Contacts of the helix formed by residues 386 - 399 (chain A) in PDB entry 5TF6
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 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A LEU* 5.5 4.9 - - - -
314A ILE* 5.4 1.8 - - - +
315A CYS* 3.9 3.3 - - - -
369A LEU* 6.1 2.9 - - + -
385A GLY* 1.3 79.1 - - - +
387A ILE* 1.3 64.8 + - - +
388A ASN 3.4 4.2 + - - -
389A ASP* 2.8 19.7 + - - +
390A MET* 3.1 19.1 + - - +
504A GOL 2.9 42.1 + - - +
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Residues in contact with ILE 387 (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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301A LEU 3.8 23.3 - - - +
302A LEU* 3.9 18.8 - - + +
310A LEU* 4.0 21.8 - - + -
313A LEU* 4.2 17.0 - - + +
315A CYS* 3.7 21.7 - - - -
356A ILE* 4.4 15.9 - - + -
386A THR* 1.3 74.1 - - - +
388A ASN* 1.3 62.7 + - - +
390A MET* 2.8 22.9 + - + +
391A LYS* 2.9 40.2 + - + +
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Residues in contact with ASN 388 (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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386A THR* 3.3 2.2 + - - -
387A ILE* 1.3 80.6 - - - +
389A ASP* 1.3 58.4 + - - +
391A LYS* 3.2 19.9 + - - +
392A ARG* 2.9 45.3 + - - +
504A GOL 3.1 35.3 + - - -
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Residues in contact with ASP 389 (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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317A PHE* 3.8 9.9 - - + -
385A GLY* 3.2 14.4 - - - -
386A THR* 2.8 42.2 + - - +
387A ILE 3.1 0.2 - - - -
388A ASN* 1.3 78.2 - - - +
390A MET* 1.3 63.0 + - - +
392A ARG* 2.7 33.4 + - - +
393A TYR* 3.0 24.1 + - - +
504A GOL 2.9 6.3 + - - -
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Residues in contact with MET 390 (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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302A LEU* 4.5 12.6 - - + -
315A CYS* 3.8 29.2 - - + -
317A PHE* 3.6 31.3 - - + +
349A VAL* 3.9 28.5 - - + -
352A PHE* 3.9 24.5 - - + +
354A GLY* 3.7 27.1 - - - -
355A ALA 4.1 3.8 - - - -
356A ILE* 4.8 0.7 - - + -
386A THR 3.1 8.6 + - - +
387A ILE* 2.8 20.2 + - + +
389A ASP* 1.3 77.6 - - - +
391A LYS* 1.3 55.4 + - + +
393A TYR* 3.3 3.6 + - - +
394A TYR* 3.0 26.7 + - - +
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Residues in contact with LYS 391 (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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302A LEU* 4.1 22.0 + - - +
352A PHE* 4.0 47.0 - - + -
387A ILE* 2.9 34.1 + - + +
388A ASN* 3.6 21.1 + - - +
390A MET* 1.3 73.3 - - + +
392A ARG* 1.3 56.9 + - - +
394A TYR* 3.0 2.3 + - - +
395A ASN* 2.7 47.6 + - - +
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Residues in contact with ARG 392 (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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388A ASN* 2.9 25.7 + - - +
389A ASP* 2.7 41.4 + - - +
391A LYS* 1.3 76.7 - - - +
393A TYR* 1.3 64.8 + - - +
395A ASN* 4.0 8.2 - - - +
396A ASN* 3.1 25.5 + - - +
504A GOL 2.9 30.0 + - - -
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Residues in contact with TYR 393 (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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317A PHE* 3.6 29.8 - + + -
318A PRO* 3.7 39.2 - - + +
352A PHE 5.9 1.6 - - - -
383A ARG* 4.0 23.2 - - - -
389A ASP 3.0 15.7 + - - +
390A MET 3.6 3.6 - - - +
392A ARG* 1.3 83.7 - - - +
394A TYR* 1.3 60.0 + - + +
396A ASN* 3.9 6.9 + - - +
397A GLN* 3.0 56.9 + - + +
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Residues in contact with TYR 394 (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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153A ARG* 5.6 2.9 + - - -
351A ASP 3.5 18.6 + - - -
352A PHE* 3.7 42.8 - + + +
353A ASN* 3.2 33.7 - - - -
390A MET 3.0 15.3 + - - +
391A LYS 3.0 4.5 + - - +
393A TYR* 1.3 75.7 - - - +
395A ASN* 1.3 65.7 + - - +
396A ASN 3.0 1.3 - - - -
397A GLN* 2.7 30.3 + - + +
398A GLN* 3.1 45.7 + - + +
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Residues in contact with ASN 395 (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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352A PHE* 4.8 8.3 - - - -
391A LYS* 2.7 35.6 + - - +
392A ARG* 4.1 6.5 + - - +
394A TYR* 1.3 80.7 - - - +
396A ASN* 1.3 57.0 + - - +
398A GLN* 3.2 27.9 + - - +
399A ASN* 3.3 14.5 + - - +
83B A 5.2 8.0 + - - +
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Residues in contact with ASN 396 (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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392A ARG 3.1 18.0 + - - +
393A TYR* 4.0 6.5 + - - +
394A TYR 3.0 1.0 - - - -
395A ASN* 1.3 74.4 - - - +
397A GLN* 1.3 79.9 + - - +
398A GLN 3.3 0.5 + - - -
399A ASN* 3.6 27.2 + - - +
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Residues in contact with GLN 397 (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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353A ASN* 5.7 3.6 - - - +
393A TYR* 3.0 53.5 + - + +
394A TYR* 2.7 18.0 + - + +
396A ASN* 1.3 89.6 - - - +
398A GLN* 1.3 65.9 + - - +
399A ASN 4.0 3.8 - - - +
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Residues in contact with GLN 398 (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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394A TYR* 3.1 50.8 + - + +
395A ASN* 3.2 15.4 + - - +
397A GLN* 1.3 79.2 - - - +
399A ASN* 1.3 68.0 + - - +
82B A 4.0 36.9 + - - +
83B A 4.3 18.6 + - - +
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Residues in contact with ASN 399 (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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395A ASN* 3.3 15.0 + - - +
396A ASN* 3.6 26.2 + - - +
397A GLN 4.0 3.5 - - - +
398A GLN* 1.3 84.7 - - - +
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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