Contacts of the helix formed by residues 393 - 412 (chain A) in PDB entry 4LEY
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 CYS 393 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A CYS* 1.3 71.7 - - - +
394A ARG* 1.3 57.5 + - - +
396A GLU* 3.5 14.0 - - + +
397A CYS* 3.0 38.3 + - - -
440A TRP* 2.6 43.1 + - - +
441A ASP 3.8 4.7 - - - -
442A PRO* 4.1 16.6 - - + -
444A ASN* 4.3 2.7 - - - -
445A LEU* 3.9 18.2 - - + -
448A CYS* 3.8 20.2 - - - -
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Residues in contact with ARG 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A TRP* 3.6 9.5 - - - +
378A HIS* 3.7 27.9 + - + -
379A GLY* 3.7 8.7 - - - -
384A CYS* 3.9 0.2 - - - -
392A CYS* 3.3 31.7 - - - +
393A CYS* 1.3 76.7 - - - +
395A LYS* 1.3 60.2 + - + +
397A CYS* 3.2 5.5 + - - +
398A LEU* 3.0 23.2 + - - +
427A ILE* 3.7 7.1 - - - +
431A TRP* 3.4 43.9 + - + +
434A ASP 4.1 1.6 + - - -
435A PRO 2.8 29.7 + - - -
436A GLN 3.9 1.0 + - - -
437A ASP* 2.4 33.3 + - - +
440A TRP* 3.6 41.5 - - + -
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Residues in contact with LYS 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU 3.4 23.5 + - - +
203A HIS* 3.5 29.4 - - + +
204A VAL* 3.8 16.7 - - + +
375A LEU* 3.3 34.8 + - + -
376A ASN* 4.2 4.8 + - - +
378A HIS* 4.1 21.4 - - + +
385A CYS* 6.4 0.7 - - - -
392A CYS* 4.9 1.0 - - - -
393A CYS 3.6 0.2 - - - -
394A ARG* 1.3 79.6 - - + +
396A GLU* 1.3 70.7 + - - +
398A LEU* 3.3 9.1 + - - +
399A LYS* 2.9 34.5 + - + +
431A TRP* 5.2 1.8 - - + -
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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
----------------------------------------------------------
154A LEU* 3.7 33.6 - - + +
158A ARG* 5.8 1.6 + - - -
385A CYS* 5.5 3.3 - - - -
392A CYS* 3.5 15.1 - - - +
393A CYS* 3.5 26.5 - - + +
395A LYS* 1.3 86.9 + - - +
397A CYS* 1.3 57.3 + - - +
399A LYS* 3.2 12.2 + - - +
400A LEU* 2.9 33.6 + - - +
445A LEU* 4.1 6.7 - - + -
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Residues in contact with CYS 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A CYS* 3.0 37.4 + - - +
394A ARG 3.4 4.7 - - - +
396A GLU* 1.3 72.7 - - - +
398A LEU* 1.3 65.5 + - - +
400A LEU* 3.3 9.4 + - - +
401A MET* 2.9 25.1 + - - +
427A ILE* 4.2 10.5 - - + -
440A TRP* 4.1 9.0 - - + -
445A LEU* 3.8 17.2 - - - +
448A CYS* 3.9 5.2 - - - -
449A PHE* 3.8 31.5 - - - -
452A LEU* 4.2 9.3 - - + +
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Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU* 5.5 0.7 - - - +
204A VAL* 3.7 30.1 - - + -
375A LEU* 4.0 18.8 - - + -
394A ARG 3.0 9.9 + - - +
395A LYS* 3.4 11.0 - - - +
397A CYS* 1.3 77.3 - - - +
399A LYS* 1.3 55.3 + - - +
401A MET* 3.5 2.7 - - + +
402A LYS* 2.9 46.6 + - + +
423A VAL* 3.9 24.7 - - + +
424A LYS* 4.3 16.4 - - + -
427A ILE* 3.6 39.8 - - + +
431A TRP* 4.7 1.8 - - + -
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Residues in contact with LYS 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 4.3 19.9 + - + +
157A LEU* 4.3 7.9 + - + -
158A ARG* 4.7 24.7 - - - +
159A LEU* 5.3 1.6 - - - +
203A HIS 3.6 23.7 + - - -
204A VAL* 4.1 13.9 - - - +
205A LYS 4.3 12.6 + - - -
206A ILE* 3.8 23.9 - - + +
395A LYS* 2.9 21.6 + - - +
396A GLU* 3.2 15.5 + - - +
398A LEU* 1.3 75.9 - - - +
400A LEU* 1.3 57.8 + - - +
402A LYS* 3.2 7.2 + - - +
403A TYR* 2.9 30.8 + - - +
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Residues in contact with LEU 400 (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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150A LEU* 3.7 36.3 - - + +
153A VAL* 3.6 33.7 - - + -
154A LEU* 3.7 19.5 - - + -
157A LEU* 4.5 1.8 - - + -
396A GLU 2.9 22.6 + - - +
397A CYS* 3.7 2.2 - - - +
399A LYS* 1.3 71.9 - - - +
401A MET* 1.3 57.5 + - - +
403A TYR* 3.3 6.0 + - - +
404A LEU* 2.9 29.6 + - - +
445A LEU* 4.1 19.5 - - + -
449A PHE* 3.6 27.6 - - + -
504A PHE* 3.9 11.1 - - + -
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Residues in contact with MET 401 (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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397A CYS 2.9 18.1 + - - +
398A LEU* 3.5 4.9 - - - +
400A LEU* 1.3 75.5 - - - +
402A LYS* 1.3 63.4 + - - +
404A LEU* 3.2 17.8 + - + +
405A LEU* 3.0 23.6 + - - +
423A VAL* 3.8 27.1 - - + -
449A PHE* 3.7 7.5 - - - -
452A LEU* 3.8 21.5 - - + -
453A LEU* 3.6 39.3 - - + +
456A PHE* 4.0 39.5 - - + -
493A ILE* 5.3 4.3 - - + -
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Residues in contact with LYS 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER* 2.8 27.2 + - - -
204A VAL* 3.1 29.1 - - + +
205A LYS* 5.1 2.1 - - - +
206A ILE* 4.1 11.9 - - + -
398A LEU* 2.9 41.0 + - + +
399A LYS* 3.6 4.5 - - - +
401A MET* 1.3 75.5 - - - +
403A TYR* 1.3 57.6 + - - +
405A LEU* 3.5 5.4 + - - +
406A GLU* 2.9 42.6 + - + +
420A SER* 4.0 28.1 + - - +
423A VAL* 3.9 20.2 - - + -
424A LYS* 6.5 0.4 - - + -
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Residues in contact with TYR 403 (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 VAL* 4.1 10.3 - - + -
156A LYS* 3.2 27.1 + - - -
157A LEU* 3.5 42.4 - - + -
206A ILE* 3.5 15.7 - - + +
207A SER* 4.1 9.2 - - - -
399A LYS 2.9 16.8 + - - +
400A LEU* 3.6 3.4 - - - +
402A LYS* 1.3 74.7 - - - +
404A LEU* 1.3 65.5 + - - +
406A GLU* 3.1 7.9 + - + +
407A GLN* 2.9 63.9 + - + +
504A PHE* 3.5 44.5 + + + -
507A LEU* 4.6 7.5 - - + +
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Residues in contact with LEU 404 (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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400A LEU 2.9 11.5 + - - +
401A MET* 3.5 28.3 - - + +
403A TYR* 1.3 75.8 - - - +
405A LEU* 1.3 60.3 + - + +
407A GLN* 3.4 2.8 + - - +
408A LEU* 3.0 43.0 + - + +
449A PHE* 5.1 0.9 - - + -
453A LEU* 4.6 7.6 - - + -
493A ILE* 4.5 30.7 - - + -
496A GLU* 4.3 20.4 - - + -
501A PHE* 4.5 8.1 - - + -
503A ILE* 4.0 15.9 - - + -
504A PHE* 3.4 33.0 - - + -
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Residues in contact with LEU 405 (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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401A MET 3.0 16.4 + - - +
402A LYS 3.8 4.9 - - - +
404A LEU* 1.3 78.3 - - + +
406A GLU* 1.3 57.1 + - + +
408A LEU* 3.7 3.3 - - + +
409A LYS* 2.9 42.8 + - + +
415A LEU* 4.9 4.7 - - + -
418A PHE* 4.3 18.2 - - + -
419A CYS* 3.4 39.0 - - - +
420A SER* 4.2 3.6 - - - +
422A HIS* 5.6 1.1 - - + -
423A VAL* 3.6 21.8 - - + -
456A PHE* 5.6 4.7 - - + -
489A LEU* 4.4 23.8 - - + -
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Residues in contact with GLU 406 (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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205A LYS* 5.4 5.1 + - - -
206A ILE* 3.3 35.0 - - - +
207A SER* 4.8 4.3 + - - -
211A GLU* 5.2 5.5 - - - +
402A LYS* 2.9 31.1 + - + +
403A TYR* 3.1 11.0 + - + +
405A LEU* 1.3 73.9 - - + +
407A GLN* 1.3 67.7 + - - +
409A LYS* 3.2 5.9 + - - +
410A LYS* 2.9 28.5 + - + +
420A SER* 6.3 2.7 - - - -
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Residues in contact with GLN 407 (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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403A TYR* 2.9 61.0 + - + +
404A LEU* 3.7 3.6 - - - +
406A GLU* 1.3 75.3 - - - +
408A LEU* 1.3 64.2 + - - +
410A LYS* 3.1 36.8 + - - +
411A GLU* 3.0 23.7 + - - +
503A ILE* 2.7 49.6 + - + +
506A LYS* 4.0 18.0 + - - +
507A LEU* 3.6 7.3 - - - +
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Residues in contact with LEU 408 (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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404A LEU* 3.0 33.8 + - + +
405A LEU* 3.7 6.3 - - + +
407A GLN* 1.3 75.3 - - - +
409A LYS* 1.3 57.8 + - - +
411A GLU* 3.1 1.9 + - - -
412A PHE* 2.9 44.9 + - + -
415A LEU* 3.5 14.3 - - + +
489A LEU* 3.9 24.7 - - + -
492A LYS* 4.0 26.5 - - + -
493A ILE* 4.3 14.4 - - + +
496A GLU* 4.6 13.7 - - + +
503A ILE* 3.6 20.6 - - + -
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Residues in contact with LYS 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A LEU* 2.9 26.9 + - + +
406A GLU* 3.7 5.2 - - - +
407A GLN 3.2 0.2 - - - -
408A LEU* 1.3 76.7 - - - +
410A LYS* 1.3 59.3 + - - +
412A PHE 3.0 21.4 - - - +
413A GLN* 5.1 0.2 - - - -
415A LEU* 3.5 27.4 - - + +
416A ASP* 3.5 26.1 + - - +
418A PHE* 2.2 37.2 + - + +
419A CYS* 4.1 9.9 - - - +
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Residues in contact with LYS 410 (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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406A GLU 2.9 15.0 + - - +
407A GLN* 3.1 38.4 - - - +
409A LYS* 1.3 76.3 - - - +
411A GLU* 1.3 61.6 + - + +
412A PHE 3.5 0.2 - - - -
506A LYS* 6.4 0.2 - - - -
507A LEU* 3.2 40.9 - - - +
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Residues in contact with GLU 411 (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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407A GLN 3.0 14.1 + - - +
408A LEU* 3.1 5.6 + - - +
410A LYS* 1.3 82.0 - - + +
412A PHE* 1.3 91.1 + - + +
503A ILE* 3.6 13.0 - - - +
506A LYS* 2.9 38.3 + - - +
433B GLN* 5.2 2.6 - - - +
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Residues in contact with PHE 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU* 2.9 31.4 + - + +
409A LYS 3.0 19.4 - - - +
410A LYS 3.5 0.8 - - - -
411A GLU* 1.3 110.9 - - + +
413A GLN* 1.3 63.3 + - - +
414A GLU* 3.4 14.9 + - - +
415A LEU* 3.5 17.1 + - + +
416A ASP* 4.7 0.3 - - - +
488A PHE* 4.1 26.0 - + + -
492A LYS* 3.2 41.3 - - + -
503A ILE* 5.7 0.2 - - + -
506A LYS* 6.0 0.2 - - - -
433B GLN* 5.1 7.2 - - - -
439B GLN* 5.5 0.2 - - - -
451B LYS* 3.4 33.7 - - - -
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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
------------------------------------------------------------
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