Contacts of the helix formed by residues 214 - 228 (chain K) in PDB entry 2X86
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 VAL 214 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10K PHE* 3.6 20.6 - - + -
11K ILE* 4.5 11.0 - - + -
14K ASN* 3.5 42.8 - - + +
170K VAL* 3.8 14.8 - - + -
171K TYR 2.9 20.6 + - - +
172K GLY* 3.8 15.9 - - - -
173K PRO* 3.9 10.8 - - + -
212K VAL 3.6 0.6 + - - -
213K TYR* 1.3 76.1 - - + +
215K GLY* 1.3 65.6 + - - +
217K VAL* 3.1 5.8 + - + +
218K ALA* 2.9 21.9 + - - +
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Residues in contact with GLY 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K ASN* 5.6 2.2 - - - -
213K TYR* 3.1 19.5 + - - -
214K VAL* 1.3 83.6 - - - +
216K ASP* 1.3 64.9 + - - +
218K ALA* 3.4 8.1 + - - +
219K ASP* 3.1 29.2 + - - +
293K LYS* 5.9 1.1 - - - -
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Residues in contact with ASP 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212K VAL* 4.4 2.6 - - + +
213K TYR* 2.9 17.6 + - - +
215K GLY* 1.3 75.2 - - - +
217K VAL* 1.3 67.5 + - - +
219K ASP* 3.0 13.6 + - - +
220K VAL* 2.9 29.3 + - - +
288K TYR* 4.4 2.6 + - - +
291K PRO 4.7 5.3 - - - +
292K PHE* 3.4 30.1 - - + +
293K LYS* 2.8 53.8 + - - +
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Residues in contact with VAL 217 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K ILE* 4.0 20.0 - - + -
167K TYR* 3.6 31.6 - - + -
170K VAL* 3.9 28.0 - - + -
212K VAL* 4.2 7.9 - - + -
213K TYR 3.8 11.0 - - - +
214K VAL* 3.3 10.1 - - + +
216K ASP* 1.3 77.4 - - - +
218K ALA* 1.3 63.2 + - - +
220K VAL* 3.3 3.3 + - - +
221K ASN* 3.0 33.5 + - - +
235K LEU* 4.1 24.2 - - + +
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Residues in contact with ALA 218 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K ASN* 3.9 30.1 - - + +
15K ILE* 4.6 6.1 - - - +
18K ALA* 4.0 13.2 - - + -
214K VAL* 2.9 11.9 + - - +
215K GLY* 3.5 11.4 - - - +
217K VAL* 1.3 79.3 - - - +
219K ASP* 1.3 63.8 + - - +
221K ASN* 3.1 9.7 + - - +
222K LEU* 3.0 27.2 + - - +
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Residues in contact with ASP 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ALA* 5.3 4.5 - - - +
215K GLY 3.1 18.7 + - - +
216K ASP* 3.0 16.0 + - - +
218K ALA* 1.3 77.5 - - - +
220K VAL* 1.3 63.1 + - - +
222K LEU* 3.2 7.5 + - - +
223K TRP* 2.9 24.9 + - - +
288K TYR* 4.0 14.9 + - + +
290K LYS* 5.7 5.3 - - + +
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Residues in contact with VAL 220 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K PHE* 3.6 26.2 - - + -
216K ASP 2.9 17.0 + - - +
217K VAL 3.6 6.7 - - - +
219K ASP* 1.3 75.6 - - - +
221K ASN* 1.3 64.8 + - - +
223K TRP* 3.1 2.1 + - - +
224K PHE* 3.0 36.2 + - + -
235K LEU* 3.6 31.9 - - + -
283K LEU* 4.6 5.4 - - + -
288K TYR* 3.6 37.0 - - + +
292K PHE* 4.1 6.3 - - + -
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Residues in contact with ASN 221 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K ILE* 3.5 22.2 - - + +
73K PHE* 3.4 30.6 - - + -
75K GLU* 3.8 3.3 - - - +
112K LEU* 4.1 2.1 - - - +
165K PHE* 3.3 30.4 - - - -
167K TYR* 3.1 24.0 + - - -
217K VAL* 3.0 30.5 + - - +
218K ALA 3.1 8.7 + - - +
220K VAL* 1.3 78.9 - - - +
222K LEU* 1.3 65.5 + - + +
224K PHE* 3.3 3.5 + - - +
225K LEU* 3.1 19.8 + - - +
235K LEU* 4.7 0.4 - - - +
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Residues in contact with LEU 222 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K ILE* 4.4 10.3 - - + -
18K ALA* 3.8 36.1 - - + +
19K LEU* 3.9 29.8 - - + +
22K LYS* 3.8 29.2 - - + -
73K PHE* 4.1 14.1 - - + -
218K ALA 3.0 18.1 + - - +
219K ASP* 3.9 7.4 - - - +
221K ASN* 1.3 79.0 - - - +
223K TRP* 1.3 63.0 + - - +
225K LEU* 3.2 7.3 + - + +
226K GLU* 3.0 37.2 + - - +
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Residues in contact with TRP 223 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219K ASP 2.9 16.2 + - - +
220K VAL 3.1 4.9 + - - +
222K LEU* 1.3 77.9 - - - +
224K PHE* 1.3 90.4 + + - +
226K GLU* 3.2 7.6 + - - -
227K ASN* 2.7 75.4 + - + +
229K VAL* 4.5 3.8 - - + -
286K ALA 3.6 15.7 - - - -
287K GLY* 3.5 33.4 + - - -
288K TYR* 3.5 36.7 - + + +
289K ASP* 5.9 0.8 + - - -
290K LYS* 4.1 22.6 - - - +
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Residues in contact with PHE 224 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112K LEU* 4.0 7.2 - - + -
161K GLN* 2.9 12.0 + - - +
163K VAL* 4.1 7.2 - - + -
165K PHE* 3.5 32.8 - + + -
220K VAL* 3.0 26.1 + - + +
221K ASN 3.8 2.0 - - - +
223K TRP* 1.3 97.9 - + - +
225K LEU* 1.3 63.8 + - - +
227K ASN* 4.4 0.4 - - - +
228K GLY 2.9 21.8 + - - -
229K VAL* 3.8 35.2 - - + -
233K PHE* 3.6 36.8 - + - -
283K LEU* 3.7 26.0 - - + -
286K ALA* 4.2 13.9 - - + -
288K TYR* 4.5 1.6 - - + -
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Residues in contact with LEU 225 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K ILE* 4.2 18.4 - - + -
19K LEU* 5.0 5.6 - - + -
24K ILE* 6.2 0.9 - - + -
70K GLU* 4.5 14.4 - - + +
71K ALA* 3.6 24.2 - - + -
73K PHE* 3.7 30.1 - - + -
110K PRO* 4.4 7.4 - - + -
112K LEU* 3.9 11.3 - - + +
161K GLN* 4.2 11.6 - - - +
221K ASN 3.1 12.5 + - - +
222K LEU* 3.2 11.2 + - + +
224K PHE* 1.3 79.3 - - - +
226K GLU* 1.3 66.6 + - + +
228K GLY* 3.8 5.7 + - - -
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Residues in contact with GLU 226 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K LYS* 3.1 36.6 + - - +
222K LEU* 3.0 23.6 + - - +
223K TRP* 3.2 10.2 + - - +
225K LEU* 1.3 80.5 - - + +
227K ASN* 1.3 66.9 + - - +
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Residues in contact with ASN 227 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223K TRP* 2.7 80.6 + - + +
224K PHE 4.3 0.9 - - - +
226K GLU* 1.3 89.7 + - - +
228K GLY* 1.3 57.6 + - - +
229K VAL* 3.2 16.7 + - + +
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Residues in contact with GLY 228 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161K GLN* 3.2 30.1 + - - +
224K PHE 2.9 7.9 + - - -
225K LEU 3.8 2.6 + - - -
226K GLU 3.6 2.4 - - - -
227K ASN* 1.3 76.5 - - - +
229K VAL* 1.3 62.3 + - - +
230K SER* 3.7 3.1 + - - -
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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