Contacts of the helix formed by residues 224 - 234 (chain A) in PDB entry 2KTY
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 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A ASP* 3.4 11.2 + - - +
179A LYS* 3.4 42.6 + - + +
223A GLY* 1.3 70.1 - - - -
225A ILE* 1.3 52.3 + - - +
226A GLU* 2.8 13.4 + - - +
227A PHE* 2.9 4.9 + - - +
228A THR* 2.7 28.7 + - - -
265A LEU* 5.9 2.0 - - - -
352A LYS* 6.6 0.2 - - - -
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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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223A GLY 3.3 5.3 + - - -
224A THR* 1.3 70.7 - - - +
226A GLU* 1.3 66.2 + - - +
227A PHE 3.1 0.7 + - - -
228A THR* 3.4 16.5 + - + -
229A SER* 3.4 8.1 + - - +
233A HIS* 3.3 56.5 - - + +
265A LEU* 3.7 20.2 - - + +
267A ASP 5.0 0.9 - - - +
268A PRO* 3.7 9.2 - - + -
271A VAL* 3.3 49.7 - - + +
275A LYS* 4.2 0.5 + - - -
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Residues in contact with GLU 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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142A TYR* 4.7 8.2 + - - -
147A LYS* 5.0 1.7 + - - -
179A LYS* 3.3 20.1 + - - -
224A THR* 2.8 11.4 + - - +
225A ILE* 1.3 83.5 - - - +
227A PHE* 1.3 90.4 + - + +
229A SER* 5.5 0.2 - - - -
249A TYR* 5.9 1.6 - - - +
253A GLN* 4.2 8.1 + - - -
259A LEU* 5.5 5.1 - - + +
261A TRP* 4.2 19.5 + - - +
262A GLU* 4.2 13.7 - - + +
265A LEU* 3.5 43.8 - - + +
271A VAL* 5.7 0.7 - - - -
275A LYS* 4.8 3.5 + - - -
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Residues in contact with PHE 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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142A TYR* 6.0 3.8 - + - -
176A GLY 3.5 4.2 - - - +
177A ASP* 4.4 2.2 - - - -
178A ILE* 3.6 20.2 - - + +
179A LYS* 3.3 60.1 - - + +
180A ALA* 4.6 4.3 - - + -
224A THR* 2.9 5.7 + - - +
226A GLU* 1.3 100.9 - - + +
228A THR* 1.3 65.3 + - - +
229A SER* 2.9 8.1 + - - -
246A ILE* 3.3 24.5 - - + +
249A TYR* 6.0 2.2 - - + -
250A CYS* 3.5 29.6 - - + -
253A GLN* 3.5 32.1 - - + -
254A TRP* 4.8 6.5 - + - -
259A LEU* 5.8 3.1 - - + -
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Residues in contact with THR 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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176A GLY 4.1 7.1 - - - +
177A ASP* 3.0 13.0 + - - -
221A HIS* 5.3 2.7 - - - -
222A ASP* 3.0 25.6 + - - -
223A GLY 3.5 10.1 + - - +
224A THR 2.7 18.0 + - - -
225A ILE* 3.4 12.3 + - + -
227A PHE* 1.3 77.7 - - - +
229A SER* 1.3 83.2 + - - +
231A ASP* 4.5 0.7 - - - +
232A ALA* 3.2 18.5 + - + +
233A HIS* 3.1 28.0 - - + +
246A ILE* 4.5 2.4 - - - +
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Residues in contact with SER 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 ILE* 3.4 6.7 + - - -
227A PHE* 2.9 7.3 + - - +
228A THR* 1.3 104.8 - - - +
230A ILE* 1.3 62.2 + - - +
231A ASP* 4.1 9.2 - - - -
233A HIS* 2.9 11.5 + - - +
245A GLU* 5.6 1.3 - - - -
246A ILE* 3.2 30.6 + - - +
249A TYR* 3.4 27.3 - - - +
275A LYS* 3.8 15.8 - - - +
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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
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229A SER* 1.3 71.5 - - - +
231A ASP* 1.3 71.2 + - - +
233A HIS* 3.9 10.1 - - + -
234A ASN* 2.7 46.4 + - - +
241A ARG* 5.5 0.9 - - - +
245A GLU* 5.4 7.9 - - + +
249A TYR* 5.4 0.4 - - - +
271A VAL* 4.7 2.5 - - + +
272A ARG* 4.7 16.6 - - + +
275A LYS* 3.2 38.2 - - + +
276A ILE* 5.9 2.2 - - + -
279A ARG* 3.3 42.2 - - - +
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Residues in contact with ASP 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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228A THR 4.5 3.6 - - - +
229A SER* 3.1 5.5 - - - -
230A ILE* 1.3 96.9 - - - +
232A ALA* 1.3 63.3 + - + +
234A ASN 3.0 5.9 + - - -
236A VAL* 3.0 47.2 + - - +
237A ALA 4.0 1.4 - - - +
238A PRO* 3.3 23.0 - - + +
239A SER 4.6 0.3 + - - -
241A ARG* 4.7 4.7 + - - +
242A GLY* 3.0 36.2 + - - +
245A GLU* 4.7 6.1 - - - +
246A ILE* 5.0 2.9 - - + -
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Residues in contact with ALA 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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176A GLY* 5.2 8.3 - - - -
202A TYR* 5.4 5.6 - - + -
220A CYS* 3.1 23.5 - - - -
221A HIS 3.4 5.1 + - - -
222A ASP* 3.2 27.1 - - - +
228A THR* 3.2 26.6 + - - +
231A ASP* 1.3 80.3 - - + +
233A HIS* 1.3 56.0 + - - +
234A ASN 3.0 0.2 - - - -
235A GLY 2.9 15.6 + - - +
236A VAL 3.9 4.9 + - - -
238A PRO* 5.5 2.2 - - + +
246A ILE* 6.3 0.2 - - + -
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Residues in contact with HIS 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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219A ARG* 2.9 42.5 - - + +
221A HIS* 4.8 8.6 - - - +
225A ILE* 3.3 28.2 - - + +
228A THR* 3.1 13.2 - - + +
229A SER 2.9 20.7 + - - +
230A ILE* 3.7 7.9 - - - +
232A ALA* 1.3 75.6 - - - +
234A ASN* 1.3 71.0 + - - +
235A GLY 3.4 0.2 - - - -
268A PRO* 3.2 38.5 + - + +
271A VAL* 5.1 1.1 - - + -
272A ARG* 4.4 20.4 + - + +
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Residues in contact with ASN 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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216A ASP 2.6 22.5 - - - +
217A PRO* 4.6 2.8 - - - +
219A ARG* 4.0 7.2 + - - +
230A ILE* 2.7 30.3 + - - +
231A ASP 3.6 3.8 - - - +
233A HIS* 1.3 97.4 + - - +
235A GLY* 1.3 51.4 + - - +
236A VAL* 3.1 16.9 + - + +
272A ARG* 3.1 34.6 + - - +
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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