Contacts of the helix formed by residues 247 - 261 (chain A) in PDB entry 3KTC
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 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A PHE* 4.8 3.4 - - + -
206A LEU* 3.4 21.2 - - + +
232A ASP* 2.8 35.6 + - - +
233A ASN 2.8 22.4 + - - -
234A LEU* 4.3 2.7 - - - -
235A ARG* 3.5 28.1 + - + +
244A GLY* 5.2 0.7 - - - -
246A VAL* 1.3 88.2 - - + +
248A MSE 1.3 64.8 + - - +
249A THR 3.2 3.3 + - - +
250A GLU* 3.3 31.1 + - + +
251A ILE* 3.1 23.6 + - - +
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Residues in contact with MSE 248 (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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244A GLY* 3.3 28.7 - - - +
245A THR 4.6 2.9 - - - +
246A VAL 4.0 12.7 + - - +
247A HIS* 1.3 73.8 - - - +
249A THR* 1.3 64.5 + - - +
251A ILE* 2.9 23.9 - - - +
252A PHE* 2.9 11.8 + - - +
288A PHE* 3.6 22.2 - - + -
292A ILE* 4.6 0.9 - - - +
324A LEU* 3.9 16.4 - - + +
325A LEU* 5.5 11.2 - - + -
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Residues in contact with THR 249 (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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247A HIS* 3.2 1.0 - - - +
248A MSE 1.3 78.4 - - - +
250A GLU* 1.3 59.3 + - - +
252A PHE* 3.2 5.2 + - - +
253A GLU 2.9 22.5 + - - -
317A GLN* 3.9 29.3 + - - +
320A VAL* 4.6 6.0 - - + +
324A LEU* 3.9 16.0 - - - +
135B PRO* 4.1 16.4 - - + -
136B PHE* 3.5 15.0 - - + -
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Residues in contact with GLU 250 (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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202A PHE* 3.5 18.1 - - + -
206A LEU* 3.8 7.3 - - + +
211A SER* 5.8 1.2 - - - -
212A PRO* 4.9 9.1 - - + +
213A ALA* 5.3 1.0 + - - +
235A ARG* 2.8 45.2 + - - -
247A HIS* 3.3 20.7 + - + +
249A THR* 1.3 75.2 - - + +
251A ILE* 1.3 65.9 + - - +
253A GLU* 3.3 12.0 + - - +
254A PHE* 3.0 22.5 + - - +
132B TRP* 5.4 5.4 - - - -
135B PRO* 3.7 32.6 - - + +
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Residues in contact with ILE 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PHE* 3.7 38.9 - - + -
230A VAL* 4.0 8.5 - - + -
232A ASP* 5.9 0.4 - - - +
243A VAL* 3.8 25.1 - - + -
244A GLY* 4.7 4.5 - - - +
247A HIS 3.1 17.9 + - - +
248A MSE 2.9 30.1 - - - +
250A GLU* 1.3 77.6 - - - +
252A PHE* 1.3 60.1 + - - +
254A PHE* 3.1 6.1 + - + +
255A PHE* 3.1 51.1 + - + -
288A PHE* 3.7 22.7 - - + -
292A ILE* 4.3 2.2 - - + -
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Residues in contact with PHE 252 (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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248A MSE 2.9 14.8 + - - +
249A THR 3.4 7.6 - - - +
251A ILE* 1.3 78.4 - - - +
253A GLU* 1.3 55.9 + - - +
255A PHE* 3.3 2.3 + - - -
256A TYR* 2.8 29.5 + - - +
292A ILE* 3.8 27.6 - - + -
295A ALA* 3.6 39.0 - - + -
296A LEU* 3.6 24.0 - - + -
299A LEU* 4.2 21.8 - - + -
320A VAL* 3.8 33.4 - - + -
323A ALA* 4.1 5.2 - - + -
324A LEU* 4.0 16.6 - - + -
136B PHE* 3.7 18.6 - + - -
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Residues in contact with GLU 253 (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 SER* 4.4 4.7 + - - -
212A PRO* 6.1 0.7 - - - +
213A ALA* 3.6 19.5 - - + +
249A THR 2.9 9.9 + - - +
250A GLU* 3.6 14.0 - - - +
251A ILE 3.2 0.2 - - - -
252A PHE* 1.3 75.2 - - - +
254A PHE* 1.3 57.3 + - - +
256A TYR* 3.2 5.7 + - + +
257A VAL* 2.9 30.1 + - + +
308A GLN* 5.3 0.9 + - - +
135B PRO* 3.8 15.6 - - - +
136B PHE* 3.0 60.9 + - + -
138B VAL 4.6 1.2 - - - +
140B HIS* 2.9 26.1 + - - -
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Residues in contact with PHE 254 (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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200A LEU* 3.7 44.6 - - + -
202A PHE* 3.8 21.3 - + + -
212A PRO* 3.6 26.2 - - + -
213A ALA* 4.1 9.1 - - - +
216A ALA* 4.1 7.1 - - + +
225A LEU* 6.0 0.7 - - + -
228A MSE 4.2 20.2 - - + -
230A VAL* 4.0 17.7 - - + -
250A GLU 3.0 13.1 + - - +
251A ILE* 3.3 10.1 - - + +
253A GLU* 1.3 76.1 - - - +
255A PHE* 1.3 78.9 + + - +
257A VAL* 3.2 5.9 + - - +
258A LEU* 3.1 44.4 + - + +
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Residues in contact with PHE 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A MSE 4.0 13.5 - - + -
230A VAL* 3.9 21.5 - - + -
251A ILE* 3.1 52.4 + - + +
252A PHE 4.0 1.6 - - - +
254A PHE* 1.3 76.6 - + - +
256A TYR* 1.3 66.3 + - - +
258A LEU* 3.3 16.5 + - + +
259A LYS* 2.9 23.4 + - - +
267A TRP* 3.3 45.7 - + + -
289A LEU* 3.8 24.5 - - + -
292A ILE* 3.8 27.6 - - + -
296A LEU* 4.0 12.7 - - + +
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Residues in contact with TYR 256 (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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252A PHE 2.8 17.9 + - - +
253A GLU* 3.2 9.4 + - + +
255A PHE* 1.3 77.4 - - - +
257A VAL* 1.3 71.8 + - + +
259A LYS* 3.2 4.3 + - + +
260A ILE* 3.0 59.8 + - + +
296A LEU* 3.7 16.0 - - + +
299A LEU* 3.7 17.5 - - + -
301A ILE* 4.0 17.3 - - + -
304A LEU* 3.7 20.9 - - + +
305A GLN* 3.1 34.7 + - - +
308A GLN* 3.9 17.0 + - - -
136B PHE* 3.8 21.8 - + + -
139B SER* 6.5 0.2 - - - -
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Residues in contact with VAL 257 (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 ALA* 3.6 38.4 - - + +
216A ALA* 4.0 7.9 - - + -
217A GLN* 3.8 20.4 - - + +
220A ILE* 4.9 0.7 - - + -
253A GLU* 2.9 18.4 + - + +
254A PHE 3.2 7.2 + - - +
256A TYR* 1.3 88.6 - - + +
258A LEU* 1.3 64.6 + - - +
260A ILE* 3.4 9.4 + - + -
261A ASN* 2.8 44.8 + - - +
140B HIS* 4.5 10.8 - - + +
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Residues in contact with LEU 258 (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 ALA* 4.1 12.6 - - + -
220A ILE* 3.9 12.6 - - + -
225A LEU* 3.6 30.1 - - + -
228A MSE 3.7 30.3 - - + -
254A PHE* 3.1 32.6 + - + +
255A PHE* 3.3 21.0 + - + +
257A VAL* 1.3 76.2 - - - +
259A LYS* 1.3 63.0 + - - +
261A ASN 3.4 0.3 + - - -
262A ASN 3.3 2.8 + - - -
263A TRP* 3.0 50.7 + - + +
267A TRP* 5.4 1.8 - - - +
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Residues in contact with LYS 259 (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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255A PHE 2.9 13.2 + - - +
256A TYR* 3.2 9.2 + - - +
258A LEU* 1.3 76.7 - - - +
260A ILE* 1.3 61.1 + - + +
262A ASN* 3.0 20.0 + - - +
263A TRP 5.3 1.3 - - - -
296A LEU* 4.0 42.9 + - + +
297A ASP* 5.3 3.2 - - - +
301A ILE* 3.6 30.5 - - + -
338A UNL 3.8 15.2 + - - +
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Residues in contact with ILE 260 (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 GLN* 4.9 1.8 - - - +
256A TYR* 3.0 68.6 + - + +
257A VAL* 3.5 12.8 - - + +
259A LYS* 1.3 78.5 - - + +
261A ASN* 1.3 64.4 + - - +
262A ASN* 3.3 2.5 + - - +
301A ILE* 4.4 9.2 - - + -
305A GLN* 4.0 13.5 - - - +
338A UNL 4.3 14.6 - - - +
344A EDO 3.5 40.2 - - - +
139B SER* 6.0 1.6 - - - +
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Residues in contact with ASN 261 (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 GLN* 2.8 43.8 + - - -
220A ILE* 3.7 32.9 - - + +
221A ASP* 4.5 1.0 - - - +
257A VAL* 2.8 32.8 + - - +
258A LEU 3.9 2.9 - - - +
259A LYS 3.1 1.0 - - - -
260A ILE* 1.3 83.7 - - - +
262A ASN* 1.3 68.9 + - - +
263A TRP* 3.1 3.2 + - - +
344A EDO 3.5 14.1 + - - -
141B LYS* 5.0 0.3 - - - +
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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