225A TYR* 3.8 5.2 + - - +
226A LYS* 3.1 25.2 + - - +
255A LYS* 5.1 13.1 + - - +
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Residues in contact with ASN 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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214A LEU* 4.6 12.1 - - + -
217A GLU* 3.1 30.1 + - - +
218A ARG* 4.0 18.4 + - - +
219A SER 4.2 1.1 + - - +
220A THR* 3.0 29.6 + - + +
222A GLU* 1.3 79.1 - - - +
224A ILE* 1.3 60.5 + - - +
226A LYS* 3.2 22.1 - - + +
227A LYS* 2.9 34.9 + - + +
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Residues in contact with ILE 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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179A ILE* 4.8 13.7 - - + -
181A LEU* 3.6 39.9 - - + -
192A LEU* 3.9 26.3 - - + +
214A LEU* 4.4 11.2 - - + -
219A SER* 3.7 12.6 - - - +
220A THR 3.2 16.4 + - - +
221A ALA* 3.8 3.8 - - - +
222A GLU 3.3 0.4 - - - -
223A ASN* 1.3 74.1 - - - +
225A TYR* 1.3 57.5 + - - +
226A LYS 3.0 1.1 - - - -
227A LYS* 3.1 3.4 + - - +
228A LEU* 2.7 37.1 + - + +
252A ASN* 3.8 15.5 - - + -
253A VAL* 4.6 5.2 - - + +
256A SER* 3.6 15.7 - - - +
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Residues in contact with TYR 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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221A ALA 3.2 7.3 + - - +
222A GLU* 4.1 5.2 - - - +
224A ILE* 1.3 73.3 - - - +
226A LYS* 1.3 62.1 + - - +
228A LEU* 3.8 22.2 - - + +
229A LYS* 3.2 54.1 + - + +
240A LEU* 3.3 37.1 - - + +
256A SER* 2.8 39.9 + - - +
257A LEU* 6.1 2.9 - - + -
259A ASN* 3.6 27.6 + - + -
260A ASN* 4.4 11.2 + - - -
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Residues in contact with LYS 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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217A GLU* 5.2 5.8 + - - +
222A GLU 3.1 15.9 + - - +
223A ASN* 3.2 30.4 - - - +
224A ILE 3.0 0.4 - - - -
225A TYR* 1.3 75.9 - - - +
227A LYS* 1.3 72.2 + - + +
229A LYS* 3.2 11.6 + - - +
230A ALA* 3.2 18.9 + - - +
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Residues in contact with LYS 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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192A LEU* 3.8 14.6 - - + -
212A LYS* 4.5 23.4 - - + +
213A SER 2.7 31.9 + - - -
214A LEU* 3.8 27.6 - - + +
215A ASP* 4.3 4.2 + - - -
217A GLU* 5.4 10.3 + - - +
223A ASN 2.9 25.0 + - - +
224A ILE* 3.1 3.3 + - - +
226A LYS* 1.3 83.9 - - + +
228A LEU* 1.3 62.3 - - - +
230A ALA* 3.1 10.6 + - + +
231A ILE* 3.0 26.9 + - - +
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Residues in contact with LEU 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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179A ILE* 4.0 30.5 - - + -
192A LEU* 4.0 10.0 - - + +
194A VAL* 4.7 6.7 - - + -
224A ILE* 2.7 22.5 + - + +
225A TYR* 3.8 27.8 - - + +
227A LYS* 1.3 73.5 - - - +
229A LYS* 1.3 64.0 + - + +
231A ILE* 3.4 9.4 + - - +
232A PHE* 3.2 48.6 + - + -
245A PHE* 3.8 29.4 - - + -
257A LEU* 4.4 8.1 - - + -
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Residues in contact with LYS 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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225A TYR* 3.2 56.0 + - + +
226A LYS* 3.5 10.3 - - - +
227A LYS 3.2 0.2 - - - -
228A LEU* 1.3 77.9 - - + +
230A ALA* 1.3 54.0 + - - +
232A PHE* 2.9 8.3 + - + +
233A SER* 2.5 40.0 + - - +
238A GLU* 3.3 23.9 - - + +
240A LEU* 6.1 1.1 - - - -
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Residues in contact with ALA 230 (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* 3.2 26.3 + - + +
226A LYS 3.2 9.3 + - - +
227A LYS* 3.1 18.7 + - + +
229A LYS* 1.3 78.3 - - - +
231A ILE* 1.3 61.8 + - - +
233A SER* 3.5 14.3 + - - -
234A GLN* 3.3 14.4 + - - +
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Residues in contact with ILE 231 (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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192A LEU* 4.6 10.8 - - + +
194A VAL* 3.7 30.3 - - + -
209A LEU* 3.7 39.3 - - + +
210A GLY* 4.3 12.1 - - - +
212A LYS* 3.8 26.2 - - + +
227A LYS 3.0 15.6 + - - +
228A LEU* 3.6 9.4 - - - +
229A LYS 3.1 0.2 - - - -
230A ALA* 1.3 75.1 - - - +
232A PHE* 1.3 68.2 + - + +
234A GLN* 3.0 29.9 + - - +
235A PHE* 3.5 10.2 - - + -
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Residues in contact with PHE 232 (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 ILE* 6.4 1.6 - - + -
177A ALA* 5.1 3.8 - - + -
194A VAL* 4.7 9.4 - - + -
196A LEU* 5.3 3.8 - - + -
209A LEU* 3.6 31.6 - - + -
228A LEU* 3.2 40.3 + - + -
229A LYS* 2.9 10.8 + - + +
231A ILE* 1.3 80.5 - - + +
233A SER* 1.3 57.1 + - - +
234A GLN 3.1 0.2 - - - -
235A PHE* 3.1 9.0 + + - +
236A ASN 2.9 22.5 + - - -
237A VAL* 3.0 41.1 + - + +
238A GLU* 4.7 2.0 - - - +
243A ILE* 3.7 31.9 - - + -
245A PHE* 3.9 16.6 - + - -
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Residues in contact with SER 233 (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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229A LYS* 2.5 25.7 + - - +
230A ALA* 3.7 12.3 - - - -
231A ILE 3.2 0.4 - - - -
232A PHE* 1.3 72.4 - - - +
234A GLN* 1.3 60.7 + - - +
236A ASN* 3.6 15.4 + - - +
238A GLU* 2.7 27.2 + - - -
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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