Contacts of the helix formed by residues 221 - 233 (chain A) in PDB entry 2KXH
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 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A ASP 3.1 13.2 + - - -
220A LEU* 1.3 71.9 - - - +
222A ASP* 1.3 73.6 + - - +
223A ASP* 3.4 3.4 - - - -
224A ASP* 2.7 22.5 + - - +
225A ILE* 2.9 24.4 + - - +
240A LEU* 3.7 6.3 - - - -
242A ARG* 5.6 1.6 - - - -
249A HIS* 4.3 6.8 - - - -
44B LYS* 5.8 0.4 - - - -
45B ILE* 4.0 5.2 - - - +
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Residues in contact with ASP 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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221A SER* 1.3 75.6 - - - +
223A ASP* 1.3 69.6 + - - +
225A ILE* 3.1 8.3 + - - +
226A LYS* 3.0 23.6 + - - +
238A CYS* 4.1 20.3 - - - +
239A THR* 3.4 5.0 - - - +
240A LEU* 2.6 45.6 + - + +
242A ARG* 2.6 39.1 + - - -
249A HIS* 5.7 0.5 - - - -
255A ILE* 5.4 0.9 - - - +
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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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221A SER* 3.4 2.3 - - - -
222A ASP* 1.3 86.1 - - - +
224A ASP* 1.3 63.4 + - - +
226A LYS* 3.0 36.1 + - + +
227A SER* 3.5 5.5 + - - -
238A CYS* 5.4 5.9 - - - -
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Residues in contact with ASP 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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220A LEU* 3.7 8.7 - - + -
221A SER* 2.7 42.9 + - - +
223A ASP* 1.3 76.6 - - - +
225A ILE* 1.3 57.7 + - - +
226A LYS 3.0 1.3 - - - -
227A SER* 2.8 27.7 + - - -
41B ILE* 2.9 37.2 - - + +
44B LYS* 2.6 39.1 + - - -
45B ILE* 3.4 9.2 - - - +
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Residues in contact with ILE 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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213A VAL* 3.9 14.6 - - + -
216A VAL* 3.6 24.2 - - + -
220A LEU* 3.5 26.9 - - + -
221A SER 2.9 13.2 + - - +
222A ASP* 3.1 5.8 + - - +
224A ASP* 1.3 75.0 - - - +
226A LYS* 1.3 61.0 + - - +
228A VAL* 3.1 24.0 - - - +
229A PHE* 3.1 35.4 - - + -
240A LEU* 4.0 19.7 - - + -
255A ILE* 3.9 10.5 - - + -
273A PHE* 3.7 18.4 - - + -
275A LEU* 4.3 1.8 - - + -
280A LEU* 5.0 0.4 - - + -
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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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222A ASP 3.0 18.0 + - - +
223A ASP* 3.0 26.0 + - + +
225A ILE* 1.3 77.0 - - - +
227A SER* 1.3 56.7 + - - +
229A PHE* 4.6 1.8 - - - +
230A GLU* 2.7 81.1 + - + +
235A ILE* 3.7 29.4 + - + +
238A CYS* 3.4 39.9 - - + -
255A ILE* 5.1 4.5 - - + +
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Residues in contact with SER 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 3.5 4.3 + - - -
224A ASP 2.8 21.4 + - - -
226A LYS* 1.3 79.1 - - - +
228A VAL* 1.3 59.1 + - - +
231A ALA* 3.1 26.2 + - - +
34B ALA* 3.8 2.6 - - - -
37B ARG* 3.2 42.6 + - - +
38B ALA* 4.4 0.2 - - - -
41B ILE* 3.0 29.4 - - - +
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A ILE 3.1 19.3 - - - +
227A SER* 1.3 75.0 - - - +
229A PHE* 1.3 67.0 + - - +
231A ALA* 3.2 4.5 + - - +
232A PHE* 3.0 28.0 - - + -
270A MET* 3.4 34.5 - - + -
273A PHE* 3.4 22.7 - - + -
34B ALA* 3.3 28.0 - - + +
35B LEU* 3.5 14.8 - - + -
38B ALA* 3.4 20.9 - - + -
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Residues in contact with PHE 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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211A ILE* 3.5 31.0 - - + -
213A VAL* 3.3 24.5 - - + -
225A ILE* 3.1 41.7 - - + +
226A LYS* 3.3 3.7 + - - +
228A VAL* 1.3 83.8 - - + +
230A GLU* 1.3 58.6 + - - +
232A PHE* 3.2 6.8 + - - +
233A GLY 3.0 19.2 + - - +
235A ILE* 3.6 13.7 - - + -
255A ILE* 3.6 11.0 - - + -
257A TYR* 2.9 43.4 + + - +
266A ALA* 4.0 0.4 - - + -
270A MET* 3.4 39.3 - - + -
282A VAL* 3.8 9.2 - - + -
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A LYS* 2.7 59.2 + - - +
227A SER 4.8 0.2 - - - +
229A PHE* 1.3 71.6 - - - +
231A ALA* 1.3 61.5 + - - +
232A PHE 3.2 0.6 - - - -
233A GLY 3.0 22.7 + - - +
234A LYS* 4.8 4.7 - - + +
235A ILE* 3.6 15.7 + - + +
37B ARG* 4.7 15.3 + - - +
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Residues in contact with ALA 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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227A SER 3.1 20.5 + - - +
228A VAL 3.2 3.3 + - - +
229A PHE 3.2 0.6 - - - -
230A GLU* 1.3 78.4 - - - +
232A PHE* 1.3 62.5 + - - +
30B ALA* 3.6 18.9 - - - +
33B ASP* 4.0 5.8 - - - +
34B ALA* 3.5 29.8 - - - +
37B ARG* 3.8 23.3 - - - +
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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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228A VAL 3.0 20.0 - - - -
229A PHE* 3.2 4.9 + - - +
230A GLU 4.4 0.4 - - - -
231A ALA* 1.3 80.1 - - - +
233A GLY* 1.3 57.3 + - - +
257A TYR* 4.6 1.3 - - - +
262A SER* 5.4 2.1 - - - +
265A ASP* 4.8 10.5 - - + -
266A ALA* 3.6 32.1 - - + +
269A SER* 4.4 5.8 - - - -
270A MET* 3.4 33.7 - - + -
27B VAL* 4.7 7.4 - - + -
30B ALA* 3.5 26.6 - - + +
31B PHE* 3.3 35.2 - + + -
34B ALA* 3.0 22.2 - - + -
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Residues in contact with GLY 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 PHE 3.0 4.2 + - - -
230A GLU* 3.0 31.1 - - - +
232A PHE* 1.3 81.1 - - - +
234A LYS* 1.3 60.2 + - - -
257A TYR* 3.8 15.8 - - - -
262A SER* 4.2 13.5 - - - -
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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