Contacts of the helix formed by residues 364 - 377 (chain J) in PDB entry 5XTE
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 ILE 364 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360J THR* 2.9 37.9 + - + +
363J LEU* 1.3 83.7 - - + +
365J LEU* 1.3 76.4 + - + +
367J PRO* 3.4 6.9 - - - +
368J THR* 3.3 28.7 - - + +
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Residues in contact with LEU 365 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324J LEU* 4.2 26.5 - - + -
327J LEU* 5.8 0.9 - - + -
357J LEU* 6.0 0.9 - - + -
360J THR* 2.9 24.7 + - - +
361J THR* 3.8 33.4 - - + +
364J ILE* 1.3 82.4 - - + +
366J MET* 1.3 64.0 + - - +
368J THR* 2.5 25.0 + - - +
369J ILE* 3.3 15.1 + - + +
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Residues in contact with MET 366 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315J MET* 4.9 12.8 - - + +
318J ARG* 4.9 2.2 - - - -
321J SER* 3.8 42.8 - - - +
324J LEU* 4.3 21.1 - - + +
325J TYR* 4.8 8.5 - - + +
328J LEU* 6.3 2.7 - - + -
361J THR* 3.5 18.1 + - - +
362J ILE* 5.0 6.1 - - - +
365J LEU* 1.3 79.5 - - - +
367J PRO* 1.4 69.6 - - + +
369J ILE* 3.4 1.2 + - - +
370J SER* 2.8 33.8 + - - +
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Residues in contact with PRO 367 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307J LEU* 3.8 28.3 - - + +
309J MET* 3.9 21.9 - - + +
362J ILE 4.9 1.3 - - - +
363J LEU 3.2 28.3 - - - +
364J ILE 3.4 6.5 - - - +
366J MET* 1.4 94.8 - - + +
368J THR* 1.3 57.8 + - + +
370J SER* 3.2 10.3 + - - +
371J LEU* 2.9 34.3 + - + +
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Residues in contact with THR 368 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364J ILE* 3.3 22.2 + - + +
365J LEU* 2.5 26.9 + - - +
367J PRO* 1.3 78.2 - - + +
369J ILE* 1.3 65.1 + - - +
371J LEU* 3.0 16.5 + - + +
372J ILE* 2.9 33.0 + - - +
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Residues in contact with ILE 369 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320J LEU* 3.7 44.6 - - + +
321J SER* 4.5 3.6 - - - +
324J LEU* 3.5 33.0 - - + -
365J LEU* 3.3 15.9 + - + +
366J MET 4.2 2.2 - - - +
368J THR* 1.3 83.2 + - - +
370J SER* 1.3 60.1 + - - +
372J ILE* 4.0 19.3 - - + -
373J GLU* 2.9 34.2 + - - +
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Residues in contact with SER 370 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308J HIS* 5.7 0.9 + - - -
309J MET* 4.0 4.5 + - - -
310J SER* 3.7 28.6 + - - -
318J ARG* 4.2 13.3 + - - -
321J SER* 4.5 1.1 + - - -
366J MET* 2.8 28.6 + - - +
367J PRO* 3.2 13.9 - - - +
368J THR 3.1 0.2 - - - -
369J ILE* 1.3 79.0 - - - +
371J LEU* 1.3 56.8 + - - +
373J GLU* 3.5 10.6 + - - +
374J ASN* 2.9 35.0 + - - +
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Residues in contact with LEU 371 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309J MET* 3.9 33.0 - - + -
367J PRO* 2.9 20.0 + - + +
368J THR* 3.0 16.6 + - + +
370J SER* 1.3 74.9 - - - +
372J ILE* 1.3 61.1 + - + +
374J ASN* 3.0 21.1 + - + +
375J LYS* 2.9 42.5 + - - +
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Residues in contact with ILE 372 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320J LEU* 5.0 13.7 - - + -
368J THR* 2.9 24.2 + - - +
369J ILE* 3.8 23.6 - - + +
371J LEU* 1.3 76.1 - - + +
373J GLU* 1.3 58.6 + - - +
375J LYS* 3.1 10.8 + - + +
376J MET* 2.9 47.3 + - + +
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Residues in contact with GLU 373 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F TYR* 3.2 31.5 + - + +
318J ARG* 3.1 37.1 + - - +
320J LEU* 3.1 19.1 + - + +
321J SER* 3.1 36.5 + - - -
369J ILE* 2.9 25.4 + - + +
370J SER* 3.8 5.3 - - - +
372J ILE* 1.3 74.7 - - + +
374J ASN* 1.3 66.6 + - - +
375J LYS 3.4 0.2 + - - -
376J MET* 3.5 12.3 + - - +
377J LEU* 3.6 22.0 + - - +
379J TRP* 4.5 2.0 - - + -
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Residues in contact with ASN 374 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309J MET 3.0 27.7 + - - -
310J SER* 3.5 3.8 + - - +
311J LYS* 3.2 22.7 + - + +
370J SER 2.9 26.3 + - - +
371J LEU* 3.0 23.8 + - + +
373J GLU* 1.3 79.8 - - - +
375J LYS* 1.3 59.0 + - + +
377J LEU 3.9 0.3 + - - -
378J LYS 3.7 1.9 + - - -
379J TRP* 3.1 66.4 + - + +
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Residues in contact with LYS 375 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ARG* 3.5 21.7 + - - +
371J LEU* 2.9 27.0 + - - +
372J ILE* 3.1 10.1 + - + +
374J ASN* 1.3 79.1 - - + +
376J MET* 1.3 64.6 + - - +
377J LEU 3.1 1.8 - - - -
378J LYS* 3.2 11.4 + - - +
379J TRP 4.7 8.7 - - - +
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Residues in contact with MET 376 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LEU* 5.8 2.9 - - - -
17F ILE* 3.6 47.8 - - + +
18F ARG* 3.2 40.9 - - + +
20F TRP* 5.0 4.7 - - + -
21F TYR* 3.8 37.0 - - + -
320J LEU* 6.0 1.6 - - + -
372J ILE* 2.9 36.4 + - + +
373J GLU* 4.0 7.4 - - - +
374J ASN 3.5 0.2 - - - -
375J LYS* 1.3 78.7 - - - +
377J LEU* 1.3 62.2 + - - +
378J LYS* 3.3 0.8 - - - +
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Residues in contact with LEU 377 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ARG 5.6 0.7 - - - +
21F TYR* 3.6 39.5 - - + +
22F TYR* 4.6 15.0 - - + -
25F ALA* 5.5 0.2 - - + -
27F PHE* 4.4 22.9 - - + -
34F ARG* 3.0 37.1 + - + +
89F PHE* 5.5 0.3 - - - -
312J GLN* 4.0 12.6 - - - +
317J PHE 5.7 0.9 - - - +
318J ARG* 6.5 0.2 - - + -
373J GLU 3.6 10.9 + - - +
374J ASN 3.9 0.2 + - - -
375J LYS 3.1 0.2 - - - -
376J MET* 1.3 79.8 - - - +
378J LYS* 1.3 72.2 + - - +
379J TRP* 3.6 38.1 + - + -
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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