Contacts of the helix formed by residues 241 - 257 (chain A) in PDB entry 3QTC
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 ASN 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A ARG 4.0 0.8 + - - -
240A GLU* 1.3 73.9 - - - +
242A TYR* 1.3 53.6 + - - +
243A LEU* 2.9 31.5 + - - +
244A GLY* 3.2 12.4 + - - +
245A LYS* 2.8 36.0 + - - +
248A ARG* 4.7 2.6 - - - +
447A TYR* 3.5 29.7 + - + +
448A ASN* 3.5 3.7 + - - -
815A EDO 3.0 25.2 + - - -
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Residues in contact with TYR 242 (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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238A GLU* 5.7 4.3 - - - -
240A GLU 4.7 1.8 - - - -
241A ASN* 1.3 72.3 + - - +
243A LEU* 1.3 58.8 + - - +
245A LYS* 4.4 6.5 - - + -
246A LEU* 2.9 31.7 + - - +
428A LEU* 4.0 11.2 - - + +
432A HIS* 3.5 45.8 + + - -
434A PHE* 4.2 7.0 - + - -
448A ASN* 2.8 63.2 + - + +
814A EDO 3.5 22.8 - - - -
815A EDO 3.9 12.8 - - - +
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ASN* 2.9 11.3 + - - +
242A TYR* 1.3 76.7 - - - +
244A GLY* 1.3 65.9 + - - +
246A LEU* 3.5 1.9 + - + +
247A GLU* 3.1 23.0 + - - +
343A THR* 3.9 13.0 - - + +
424A LEU* 3.9 30.4 - - + +
425A GLU* 3.8 26.2 - - + +
428A LEU* 4.0 17.0 - - + +
440A ALA 4.2 3.8 - - - +
441A ALA 4.5 0.7 - - - -
442A ARG* 3.9 41.7 - - + +
815A EDO 4.1 8.4 - - - -
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Residues in contact with GLY 244 (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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241A ASN* 3.2 14.4 + - - -
243A LEU* 1.3 77.8 - - - +
245A LYS* 1.3 62.1 + - - +
247A GLU* 3.3 10.2 + - - +
248A ARG* 3.0 44.4 + - - +
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Residues in contact with LYS 245 (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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238A GLU* 2.8 41.1 + - - +
240A GLU* 3.4 25.4 - - + +
241A ASN 2.8 18.2 + - - +
242A TYR* 5.4 4.6 - - + -
244A GLY* 1.3 73.6 - - - +
246A LEU* 1.3 60.2 + - - +
248A ARG* 3.1 15.9 + - + +
249A GLU* 2.9 54.0 + - + +
814A EDO 3.8 24.5 + - - -
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Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A TYR 2.9 19.6 + - - +
243A LEU* 4.0 3.6 - - - +
245A LYS* 1.3 75.6 - - - +
247A GLU* 1.3 65.0 + - - +
249A GLU* 3.2 15.1 + - - +
250A ILE* 2.8 47.7 + - + +
370A LEU* 4.0 20.4 - - + -
372A ILE* 6.2 0.7 - - + -
424A LEU* 3.6 39.5 - - + +
427A LEU* 4.1 13.5 - - + -
428A LEU* 3.8 17.3 - - + -
431A LYS* 5.7 4.9 - - + +
814A EDO 3.6 13.4 - - - +
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Residues in contact with GLU 247 (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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243A LEU 3.1 15.2 + - - +
244A GLY* 3.5 12.2 - - - +
245A LYS 3.3 0.2 - - - -
246A LEU* 1.3 77.3 - - - +
248A ARG* 1.3 60.3 + - + +
250A ILE 3.4 0.2 + - - -
251A THR* 2.8 38.3 + - - +
261A GLU* 5.3 1.0 - - - +
263A LYS* 2.9 31.7 + - - +
325A ILE* 3.6 29.9 - - + +
326A GLY* 5.4 1.4 - - - -
343A THR* 5.1 4.7 - - - +
424A LEU* 4.0 15.6 - - + +
442A ARG* 5.9 1.4 + - - -
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Residues in contact with ARG 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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240A GLU* 2.8 43.8 + - - +
241A ASN* 4.3 3.0 + - - +
244A GLY* 3.0 34.5 + - - +
245A LYS* 3.1 20.0 + - + +
247A GLU* 1.3 81.7 - - + +
249A GLU* 1.3 56.4 + - + +
251A THR* 3.4 7.6 + - - -
252A ARG* 3.0 32.4 + - - +
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Residues in contact with GLU 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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245A LYS* 2.9 38.6 + - + +
246A LEU* 3.6 17.0 - - + +
248A ARG* 1.3 74.1 - - + +
250A ILE* 1.3 64.9 + - - +
252A ARG* 3.4 7.6 + - - +
253A PHE* 3.1 22.0 + - - +
369A HIS* 4.8 9.9 + - - +
370A LEU* 4.6 13.0 - - + +
431A LYS* 4.3 5.4 + - - -
814A EDO 2.5 30.3 + - - -
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Residues in contact with ILE 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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246A LEU* 2.8 50.4 + - + +
249A GLU* 1.3 69.5 - - - +
251A THR* 1.3 66.1 + - - +
253A PHE* 3.2 6.4 + - - +
254A PHE* 3.1 36.0 + - + -
323A PHE* 5.3 0.2 - - + -
325A ILE* 3.6 19.7 - - + -
345A LEU* 3.7 23.6 - - + -
366A PHE* 3.9 24.7 - - + -
370A LEU* 4.6 2.9 - - + -
424A LEU* 3.8 27.1 - - + -
427A LEU* 4.2 7.0 - - + -
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Residues in contact with THR 251 (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 GLU* 2.8 29.1 + - - +
248A ARG* 3.5 8.6 - - - -
249A GLU 3.3 0.2 - - - -
250A ILE* 1.3 77.2 - - - +
252A ARG* 1.3 63.9 + - - +
254A PHE 3.3 0.2 + - - -
255A VAL* 2.9 42.7 + - + +
261A GLU* 3.9 25.0 + - - +
263A LYS* 5.8 0.7 + - - -
323A PHE* 3.8 23.9 - - + -
325A ILE* 3.4 12.3 - - - +
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Residues in contact with ARG 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 ARG 3.0 15.3 + - - +
249A GLU* 3.6 11.0 - - - +
250A ILE 3.3 0.2 - - - -
251A THR* 1.3 82.5 - - - +
253A PHE* 1.3 62.5 + - - +
255A VAL* 4.0 25.7 - - - +
256A ASP* 2.9 52.9 + - - +
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Residues in contact with PHE 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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249A GLU 3.1 13.4 + - - +
250A ILE* 3.2 11.0 + - - +
252A ARG* 1.3 78.2 - - - +
254A PHE* 1.3 92.0 + + - +
256A ASP* 3.8 5.4 - - - +
257A ARG* 3.2 71.3 + - - +
362A ILE* 4.3 5.4 - - + -
365A ASP* 3.8 7.6 - - + -
366A PHE* 3.4 45.5 - + + -
369A HIS* 3.7 35.2 + + + +
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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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250A ILE* 3.1 31.3 + - + +
253A PHE* 1.3 97.7 - + - +
255A VAL* 1.3 65.7 + - - +
257A ARG* 3.1 9.0 + - + +
258A GLY 3.3 0.5 + - - -
259A PHE* 3.0 47.0 + + + +
323A PHE* 3.7 26.0 - + + -
345A LEU* 3.7 26.9 - - + -
347A PHE* 3.5 42.0 - + + -
362A ILE* 3.9 17.3 - - + -
366A PHE* 3.8 18.4 - + - -
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Residues in contact with VAL 255 (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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251A THR* 2.9 29.3 + - + +
252A ARG* 4.0 24.2 - - - +
254A PHE* 1.3 75.4 - - - +
256A ASP* 1.3 67.2 + - - +
258A GLY* 3.1 15.1 + - - -
259A PHE 3.6 10.8 + - - +
261A GLU* 4.4 10.8 - - + +
323A PHE* 3.8 19.3 - - + -
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Residues in contact with ASP 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 ARG* 2.9 48.8 + - - +
253A PHE* 3.8 5.5 - - - +
255A VAL* 1.3 82.9 - - - +
257A ARG* 1.3 58.4 + - + +
258A GLY 3.3 2.6 + - - -
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Residues in contact with ARG 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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253A PHE* 3.2 54.5 + - + +
254A PHE* 3.1 7.0 + - - +
256A ASP* 1.3 81.1 - - + +
258A GLY* 1.3 56.0 + - - +
259A PHE* 3.4 19.2 - - + -
321A LYS* 3.0 23.6 + - - -
362A ILE* 5.5 7.9 - - - +
365A ASP* 2.8 40.4 + - - +
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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