Contacts of the helix formed by residues 225 - 240 (chain A) in PDB entry 4KYW
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 HIS 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ASN* 2.9 12.6 + - - +
224A ASN* 1.3 95.4 + - + +
226A ILE* 1.3 63.9 + - - +
228A GLU* 3.2 27.8 - - - +
229A LYS* 3.2 18.7 + - - +
5E 6MA 2.8 59.4 + + + +
6E T 3.5 40.5 + - + -
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Residues in contact with ILE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A TRP* 4.0 14.1 - - + -
213A GLU* 3.7 40.8 - - + +
216A LEU* 4.3 10.1 - - + -
217A LYS* 4.1 30.3 - - + +
220A PHE 4.3 1.1 - - - +
223A ASN* 3.4 39.5 - - + +
224A ASN 3.8 1.7 - - - -
225A HIS* 1.3 76.2 - - - +
227A LYS* 1.3 53.5 + - - +
229A LYS* 3.1 5.9 + - - +
230A ILE* 2.8 49.5 + - + +
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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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210A TYR* 3.7 51.7 - - + +
213A GLU* 2.8 39.6 + - + +
225A HIS 3.3 0.2 - - - -
226A ILE* 1.3 74.4 - - - +
228A GLU* 1.3 71.1 + - - +
230A ILE* 3.3 6.1 + - - +
231A ARG* 3.0 39.1 + - - +
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Residues in contact with GLU 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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225A HIS* 3.2 38.9 - - - +
227A LYS* 1.3 81.0 + - - +
229A LYS* 1.3 58.2 + - - +
231A ARG* 3.4 26.5 + - - +
232A GLN* 3.0 24.1 + - - +
5E 6MA 3.8 6.1 - - - -
6E T 3.2 43.9 - - + +
7E C 4.6 3.5 + - - +
5F 6MA 3.2 13.1 - - - +
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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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188A TRP* 3.6 57.0 - - + +
223A ASN* 4.0 4.3 - - - +
225A HIS 3.2 13.6 + - - +
226A ILE* 3.1 12.4 + - - +
228A GLU* 1.3 74.5 - - - +
230A ILE* 1.3 60.0 + - - +
232A GLN* 2.5 33.1 + - - +
233A GLN* 2.9 40.9 + - + +
3E G 3.6 17.0 + - - -
4E G 2.9 38.2 + - + +
5E 6MA 3.9 8.0 - - - +
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Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A TRP* 4.9 1.1 - - + -
192A ILE* 3.5 16.7 - - + +
206A LEU* 4.4 4.9 - - + -
209A MET* 3.7 48.0 - - + +
210A TYR* 4.3 11.0 - - + -
212A PHE 5.5 0.4 - - - -
213A GLU* 5.6 0.9 - - + -
216A LEU* 3.1 36.8 - - + -
226A ILE* 2.8 39.3 + - + +
227A LYS* 3.4 9.2 - - - +
229A LYS* 1.3 73.0 - - - +
231A ARG* 1.3 62.2 + - - +
233A GLN* 3.3 2.5 + - - +
234A LEU* 3.0 35.2 + - + +
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Residues in contact with ARG 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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206A LEU* 3.8 9.6 - - + -
210A TYR* 3.0 29.4 + - - +
227A LYS* 3.0 33.9 + - - +
228A GLU* 3.5 32.9 - - - +
229A LYS 3.2 0.2 - - - -
230A ILE* 1.3 76.4 - - - +
232A GLN* 1.3 61.2 + - - +
234A LEU* 3.4 11.3 + - - +
235A GLN* 3.1 28.9 + - - +
245A PHE* 4.8 0.9 - - - -
7E C 4.2 2.0 - - - +
3F G 3.4 44.3 + - - -
4F G 2.9 57.0 + - + +
5F 6MA 4.2 0.9 - - - -
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Residues in contact with GLN 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 GLU 3.0 15.0 + - - +
229A LYS* 2.5 38.5 + - - +
231A ARG* 1.3 75.6 - - - +
233A GLN* 1.3 74.4 + - - +
235A GLN* 3.3 18.0 + - - +
236A ILE* 3.1 28.3 + - + +
3E G 5.5 0.2 + - - -
4E G 2.7 27.1 + - - -
5E 6MA 3.4 6.6 + - - -
5F 6MA 4.1 0.7 - - - -
6F T 3.2 35.1 + - + +
7F C 3.6 6.3 - - - +
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Residues in contact with GLN 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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188A TRP* 3.7 22.2 - - + +
189A THR* 2.7 42.2 + - - +
192A ILE* 3.9 30.5 - - + -
229A LYS* 2.9 25.6 + - + +
230A ILE 3.6 4.3 - - - +
232A GLN* 1.3 97.9 + - - +
234A LEU* 1.3 60.1 + - - +
236A ILE* 3.0 15.8 + - - +
237A LEU* 3.0 32.9 + - + +
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Residues in contact with LEU 234 (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 ILE* 4.8 3.6 - - + -
196A ILE* 4.5 9.6 - - + -
204A PHE* 4.1 20.6 - - + -
206A LEU* 3.5 31.6 - - + -
209A MET* 4.3 14.1 - - + -
230A ILE* 3.0 27.7 + - + +
231A ARG* 3.7 8.5 - - - +
232A GLN 3.4 0.2 - - - -
233A GLN* 1.3 76.1 - - - +
235A GLN* 1.3 56.6 + - - +
237A LEU* 3.4 1.2 + - - -
238A ARG 2.9 23.2 + - - -
243A ILE* 3.5 23.5 - - + +
245A PHE* 3.3 23.6 - - + -
251A TYR* 3.6 19.3 - - + +
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Residues in contact with GLN 235 (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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231A ARG 3.1 25.3 + - - +
232A GLN* 3.4 10.1 - - - +
233A GLN 3.2 0.4 - - - -
234A LEU* 1.3 73.5 - - - +
236A ILE* 1.3 66.9 + - + +
238A ARG* 3.4 15.2 + - - +
239A ASP* 3.1 31.0 + - - +
245A PHE* 3.8 18.2 - - + -
4F G 3.7 18.1 - - + +
5F 6MA 2.9 61.9 + - - +
6F T 3.5 12.5 - - - +
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Residues in contact with ILE 236 (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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177A PHE* 3.9 29.2 - - + -
189A THR* 4.4 10.3 - - + +
232A GLN* 3.1 22.9 + - + +
233A GLN* 3.0 26.9 + - - +
235A GLN* 1.3 80.0 - - + +
237A LEU* 1.3 62.8 + - - +
239A ASP* 3.3 19.4 + - - +
240A LYS* 3.3 16.7 + - + +
6F T 6.4 1.3 - - + -
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Residues in contact with LEU 237 (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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177A PHE* 4.4 3.6 - - + -
189A THR* 3.6 26.9 - - + +
192A ILE* 4.0 17.9 - - + -
193A LEU* 3.5 29.4 - - + -
196A ILE* 3.2 34.8 - - + -
233A GLN* 3.0 18.1 + - + +
234A LEU* 3.8 5.2 - - - +
236A ILE* 1.3 72.1 - - - +
238A ARG* 1.3 62.3 + - - +
240A LYS* 3.5 4.8 + - - +
242A ILE* 3.0 49.7 + - + +
243A ILE* 3.4 14.8 + - + -
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Residues in contact with ARG 238 (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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234A LEU 2.9 18.5 + - - +
235A GLN* 3.5 16.2 + - - +
237A LEU* 1.3 72.0 - - - +
239A ASP* 1.3 88.4 + - - +
240A LYS 3.0 4.3 - - - -
241A GLU* 2.8 24.1 + - - +
243A ILE* 3.3 20.3 - - - +
244A GLU* 4.9 0.9 - - - -
245A PHE* 3.4 52.7 - - + +
4F G 4.4 0.8 - - - -
5F 6MA 2.9 32.8 + - - -
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Residues in contact with ASP 239 (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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235A GLN* 3.1 19.2 + - - +
236A ILE* 3.3 13.1 + - - +
238A ARG* 1.3 105.5 + - - +
240A LYS* 1.3 65.6 + - + +
241A GLU* 3.4 6.7 + - - +
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Residues in contact with LYS 240 (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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173A LYS* 3.5 18.6 - - + +
176A LEU* 6.2 4.6 - - + +
177A PHE* 3.8 25.6 - - + -
236A ILE* 3.3 14.5 + - + +
237A LEU 3.9 2.9 - - - +
238A ARG 3.0 1.4 - - - -
239A ASP* 1.3 81.7 - - + +
241A GLU* 1.3 72.1 + - - +
242A ILE* 3.1 23.1 + - + +
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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
------------------------------------------------------------
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