Contacts of the helix formed by residues 356 - 366 (chain f) in PDB entry 5T0J
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 ALA 356 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345f VAL* 4.1 9.7 - - - +
348f ASP* 3.4 31.9 - - + +
350f LYS* 3.3 34.9 + - + +
352f SER 3.7 2.0 + - - -
355f VAL* 1.3 77.9 - - - +
357f GLY* 1.3 62.0 + - - +
358f VAL 3.4 1.3 - - - -
359f THR* 3.4 21.1 - - - +
360f ALA* 3.6 10.2 + - - +
386f LYS* 6.1 0.4 - - + -
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Residues in contact with GLY 357 (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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350f LYS* 3.4 18.4 - - - +
352f SER 3.4 5.6 + - - -
353f MET* 3.2 40.5 + - - +
356f ALA* 1.3 76.5 - - - +
358f VAL* 1.3 64.1 + - - +
360f ALA 3.4 0.6 + - - -
361f LEU 3.1 16.3 + - - -
395f TYR* 3.5 5.1 - - - -
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Residues in contact with VAL 358 (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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317f THR* 4.8 2.5 - - - +
319f ARG* 3.2 31.9 - - + +
320f LEU* 3.5 41.3 - - + +
323f ILE* 3.6 22.0 - - + -
324f PHE 5.0 0.4 - - - +
353f MET* 3.0 21.4 + - + +
354f GLU* 4.4 12.6 - - - +
355f VAL 4.7 3.8 - - - +
356f ALA 3.4 0.6 - - - -
357f GLY* 1.3 74.9 - - - +
359f THR* 1.3 55.5 + - - +
361f LEU* 2.7 26.9 + - - +
362f ALA* 3.1 8.8 + - - +
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Residues in contact with THR 359 (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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319f ARG* 5.0 5.4 - - - +
323f ILE* 3.9 24.8 - - - +
341f LEU 3.2 19.6 + - - +
344f PRO* 3.4 44.6 - - + +
345f VAL* 3.3 14.2 - - - +
348f ASP* 5.3 0.2 - - + -
355f VAL 4.9 2.7 - - - +
356f ALA* 3.4 20.2 - - - +
358f VAL* 1.3 77.4 - - - +
360f ALA* 1.3 63.5 + - - +
362f ALA* 3.3 16.1 + - - +
363f CYS 3.9 3.8 + - - -
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Residues in contact with ALA 360 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345f VAL* 3.7 24.2 - - + -
350f LYS* 3.5 20.6 - - - +
356f ALA 3.6 5.1 + - - +
357f GLY 3.4 2.0 + - - +
358f VAL 3.1 0.8 - - - -
359f THR* 1.3 82.7 - - - +
361f LEU* 1.3 59.7 - - - +
362f ALA 3.7 0.2 + - - -
363f CYS* 4.3 3.3 + - - +
364f GLY* 4.1 9.7 + - - -
379f ILE* 6.1 1.0 - - - +
386f LYS* 3.9 4.0 - - - +
395f TYR* 2.8 35.6 + - + +
399f LEU* 5.4 0.7 - - - +
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Residues in contact with LEU 361 (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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320f LEU* 4.0 15.0 - - + -
324f PHE* 5.5 5.8 - - + -
353f MET* 4.0 13.9 - - + -
357f GLY 3.1 11.4 + - - +
358f VAL 2.7 17.1 + - - +
360f ALA* 1.3 71.3 - - - +
362f ALA* 1.3 63.7 + - - -
364f GLY* 3.1 3.4 + - - +
365f MET* 2.8 46.7 + - + +
395f TYR* 3.8 7.8 - - + -
398f TRP* 3.5 67.3 - - + +
401f LEU* 5.5 0.7 - - + -
693f VAL* 5.0 4.7 - - + -
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Residues in contact with ALA 362 (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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323f ILE* 4.3 11.9 - - + +
324f PHE* 5.3 3.4 - - - +
341f LEU* 3.6 27.6 - - + +
358f VAL 3.1 5.8 + - - +
359f THR* 3.3 21.4 + - - +
361f LEU* 1.3 75.3 - - - +
363f CYS* 1.3 58.4 + - - +
366f ILE* 2.8 51.9 + - + +
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Residues in contact with CYS 363 (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 VAL* 5.0 14.6 - - - -
341f LEU* 3.7 20.1 - - + +
342f LEU* 4.0 35.2 - - + +
345f VAL* 5.8 0.7 - - + -
359f THR 3.9 5.9 + - - +
360f ALA 4.9 4.5 - - - +
361f LEU 3.5 0.2 - - - -
362f ALA* 1.3 79.4 - - - +
364f GLY* 1.3 60.3 + - - +
367f ALA* 3.2 22.8 + - - +
375f VAL* 3.8 26.9 - - - -
378f THR* 5.7 1.3 - - - -
379f ILE* 3.9 9.7 - - + +
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Residues in contact with GLY 364 (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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360f ALA 4.1 6.2 + - - -
361f LEU* 3.1 8.6 + - - -
362f ALA 3.1 0.8 - - - -
363f CYS* 1.3 81.5 - - - +
365f MET* 1.3 62.2 + - - +
367f ALA* 3.4 12.1 - - - +
368f VAL 4.8 0.3 + - - -
379f ILE* 3.7 20.0 - - - +
399f LEU* 5.9 3.4 - - - -
401f LEU 4.4 0.5 - - - +
402f GLY* 3.4 27.0 - - - -
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Residues in contact with MET 365 (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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324f PHE* 3.5 31.4 - - + -
361f LEU* 2.8 33.7 + - + +
364f GLY* 1.3 68.8 - - - +
366f ILE* 1.3 61.3 + - - +
367f ALA 3.1 6.1 + - - -
368f VAL* 3.5 15.2 + - - +
398f TRP* 4.0 19.3 - - + -
401f LEU* 5.0 13.2 - - + +
402f GLY* 5.2 0.2 - - - -
405f LEU* 5.8 4.8 - - + +
672f VAL* 3.8 37.0 - - + -
693f VAL* 3.7 29.4 - - + +
694f VAL* 5.2 5.2 - - + -
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Residues in contact with ILE 366 (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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324f PHE* 3.2 53.2 - - + +
327f GLY* 3.6 22.0 - - - +
328f LEU* 3.4 34.3 - - + +
331f ALA* 4.2 15.4 - - + +
341f LEU* 4.2 8.1 - - + -
362f ALA* 2.8 38.6 + - + +
365f MET* 1.3 70.2 - - - +
367f ALA* 1.3 67.8 + - - +
368f VAL* 3.5 10.5 - - + +
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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