Contacts of the helix formed by residues 383 - 399 (chain A) in PDB entry 5TDE
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 ASN 383 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A ASN* 3.2 29.1 + - - +
351A ALA* 3.6 23.0 + - + +
381A GLY 3.2 1.4 + - - -
382A PRO* 1.3 75.4 - - - +
384A TYR* 1.3 64.8 + - - +
385A GLN 3.2 3.9 + - - +
386A GLU* 3.3 7.4 + - + +
387A GLY 3.2 15.6 + - - -
642B MET* 4.4 10.5 - - - +
644B ASP* 5.8 0.8 + - - -
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Residues in contact with TYR 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A VAL* 3.7 19.7 - - + +
379A ARG 3.6 16.4 - - - +
380A GLY* 3.8 10.3 - - - -
381A GLY 3.0 39.0 + - - +
382A PRO 3.2 0.4 - - - -
383A ASN* 1.3 77.3 - - - +
385A GLN* 1.3 94.6 + - + +
387A GLY* 3.5 0.3 - - - -
388A LEU* 2.8 41.9 + - + +
407A THR* 3.8 24.4 + - + +
431A GLN 3.6 20.3 + - - -
644B ASP* 5.1 9.9 - - - -
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Residues in contact with GLN 385 (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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383A ASN 3.2 1.2 - - - -
384A TYR* 1.3 117.6 + - + +
386A GLU* 1.3 58.7 + - - +
388A LEU* 3.3 4.1 + - - +
389A ARG* 3.0 26.7 + - - +
430A PHE* 2.7 34.1 + - - +
431A GLN* 3.9 4.0 + - - +
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Residues in contact with GLU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ALA* 4.1 15.7 - - + -
355A LYS* 4.2 18.6 + - - +
383A ASN* 3.3 11.0 + - + +
384A TYR 3.3 0.4 - - - -
385A GLN* 1.3 76.0 - - - +
387A GLY* 1.3 66.4 + - - +
389A ARG* 2.8 47.3 + - - -
390A VAL* 3.0 30.5 + - - +
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Residues in contact with GLY 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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350A VAL* 4.0 3.1 - - - -
351A ALA* 4.0 13.1 - - - +
354A PHE* 3.6 27.0 - - - -
383A ASN 3.2 9.2 + - - -
384A TYR 3.1 7.2 + - - -
386A GLU* 1.3 76.0 - - - +
388A LEU* 1.3 60.9 + - - +
390A VAL* 3.2 19.9 - - - +
391A MET* 3.2 13.7 + - - +
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Residues in contact with LEU 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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350A VAL* 5.7 0.2 - - + -
354A PHE* 4.2 9.4 - - + -
377A VAL* 4.2 13.5 - - + -
379A ARG* 4.1 10.1 - - + +
384A TYR* 2.8 37.3 + - + +
385A GLN* 3.7 6.5 - - - +
387A GLY* 1.3 73.4 - - - +
389A ARG* 1.3 62.0 + - - +
391A MET* 3.3 4.2 + - - +
392A GLY 3.0 18.9 + - - -
404A VAL* 3.6 20.7 - - + +
405A PHE 3.5 20.4 - - - +
406A GLY* 3.7 27.1 - - - +
430A PHE* 3.6 36.5 - - + +
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Residues in contact with ARG 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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385A GLN 3.0 14.6 + - - +
386A GLU* 2.8 46.2 + - - +
388A LEU* 1.3 77.9 - - - +
390A VAL* 1.3 70.7 + - - +
392A GLY* 3.2 2.3 + - - +
393A GLU* 2.9 53.5 + - - +
396A LYS* 5.5 0.7 + - - +
430A PHE* 4.6 8.7 - - + -
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Residues in contact with VAL 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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354A PHE 4.4 5.8 - - - -
355A LYS* 4.2 28.7 - - + -
358A VAL* 3.6 30.4 - - + +
362A ARG* 5.1 0.5 + - - -
386A GLU* 3.0 37.4 + - - +
387A GLY* 3.2 20.0 - - - +
389A ARG* 1.3 87.4 - - - +
391A MET* 1.3 56.8 + - - +
393A GLU* 3.8 7.1 - - + +
394A VAL* 3.0 24.4 + - - +
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Residues in contact with MET 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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340A ILE* 4.1 11.4 - - + -
354A PHE* 3.7 42.6 - - + +
357A ILE* 3.7 33.0 - - + -
358A VAL* 3.9 11.9 - - + -
361A ILE* 4.3 14.6 - - - -
377A VAL* 4.1 16.4 - - + -
387A GLY 3.2 14.0 + - - +
388A LEU* 3.5 9.0 - - - +
389A ARG 3.2 0.4 - - - -
390A VAL* 1.3 74.1 - - - +
392A GLY* 1.3 64.6 + - - +
394A VAL* 3.4 6.8 - - - +
395A GLY* 3.3 16.8 + - - -
402A ILE* 3.8 11.8 - - + +
404A VAL* 3.9 17.7 - - + -
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Residues in contact with GLY 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 LEU 3.0 14.0 + - - -
389A ARG 3.7 2.9 - - - -
391A MET* 1.3 76.2 - - - +
393A GLU* 1.3 61.8 + - - +
395A GLY* 3.4 2.9 + - - -
396A LYS* 3.2 33.6 + - - +
402A ILE* 5.4 3.1 - - - -
404A VAL* 3.9 9.5 - - - +
430A PHE* 4.2 19.3 - - - -
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Residues in contact with GLU 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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362A ARG* 4.5 7.4 - - - +
389A ARG* 2.9 37.1 + - - +
390A VAL* 3.8 7.9 - - - +
391A MET 3.2 0.4 - - - -
392A GLY* 1.3 75.2 - - - +
394A VAL* 1.3 60.2 + - - +
396A LYS* 3.1 30.7 + - - +
397A THR* 2.9 45.5 + - + +
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Residues in contact with VAL 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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358A VAL* 3.8 26.5 - - + +
361A ILE* 4.2 16.4 - - + -
362A ARG* 3.5 42.5 - - + +
390A VAL 3.0 15.2 + - - +
391A MET* 3.4 12.6 - - - +
393A GLU* 1.3 76.2 - - - +
395A GLY* 1.3 63.9 + - - +
397A THR* 3.5 4.3 - - - -
398A THR* 2.8 42.2 + - + +
402A ILE* 3.7 14.8 - - + -
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Residues in contact with GLY 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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391A MET 3.3 5.6 + - - -
392A GLY 3.4 3.8 + - - -
393A GLU 3.2 1.0 - - - -
394A VAL* 1.3 83.5 - - - +
396A LYS* 1.3 56.1 + - - +
398A THR* 3.9 1.8 - - - -
399A GLY* 2.9 31.2 + - - -
400A ILE 3.4 22.0 - - - +
402A ILE* 3.7 16.6 - - - -
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Residues in contact with LYS 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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389A ARG* 5.5 0.8 + - - +
392A GLY* 3.2 21.0 + - - +
393A GLU* 3.1 34.2 + - - +
395A GLY* 1.3 78.3 - - - +
397A THR* 1.3 63.5 + - + +
399A GLY* 3.7 5.7 + - - -
430A PHE* 4.6 17.2 - - - -
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Residues in contact with THR 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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362A ARG* 3.1 31.9 + - - +
365A GLN* 4.8 2.1 - - - +
393A GLU* 2.9 30.2 + - + +
394A VAL* 3.2 9.5 + - - -
396A LYS* 1.3 78.5 - - + +
398A THR* 1.3 63.8 + - - +
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Residues in contact with THR 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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361A ILE* 5.0 0.6 - - + +
362A ARG* 4.7 5.8 - - + +
365A GLN* 3.7 38.4 - - + +
369A LYS* 2.7 33.3 + - - +
394A VAL* 2.8 38.4 + - + +
397A THR* 1.3 80.9 - - - +
399A GLY* 1.3 57.5 + - - +
400A ILE* 3.0 37.4 + - + +
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Residues in contact with GLY 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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369A LYS* 4.5 8.6 - - - +
395A GLY 2.9 12.0 + - - -
396A LYS 3.7 5.3 + - - -
397A THR 3.5 2.2 - - - -
398A THR* 1.3 77.0 - - - +
400A ILE* 1.3 62.5 + - - +
401A PRO* 3.6 6.8 - - - +
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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