Contacts of the helix formed by residues 393 - 412 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B CYS* 1.3 73.9 - - - +
394B ARG* 1.3 58.6 + - - +
396B GLU* 3.2 15.5 - - + +
397B CYS* 3.0 31.2 + - - -
440B TRP* 2.9 20.4 + - - -
441B ASP 3.4 23.3 - - - -
442B PRO* 3.9 16.2 - - + -
445B LEU* 3.9 26.5 - - + -
448B CYS* 4.1 20.0 - - - -
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Residues in contact with ARG 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B TRP* 4.0 4.9 - - - +
378B HIS* 3.3 40.1 + - + +
384B CYS* 3.6 19.6 - - - -
392B CYS* 3.5 16.9 - - - +
393B CYS* 1.3 74.6 - - - +
395B LYS* 1.3 68.0 + - + +
397B CYS* 3.0 6.8 + - - +
398B LEU 2.9 18.4 + - - -
427B ILE* 3.7 0.3 - - - +
431B TRP* 3.5 51.6 - - + +
434B ASP 4.2 0.6 + - - -
435B PRO 2.9 29.5 + - - -
436B GLN 3.7 1.0 + - - -
437B ASP* 2.9 26.1 + - - +
440B TRP* 3.6 39.4 - - + +
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Residues in contact with LYS 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLU 3.2 26.7 + - - +
203B HIS* 4.1 17.7 - - + +
204B VAL* 3.9 15.3 - - + +
375B LEU* 3.1 39.4 + - + -
376B ASN* 3.4 13.7 + - - +
378B HIS* 4.4 20.7 - - + +
385B CYS* 6.2 0.2 - - - -
391B LYS* 5.4 9.0 - - - +
392B CYS* 5.0 1.2 - - - -
394B ARG* 1.3 79.7 - - + +
396B GLU* 1.3 67.0 + - - +
398B LEU* 3.3 9.7 + - - +
399B LYS* 2.9 36.6 + - - +
431B TRP* 4.8 1.8 - - + -
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 3.7 32.2 - - + +
391B LYS* 3.1 28.1 + - - -
392B CYS* 3.3 9.0 - - - +
393B CYS* 3.2 29.9 - - + +
394B ARG 3.1 0.2 - - - -
395B LYS* 1.3 82.8 + - - +
397B CYS* 1.3 57.6 + - - +
399B LYS* 3.1 11.6 + - + +
400B LEU* 2.9 33.7 + - - +
445B LEU* 4.2 7.4 - - + -
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Residues in contact with CYS 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B CYS* 3.0 24.0 + - - +
394B ARG 3.0 6.9 + - - +
396B GLU* 1.3 71.5 - - - +
398B LEU* 1.3 65.6 + - - +
400B LEU* 3.9 7.6 - - - +
401B MET* 2.9 26.9 + - - +
427B ILE* 4.0 10.3 - - + -
440B TRP* 4.1 11.4 - - + -
445B LEU* 4.0 14.6 - - - -
448B CYS* 3.9 14.8 - - - -
449B PHE* 3.8 33.1 - - + -
452B LEU* 4.0 10.5 - - + +
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B VAL* 3.9 28.3 - - + -
375B LEU* 4.2 17.3 - - + -
394B ARG 2.9 9.1 + - - +
395B LYS* 3.5 11.2 - - - +
397B CYS* 1.3 76.1 - - - +
399B LYS* 1.3 58.4 + - - +
401B MET* 3.5 1.4 + - - +
402B LYS* 2.9 47.1 + - + +
423B VAL* 3.5 25.4 - - + -
424B LYS* 4.1 17.7 - - + +
427B ILE* 3.4 31.4 - - + +
431B TRP* 4.3 8.1 - - + -
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Residues in contact with LYS 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 4.1 19.5 - - + +
157B LEU* 4.2 8.4 + - + +
158B ARG* 5.3 13.3 - - - +
159B LEU* 5.8 1.6 - - - +
203B HIS 3.5 24.8 + - - -
204B VAL* 3.8 15.9 - - + +
205B LYS 4.0 11.4 + - - -
206B ILE* 3.6 26.5 - - + +
395B LYS* 2.9 22.1 + - - +
396B GLU* 3.1 13.4 + - + +
398B LEU* 1.3 73.0 - - - +
400B LEU* 1.3 60.6 + - - +
402B LYS* 3.2 7.0 + - - +
403B TYR* 2.9 30.0 + - - +
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Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU* 4.0 40.8 - - + +
153B VAL* 4.0 26.0 - - + -
154B LEU* 3.7 26.5 - - + -
157B LEU* 4.5 1.8 - - + -
396B GLU 2.9 19.9 + - - +
397B CYS* 3.9 4.5 - - - +
399B LYS* 1.3 74.9 - - - +
401B MET* 1.3 58.5 + - - +
403B TYR* 3.3 5.8 + - - +
404B LEU* 2.9 29.1 + - - +
445B LEU* 4.3 19.3 - - + -
449B PHE* 4.0 24.2 - - + -
504B PHE* 4.0 7.6 - - + -
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Residues in contact with MET 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B CYS 2.9 19.0 + - - +
398B LEU 3.7 0.7 - - - +
400B LEU* 1.3 73.1 - - - +
402B LYS* 1.3 67.0 + - - +
404B LEU* 3.4 12.2 + - + +
405B LEU* 3.0 24.9 + - + +
423B VAL* 3.5 30.1 - - + -
449B PHE* 3.6 9.6 - - + -
452B LEU* 3.7 20.2 - - + -
453B LEU* 3.5 37.0 - - + -
456B PHE* 3.7 43.5 - - + -
493B ILE* 5.0 4.5 - - + -
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Residues in contact with LYS 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B SER* 3.2 27.7 + - - -
202B GLU* 5.8 0.4 + - - -
204B VAL* 3.8 21.7 - - - +
206B ILE* 4.4 12.1 - - + -
398B LEU* 2.9 40.3 + - + +
399B LYS* 3.3 10.1 - - - +
401B MET* 1.3 75.9 - - - +
403B TYR* 1.3 57.0 + - - +
405B LEU* 3.4 4.0 + - - +
406B GLU* 2.9 37.1 + - - +
420B SER* 4.0 38.6 + - - -
423B VAL* 4.0 12.9 - - + +
424B LYS* 4.8 10.5 - - - +
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Residues in contact with TYR 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B VAL* 4.1 7.6 - - + -
156B LYS* 3.4 22.8 + - - +
157B LEU* 3.4 35.0 - - + -
206B ILE* 3.7 18.2 - - + -
207B SER* 4.0 9.2 - - - -
399B LYS 2.9 16.3 + - - +
400B LEU* 3.6 4.5 - - - +
402B LYS* 1.3 74.0 - - - +
404B LEU* 1.3 65.6 + - - +
406B GLU* 3.0 10.4 + - - +
407B GLN* 2.9 64.6 + - + +
504B PHE* 3.6 43.1 - + - -
506B LYS 3.7 4.2 + - - -
507B LEU* 3.8 10.1 - - + +
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Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU 2.9 17.8 + - - +
401B MET* 3.5 14.4 - - + +
403B TYR* 1.3 75.8 - - - +
405B LEU* 1.3 58.7 + - - +
407B GLN* 3.4 2.9 + - - +
408B LEU* 3.0 48.4 + - + +
449B PHE* 4.3 4.5 - - + -
453B LEU* 3.8 29.8 - - + -
493B ILE* 4.7 17.7 - - + -
496B GLU* 4.5 6.5 - - + -
501B PHE* 4.3 15.0 - - + -
503B ILE* 3.9 23.3 - - + -
504B PHE* 3.8 21.2 - - + -
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B MET* 3.0 16.9 + - + +
402B LYS* 3.7 4.9 - - - +
404B LEU* 1.3 76.0 - - - +
406B GLU* 1.3 65.2 + - - +
408B LEU* 3.5 6.6 + - + -
409B LYS* 2.9 42.5 + - + +
415B LEU* 5.8 1.1 - - + -
418B PHE* 4.2 14.6 - - + -
419B CYS* 3.2 39.7 - - - +
420B SER* 4.0 5.2 - - - +
422B HIS* 5.7 0.7 - - + -
423B VAL* 3.9 21.1 - - + -
456B PHE* 5.9 4.7 - - + -
489B LEU* 4.9 21.1 - - + -
493B ILE* 6.3 0.7 - - + -
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Residues in contact with GLU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LYS* 5.4 3.8 + - - -
206B ILE* 3.6 35.0 - - - +
207B SER* 4.9 4.5 + - - -
402B LYS* 2.9 19.4 + - - +
403B TYR* 3.0 17.3 + - + +
405B LEU* 1.3 75.9 - - + +
407B GLN* 1.3 62.2 + - - +
409B LYS* 3.2 8.7 + - - +
410B LYS* 2.9 48.1 + - - +
420B SER* 6.5 1.3 - - - -
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Residues in contact with GLN 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B TYR* 2.9 63.6 + - + +
404B LEU* 3.8 3.6 - - - +
406B GLU* 1.3 73.1 - - - +
408B LEU* 1.3 63.0 + - - +
409B LYS 3.0 4.0 - - - -
410B LYS* 3.0 23.6 + - - +
411B GLU* 3.0 25.1 + - - +
503B ILE* 3.4 42.6 + - + +
506B LYS* 3.5 19.2 + - - +
507B LEU* 3.9 12.6 - - - +
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Residues in contact with LEU 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B LEU* 3.0 38.9 + - + +
405B LEU* 4.0 6.5 - - + +
407B GLN* 1.3 76.2 - - - +
409B LYS* 1.3 55.5 + - - +
411B GLU 4.1 0.4 - - - -
412B PHE* 3.3 29.4 + - + -
415B LEU* 3.2 26.6 - - + +
489B LEU* 4.3 9.9 - - + -
492B LYS* 4.3 15.3 - - + -
493B ILE* 3.8 36.6 - - + +
496B GLU* 4.2 17.0 - - + +
503B ILE* 3.7 22.2 - - + -
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Residues in contact with LYS 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LEU* 2.9 39.4 + - + +
406B GLU* 3.4 7.6 - - - +
408B LEU* 1.3 76.0 - - - +
410B LYS* 1.3 63.8 + - + +
411B GLU 3.2 2.0 - - - -
412B PHE 3.2 19.6 + - - +
413B GLN* 4.9 1.0 - - - -
415B LEU* 3.1 32.9 + - + +
416B ASP* 3.8 20.7 + - - +
418B PHE 2.7 30.4 + - - +
419B CYS* 4.9 2.7 - - - +
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Residues in contact with LYS 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLU* 2.9 32.2 + - - +
407B GLN* 3.0 23.8 + - - +
409B LYS* 1.3 78.1 - - + +
411B GLU* 1.3 60.6 + - - +
507B LEU* 5.3 10.4 - - + +
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Residues in contact with GLU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B GLN 3.0 14.0 + - - +
410B LYS* 1.3 80.3 - - - +
412B PHE* 1.3 90.6 + - + +
413B GLN 4.2 1.1 + - - -
503B ILE* 3.5 18.8 - - + +
506B LYS* 3.2 33.9 + - - +
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Residues in contact with PHE 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LEU* 3.3 30.9 + - + +
409B LYS* 3.2 15.4 - - - +
410B LYS 3.6 0.2 - - - -
411B GLU* 1.3 109.1 - - + +
413B GLN* 1.3 60.7 + - - +
414B GLU* 3.1 19.1 + - - +
415B LEU* 3.4 15.5 + - + +
416B ASP* 4.1 1.4 - - - +
488B PHE* 3.3 33.9 - + + -
492B LYS* 3.5 44.6 - - + -
503B ILE* 5.5 0.9 - - + -
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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