Contacts of the helix formed by residues 382 - 398 (chain A) in PDB entry 3I5Y
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 382 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A ALA 3.4 0.4 - - - -
381A PRO* 1.3 91.3 - - + +
383A VAL* 1.3 58.9 + - - +
384A LYS 4.2 1.3 - - - -
385A PHE* 3.0 25.1 + - - +
386A THR* 2.8 32.2 + - - -
433A THR* 3.6 6.7 - - - -
532A SER* 3.0 31.7 + - - +
533A LEU* 4.2 4.2 - - + +
536A SER* 3.7 25.6 - - - -
3B U 3.9 7.6 - - - +
4B 5BU 3.5 11.9 - - - -
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Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A THR* 1.3 71.0 - - - +
384A LYS* 1.3 61.8 + - + +
386A THR* 3.4 3.7 + - - -
387A SER* 3.0 29.3 + - - -
407A HIS* 3.6 33.7 - - + +
408A GLY 4.8 0.7 - - - +
409A LYS* 3.9 24.9 - - + -
433A THR* 3.8 6.4 - - + +
4B 5BU 2.8 25.7 + - - +
5B U 3.8 29.8 - - - +
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Residues in contact with LYS 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A THR* 3.3 1.6 + - - -
383A VAL* 1.3 85.7 - - + +
385A PHE* 1.3 57.0 + - - +
387A SER* 3.5 7.1 + - - -
388A PHE* 3.1 25.5 + - - +
528A ASP* 3.9 39.3 - - + +
529A ILE* 3.7 19.1 - - + +
532A SER* 4.0 13.2 - - - +
1B U 4.6 2.7 - - - -
2B U 3.8 18.3 - - - -
3B U 2.6 29.9 + - - +
4B 5BU 4.6 0.4 + - - -
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Residues in contact with PHE 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 4.3 10.3 - + - -
356A ILE* 3.9 37.0 - - + -
380A ALA* 3.6 22.9 - - + -
381A PRO* 3.6 9.6 - - + -
382A THR* 3.0 22.6 + - - +
384A LYS* 1.3 75.0 - - - +
386A THR* 1.3 55.9 + - - +
388A PHE* 3.3 14.3 + + - +
389A LEU* 2.8 45.8 + - + +
451A ILE* 3.9 22.9 - - + -
529A ILE* 3.8 24.2 - - + +
533A LEU* 3.8 25.1 - - + -
558A THR* 5.6 2.9 - - + -
562A LEU* 5.8 1.1 - - + -
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Residues in contact with THR 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ALA* 3.4 19.4 - - - +
382A THR 2.8 22.5 + - - -
383A VAL 3.5 5.6 - - - -
385A PHE* 1.3 76.9 - - - +
387A SER* 1.3 61.1 - - - +
389A LEU* 3.1 5.9 + - - +
390A CYS* 3.0 22.7 + - - -
405A GLU* 4.5 3.1 - - + -
406A PHE 4.4 0.2 - - - +
407A HIS* 3.8 19.1 - - + -
431A VAL* 3.7 31.6 - - + +
432A CYS* 3.9 10.7 - - - -
433A THR* 3.3 17.1 - - - +
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Residues in contact with SER 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL* 3.0 17.3 + - - -
384A LYS* 3.6 8.5 - - - -
385A PHE 3.3 0.2 - - - -
386A THR* 1.3 77.3 - - - +
388A PHE* 1.3 61.5 + - - +
390A CYS* 3.2 5.7 + - - +
391A SER* 3.2 20.6 + - - -
405A GLU* 2.8 32.5 + - - +
407A HIS* 4.4 1.9 + - - -
521A GLU* 5.8 0.4 - - - -
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Residues in contact with PHE 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 4.1 7.9 - - + -
384A LYS 3.1 11.0 + - - +
385A PHE* 3.4 28.0 - + - +
387A SER* 1.3 79.2 - - - +
389A LEU* 1.3 62.1 + - - +
391A SER* 3.2 9.4 + - - -
392A ILE* 3.2 42.9 + - + +
519A VAL* 4.0 21.3 - - + -
521A GLU* 4.1 22.7 - - - -
526A ILE* 3.9 17.3 - - + -
529A ILE* 3.8 26.9 - - + +
562A LEU* 3.8 41.5 - - + -
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Residues in contact with LEU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 4.7 9.0 - - + +
359A ALA* 5.9 0.7 - - + -
360A VAL* 6.2 0.4 - - + -
378A ILE* 3.8 29.2 - - + -
379A PHE 5.2 0.2 - - - -
380A ALA* 4.1 22.7 - - + -
385A PHE* 2.8 30.9 + - + +
386A THR 3.1 6.5 + - - +
388A PHE* 1.3 74.8 - - - +
390A CYS* 1.3 57.8 + - - +
392A ILE* 3.3 21.5 + - + +
393A LEU* 3.0 48.9 + - + +
431A VAL* 4.1 9.6 - - + -
451A ILE* 3.7 25.6 - - + -
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Residues in contact with CYS 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A THR 3.0 7.9 + - - -
387A SER 3.4 10.1 - - - +
388A PHE 3.2 0.2 - - - -
389A LEU* 1.3 73.2 - - - +
391A SER* 1.3 57.0 + - - +
393A LEU* 3.9 5.1 - - - +
394A LYS* 2.7 58.0 + - - +
403A ILE* 4.3 5.8 - - + +
404A LEU 4.1 1.3 - - - -
405A GLU* 3.5 37.2 - - + +
431A VAL* 3.4 35.4 - - - -
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Residues in contact with SER 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A SER 3.2 9.7 + - - -
388A PHE* 3.4 11.0 - - - -
390A CYS* 1.3 77.9 - - - +
392A ILE* 1.3 64.7 + - - +
394A LYS* 3.7 9.6 - - - +
395A ASN* 3.0 36.3 + - - -
519A VAL* 6.5 1.1 - - - -
520A THR* 5.3 3.5 + - - -
521A GLU* 3.6 27.5 + - - -
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Residues in contact with ILE 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 3.5 27.4 - - + -
360A VAL* 3.8 27.4 - - + -
388A PHE* 3.2 41.9 + - + +
389A LEU* 3.5 14.4 - - + +
391A SER* 1.3 77.0 - - - +
393A LEU* 1.3 62.4 + - + +
395A ASN* 3.1 9.5 + - - +
396A GLU* 3.0 32.7 + - + +
515A VAL* 3.9 22.9 - - + +
519A VAL* 4.7 9.9 - - + -
562A LEU* 5.7 1.1 - - + -
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Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ALA* 5.7 1.1 - - + -
360A VAL* 4.5 15.3 - - + +
363A ILE* 3.6 24.7 - - + -
378A ILE* 4.0 19.1 - - + -
389A LEU* 3.0 34.0 + - + +
390A CYS 3.9 2.5 - - - +
392A ILE* 1.3 74.4 - - + +
394A LYS* 1.3 56.1 + - - +
397A PHE* 2.7 59.3 + - + +
398A LYS 3.7 0.3 + - - -
403A ILE* 3.9 15.6 - - + +
429A ILE* 4.3 8.3 - - + -
431A VAL* 3.6 28.7 - - + -
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Residues in contact with LYS 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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390A CYS* 2.7 38.0 + - - +
391A SER* 3.7 8.0 - - - +
393A LEU* 1.3 70.5 - - - +
395A ASN* 1.3 67.3 + - - +
398A LYS* 2.9 49.4 + - + +
403A ILE* 3.9 36.5 + - + +
405A GLU* 3.9 26.3 + - - +
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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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391A SER* 3.0 24.0 + - - +
392A ILE* 3.1 9.1 + - - +
394A LYS* 1.3 78.0 - - - +
396A GLU* 1.3 63.4 + - + +
399A LYS* 5.9 1.4 - - - +
518A ALA* 3.5 43.6 + - + +
519A VAL* 4.7 2.6 - - - +
520A THR* 5.6 2.2 + - - +
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Residues in contact with GLU 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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360A VAL* 3.9 20.5 - - + +
364A LYS* 3.6 10.2 + - - -
392A ILE* 3.0 26.4 + - + +
393A LEU* 4.6 0.2 - - - -
394A LYS 3.9 0.2 - - - -
395A ASN* 1.3 80.6 - - + +
397A PHE* 1.3 85.9 + - + +
398A LYS 3.9 0.2 - - - -
399A LYS* 4.1 17.4 + - - +
400A ASP* 4.1 6.2 - - - +
514A GLU* 2.8 45.9 - - - +
515A VAL* 3.8 18.1 - - + +
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Residues in contact with PHE 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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360A VAL* 3.3 36.8 - - + -
363A ILE* 3.4 23.3 - - + -
364A LYS* 3.4 36.6 - - + -
367A ILE* 3.3 21.8 - - + -
393A LEU* 2.7 44.7 + - + +
396A GLU* 1.3 97.4 - - + +
398A LYS* 1.3 65.6 + - - +
399A LYS 3.1 3.4 - - - -
400A ASP* 2.8 21.1 + - - -
401A LEU* 2.9 14.4 + - + +
403A ILE* 4.2 10.3 - - + -
429A ILE* 4.8 2.9 - - + -
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Residues in contact with LYS 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU 3.7 2.0 + - - -
394A LYS* 2.9 42.3 + - + +
395A ASN 5.1 0.2 + - - -
397A PHE* 1.3 75.9 - - - +
399A LYS* 1.3 61.8 + - - +
400A ASP 3.3 0.2 + - - -
401A LEU 3.1 24.2 + - - +
402A PRO* 5.7 1.1 - - + -
403A ILE* 4.5 6.7 - - + +
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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
------------------------------------------------------------
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