Contacts of the helix formed by residues 247 - 257 (chain A) in PDB entry 1TJY
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 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A GLY* 4.5 1.0 - - - -
41A PHE* 3.5 41.7 + - + +
222A ALA* 5.7 0.4 - - + +
246A SER* 1.3 79.3 + - - +
248A PRO* 1.3 73.2 - - + +
249A ASN* 5.1 0.3 - - - +
250A VAL* 3.3 26.3 + - - +
251A MET* 3.0 23.9 + - - +
263A PHE* 4.1 2.0 - - - -
265A LEU* 4.0 15.0 - - + -
268A VAL* 4.8 1.3 - - + -
340A PHE* 3.6 23.8 + - + +
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Residues in contact with PRO 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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246A SER 4.3 3.1 - - - +
247A THR* 1.3 85.0 - - - +
249A ASN* 1.3 56.5 + - - +
252A ARG* 2.9 36.0 + - - +
263A PHE* 3.9 12.3 - - + -
330A PHE* 3.8 16.4 - - + -
335A ILE* 3.8 17.7 - - + +
338A TYR* 3.8 32.1 - - + +
340A PHE* 3.4 42.0 - - + +
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Residues in contact with ASN 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 THR* 5.1 0.7 - - - +
248A PRO* 1.3 76.4 - - - +
250A VAL* 1.3 64.3 + - + +
252A ARG* 3.0 32.1 + - - +
253A PRO* 4.0 11.4 - - - +
338A TYR 3.7 1.0 - - - +
339A ASP* 2.9 26.8 + - - +
340A PHE* 3.0 38.6 + - - +
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Residues in contact with VAL 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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39A VAL* 6.3 0.4 - - + -
40A GLY* 4.7 17.7 - - - +
222A ALA 4.6 1.8 - - - +
226A PRO* 3.7 34.3 - - + -
246A SER* 3.8 9.6 - - - +
247A THR* 3.3 22.6 + - - +
248A PRO 3.3 0.2 - - - -
249A ASN* 1.3 80.7 - - + +
251A MET* 1.3 60.6 + - - +
253A PRO* 3.5 11.8 - - - +
254A TYR* 3.8 12.4 - - + -
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Residues in contact with MET 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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225A LEU* 3.7 21.5 - - + -
226A PRO* 3.8 28.9 - - + -
229A ALA* 4.7 0.2 - - + -
246A SER* 3.6 28.0 - - - -
247A THR 3.0 19.6 + - - +
250A VAL* 1.3 76.2 - - - +
252A ARG* 1.3 66.3 + - - +
253A PRO* 3.3 1.8 - - - -
254A TYR* 3.0 30.2 + - + +
255A VAL* 3.0 12.5 + - + +
260A VAL* 3.7 30.3 - - + -
263A PHE* 3.5 31.6 - - + -
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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 PRO* 2.9 21.7 + - - +
249A ASN* 3.0 31.3 + - - +
250A VAL 3.4 0.2 - - - -
251A MET* 1.3 75.4 - - - +
253A PRO* 1.3 64.5 - - + +
255A VAL* 3.2 1.4 + - - +
256A GLN* 2.8 55.6 + - + +
335A ILE* 3.0 33.9 + - + +
336A ASP* 2.9 30.5 + - - +
338A TYR 2.8 28.5 + - - -
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Residues in contact with PRO 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 ASN 4.0 7.4 - - - +
250A VAL 3.5 13.2 - - - +
251A MET 3.4 3.8 - - - -
252A ARG* 1.3 93.9 - - + +
254A TYR* 1.3 60.3 + - + +
256A GLN* 3.4 11.4 + - + +
257A ARG* 3.0 57.7 + - - +
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Residues in contact with TYR 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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226A PRO* 3.8 26.3 + - + +
229A ALA* 3.5 24.2 - - + -
230A GLN* 2.7 46.1 + - - +
233A GLU* 3.5 17.9 - - - -
250A VAL* 3.8 20.2 - - + -
251A MET* 3.0 25.1 + - + +
253A PRO* 1.3 78.2 - - + +
255A VAL* 1.3 63.6 + - - +
257A ARG* 3.3 20.0 + - - -
258A GLY 3.2 2.8 + - - -
259A THR* 3.0 29.5 + - - -
260A VAL* 3.2 6.7 + - + -
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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 MET* 3.0 12.5 + - + +
252A ARG 3.7 6.1 - - - +
254A TYR* 1.3 75.9 - - - +
256A GLN* 1.3 64.4 + - + +
258A GLY* 3.1 13.9 + - - -
260A VAL* 3.3 23.4 - - + +
261A LYS* 5.0 3.9 - - - +
263A PHE* 3.8 32.3 - - + -
331A ASN* 4.2 5.4 - - - -
332A LYS* 3.9 38.0 - - + +
335A ILE* 3.9 16.6 - - + -
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Residues in contact with GLN 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* 2.8 45.9 + - + +
253A PRO* 3.6 9.7 - - + +
255A VAL* 1.3 79.3 - - + +
257A ARG* 1.3 62.1 + - + +
258A GLY* 3.4 0.7 + - - -
335A ILE* 6.2 1.6 - - + -
336A ASP* 4.8 7.9 + - - -
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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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230A GLN* 4.2 4.2 + - - -
233A GLU* 3.0 45.3 + - - +
253A PRO* 3.0 38.1 + - - +
254A TYR* 3.3 26.4 + - - +
255A VAL 3.3 0.2 - - - -
256A GLN* 1.3 78.3 - - + +
258A GLY* 1.3 60.3 + - - +
259A THR* 3.3 4.4 + - - +
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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