Contacts of the helix formed by residues 335 - 352 (chain F) in PDB entry 5TJ4
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 GLN 335 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F GLN* 5.1 1.2 + - - -
169F PHE* 3.7 26.2 - - + -
178F ILE* 3.9 21.4 - - + +
333F ILE* 3.1 14.3 - - + +
334F PRO* 1.3 94.0 - - - +
336F MET* 1.3 59.7 + - - +
338F ALA* 2.9 21.8 + - - +
339F PHE 3.0 9.9 + - - -
1221F SER* 3.3 38.8 + - - +
1224F LEU* 3.9 29.0 + - + -
1225F ASP* 3.9 9.5 - - - +
1227F HIS* 5.2 5.7 - - - -
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Residues in contact with MET 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F ASP* 4.1 15.7 - - + +
168F ALA* 3.7 16.6 - - + -
169F PHE* 3.5 30.0 - - + -
258F PHE* 4.7 1.8 - - + -
330F MET* 5.0 4.3 - - - -
331F PRO* 3.3 60.1 - - + +
333F ILE* 3.3 15.6 + - + +
334F PRO 3.1 0.2 - - - -
335F GLN* 1.3 77.0 - - - +
337F SER* 1.3 61.5 + - - +
339F PHE* 3.2 11.1 + - + +
340F TRP* 2.9 53.7 + - + -
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Residues in contact with SER 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F ARG* 4.6 32.1 + - - +
69F GLY* 5.5 4.5 - - - -
334F PRO* 3.4 14.9 + - - +
336F MET* 1.3 76.7 - - - +
338F ALA* 1.3 63.6 + - - +
340F TRP* 3.8 4.3 - - - +
341F TYR* 3.0 25.2 + - - +
1224F LEU* 5.5 6.4 - - - +
1365F VAL* 5.6 10.1 - - - -
1368F GLN* 5.5 7.3 + - - -
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Residues in contact with ALA 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334F PRO 4.5 0.4 + - - -
335F GLN 2.9 11.6 + - - +
337F SER* 1.3 79.8 - - - +
339F PHE* 1.3 64.2 + - - +
341F TYR* 3.4 1.7 + - - -
342F ALA* 3.1 25.1 + - - +
368F ALA* 3.9 4.0 - - - +
1220F MET* 3.7 30.1 - - + -
1221F SER* 3.6 22.4 - - - +
1224F LEU* 4.3 7.4 - - + +
1361F GLN* 3.7 10.2 + - - +
1365F VAL* 5.8 2.5 - - - -
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Residues in contact with PHE 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F TRP* 3.6 30.5 - + - -
168F ALA* 3.6 35.7 - - + -
169F PHE* 3.9 16.4 - - + -
181F VAL* 4.7 5.6 - - + -
183F VAL* 3.8 16.2 - - + -
258F PHE* 3.8 14.4 - + - -
335F GLN 3.0 10.3 + - - +
336F MET* 3.2 16.4 + - - +
338F ALA* 1.3 78.4 - - - +
340F TRP* 1.3 107.1 + + - +
342F ALA* 3.2 2.3 + - - +
343F VAL* 3.1 44.5 + - + +
368F ALA* 4.3 11.4 - - + +
1221F SER* 4.8 0.4 + - - -
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Residues in contact with TRP 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ASP* 3.1 27.7 + - - -
66F ARG* 4.5 13.9 - - - +
154F PRO* 3.6 28.6 - - + +
155F TYR* 3.7 34.8 - + - -
158F TRP* 4.7 6.7 - + + -
258F PHE* 3.6 33.2 - + + -
330F MET* 3.8 16.8 - - + -
336F MET* 2.9 39.5 + - + +
337F SER 3.8 2.7 - - - +
339F PHE* 1.3 93.5 - + - +
341F TYR* 1.3 64.6 + - - +
343F VAL* 3.3 3.3 + - + +
344F ARG* 2.9 29.8 + - - +
2P GLC 3.8 29.5 + - - +
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Residues in contact with TYR 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F GLU* 6.0 1.3 - - - -
337F SER 3.0 16.8 + - - +
338F ALA* 4.1 3.1 - - - +
340F TRP* 1.3 77.5 - - - +
342F ALA* 1.3 62.6 + - - +
344F ARG* 3.4 30.2 + - - +
345F THR* 3.2 40.2 + - - -
1360F ASP* 4.9 4.0 + - + +
1361F GLN* 3.6 37.9 - - + +
1364F SER* 3.2 35.1 + - - -
1365F VAL* 5.6 9.6 - - + -
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Residues in contact with ALA 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338F ALA 3.1 18.1 + - - +
339F PHE 3.5 4.3 - - - +
341F TYR* 1.3 77.1 - - - +
343F VAL* 1.3 62.6 + - + +
345F THR* 3.6 5.5 - - - +
346F ALA* 3.1 21.5 + - - +
364F ALA* 3.5 35.5 - - + +
368F ALA* 3.8 10.5 - - + +
1361F GLN* 3.7 19.9 + - - +
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Residues in contact with VAL 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F PRO* 3.7 21.3 - - + -
158F TRP* 4.4 17.5 - - + -
161F ILE* 4.9 3.1 - - + -
183F VAL* 3.9 17.7 - - + -
339F PHE* 3.1 46.0 + - + +
340F TRP* 3.8 3.8 - - + +
342F ALA* 1.3 74.9 - - + +
344F ARG* 1.3 67.2 + - - +
346F ALA* 2.9 8.2 + - + +
347F VAL* 2.8 37.4 + - + +
361F LEU* 6.0 4.3 - - + -
364F ALA* 4.7 2.2 - - + -
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Residues in contact with ARG 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F GLU* 5.5 3.2 + - - -
45F GLU* 4.8 12.1 + - - -
66F ARG* 4.4 6.5 - - - +
152F GLN 3.8 17.7 - - - +
153F GLU* 3.1 33.3 + - - -
154F PRO* 3.8 15.1 - - + +
340F TRP* 2.9 21.2 + - - +
341F TYR* 3.5 46.9 - - - +
343F VAL* 1.3 77.6 - - - +
345F THR* 1.3 63.4 + - - +
347F VAL* 4.0 3.1 - - - +
348F ILE* 3.1 38.0 + - + +
2P GLC 3.5 27.1 + - - -
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Residues in contact with THR 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341F TYR* 3.2 28.8 + - - -
342F ALA* 3.6 9.9 - - - +
343F VAL 3.2 0.2 - - - -
344F ARG* 1.3 75.2 - - - +
346F ALA* 1.3 68.9 + - - +
348F ILE* 3.1 5.9 + - - +
349F ASN* 2.8 48.7 + - - +
355F GLN* 4.8 1.3 - - - +
1357F LEU* 4.3 18.8 - - + -
1361F GLN* 5.1 2.5 + - - +
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Residues in contact with ALA 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F LEU* 4.9 1.3 - - - -
342F ALA 3.1 11.4 + - - +
343F VAL* 2.9 10.1 + - + +
345F THR* 1.3 79.9 - - - +
347F VAL* 1.3 58.7 + - + +
349F ASN* 4.6 1.3 - - - -
350F ALA* 2.9 32.7 + - - +
355F GLN* 5.0 0.9 - - - -
360F ALA* 3.6 38.7 - - + +
361F LEU* 4.3 12.6 - - + +
364F ALA* 3.8 9.9 - - + -
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Residues in contact with VAL 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F LEU* 4.0 16.2 - - + +
152F GLN 6.2 0.2 - - - +
153F GLU 6.3 0.2 - - - -
154F PRO* 4.9 4.5 - - + -
157F THR* 3.9 31.0 - - + +
161F ILE* 3.9 22.0 - - + -
192F LEU* 4.3 13.0 - - + +
195F LEU* 4.4 11.0 - - + -
343F VAL* 2.8 39.6 + - + +
344F ARG* 4.0 4.3 - - - +
346F ALA* 1.3 71.8 - - + +
348F ILE* 1.3 57.5 + - + +
350F ALA* 3.3 2.3 + - - +
351F ALA* 2.9 32.6 + - + +
361F LEU* 6.3 0.7 - - + -
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Residues in contact with ILE 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F LEU 4.6 7.6 - - - +
152F GLN* 3.8 45.1 - - + +
344F ARG* 3.1 26.7 + - + +
345F THR* 3.7 4.7 - - - +
347F VAL* 1.3 77.4 - - + +
349F ASN* 1.3 61.2 + - - +
351F ALA* 3.7 5.4 - - - +
352F SER* 2.8 41.2 + - - +
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Residues in contact with ASN 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345F THR* 2.8 35.0 + - - +
346F ALA 3.8 2.0 - - - +
348F ILE* 1.3 85.1 - - - +
350F ALA* 1.3 56.7 + - - +
352F SER* 3.6 5.6 + - - -
353F GLY 3.2 3.1 + - - -
354F ARG* 3.0 60.1 + - + +
355F GLN* 2.8 44.7 + - + +
1357F LEU* 4.4 9.5 - - - +
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Residues in contact with ALA 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F LEU* 4.1 17.5 - - + -
196F VAL* 3.7 34.0 - - + +
346F ALA 2.9 18.3 + - - +
347F VAL 3.8 2.7 - - - +
349F ASN* 1.3 74.5 - - - +
351F ALA* 1.3 64.9 + - - +
353F GLY* 3.4 9.7 + - - -
355F GLN 3.6 14.4 - - - +
357F VAL* 4.3 14.7 - - + +
360F ALA* 4.3 3.7 - - + +
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Residues in contact with ALA 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F LEU* 5.4 4.9 - - + -
192F LEU* 5.9 0.4 - - + +
195F LEU* 5.8 2.2 - - + -
196F VAL* 4.4 7.9 - - + +
199F ILE* 3.6 37.5 - - + +
206F ALA* 3.8 21.8 - - + +
347F VAL* 2.9 23.5 + - + +
348F ILE* 3.7 5.4 - - - +
350F ALA* 1.3 78.2 - - - +
352F SER* 1.3 60.7 + - - +
353F GLY* 3.3 0.9 + - - -
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Residues in contact with SER 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F ALA* 4.4 8.4 - - - +
348F ILE* 2.8 30.9 + - - +
349F ASN* 3.5 11.4 + - - -
351F ALA* 1.3 71.9 - - - +
353F GLY* 1.3 57.9 + - - +
354F ARG* 3.2 18.4 + - - +
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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