Contacts of the helix formed by residues 393 - 412 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392C CYS* 1.3 73.0 - - - +
394C ARG* 1.3 57.4 + - - +
396C GLU* 3.2 14.9 + - + +
397C CYS* 2.9 33.7 + - - -
440C TRP* 3.0 16.9 + - - -
441C ASP 3.5 21.3 - - - -
442C PRO* 4.0 13.9 - - + -
445C LEU* 3.8 22.7 - - + -
448C CYS* 3.6 31.4 - - - -
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Residues in contact with ARG 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C TRP* 3.9 7.9 - - - +
378C HIS* 3.5 34.4 + - + -
379C GLY* 3.7 2.4 - - - -
384C CYS* 3.7 17.2 - - - -
392C CYS* 3.5 18.2 - - - +
393C CYS* 1.3 76.6 - - - +
395C LYS* 1.3 64.4 + - + +
397C CYS* 3.2 2.6 + - - +
398C LEU 3.0 17.7 + - - -
427C ILE* 3.6 10.9 - - - +
431C TRP* 3.4 46.7 + - + +
434C ASP 4.1 1.0 + - - -
435C PRO 2.9 28.9 + - - -
436C GLN 3.6 10.5 + - - -
437C ASP* 2.8 30.9 + - - +
440C TRP* 3.6 30.1 - - + +
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Residues in contact with LYS 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C GLU 3.1 15.4 + - - +
203C HIS* 4.0 27.0 - - + +
204C VAL* 4.1 13.2 - - + +
375C LEU* 3.2 31.8 + - + -
376C ASN* 3.1 25.1 + - - +
378C HIS* 3.8 22.7 - - + +
385C CYS* 6.4 0.2 - - - -
392C CYS* 5.1 0.8 - - - -
393C CYS 3.5 0.2 - - - -
394C ARG* 1.3 80.1 - - + +
396C GLU* 1.3 67.1 + - - +
398C LEU* 3.2 9.3 + - - +
399C LYS* 2.9 37.1 + - - +
431C TRP* 4.9 2.0 - - + -
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Residues in contact with GLU 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C LEU* 3.9 34.5 - - + +
391C LYS* 5.6 6.8 + - - +
392C CYS* 3.3 13.5 - - - +
393C CYS* 3.2 28.1 - - + +
395C LYS* 1.3 84.5 + - - +
397C CYS* 1.3 57.2 - - - +
399C LYS* 3.0 14.1 + - + +
400C LEU* 2.9 33.9 + - - +
445C LEU* 4.2 8.7 - - + -
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Residues in contact with CYS 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C CYS* 2.9 23.8 + - - +
394C ARG 3.2 4.7 + - - +
396C GLU* 1.3 75.6 - - - +
398C LEU* 1.3 62.4 + - - +
400C LEU* 3.4 8.6 + - - +
401C MET* 2.9 26.7 + - - +
427C ILE* 4.1 12.3 - - + -
440C TRP* 4.4 8.1 - - + -
445C LEU* 3.8 20.0 - - - -
448C CYS* 3.9 25.8 - - - -
449C PHE* 3.9 16.9 - - + -
452C LEU* 4.1 9.5 - - + +
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Residues in contact with LEU 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C GLU* 5.4 0.9 - - - +
204C VAL* 3.7 28.9 - - + -
375C LEU* 4.2 16.4 - - + -
394C ARG 3.0 13.3 + - - +
395C LYS* 3.4 10.8 - - - +
397C CYS* 1.3 77.4 - - - +
399C LYS* 1.3 56.2 + - - +
401C MET* 3.7 2.1 - - - +
402C LYS* 2.9 49.6 + - + +
423C VAL* 3.7 22.9 - - + -
424C LYS* 4.1 21.8 - - + -
427C ILE* 3.6 30.8 - - + +
431C TRP* 4.5 3.1 - - + -
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Residues in contact with LYS 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C LEU* 4.5 15.4 + - + +
157C LEU* 4.5 7.1 + - + -
158C ARG* 5.3 13.9 - - - +
203C HIS 3.8 22.9 + - - -
204C VAL* 4.0 19.3 - - + +
205C LYS 4.4 8.2 + - - -
206C ILE* 3.7 27.6 - - + +
395C LYS* 2.9 23.0 + - - +
396C GLU* 3.0 17.7 + - + +
398C LEU* 1.3 74.0 - - - +
400C LEU* 1.3 60.2 + - - +
402C LYS* 3.4 7.6 + - - +
403C TYR* 2.9 29.9 + - - +
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Residues in contact with LEU 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LEU* 3.9 36.1 - - + +
153C VAL* 3.7 30.1 - - + -
154C LEU* 3.7 25.8 - - + -
157C LEU* 4.1 2.9 - - + -
396C GLU 2.9 20.3 + - - +
397C CYS* 3.9 3.8 - - - +
399C LYS* 1.3 75.1 - - - +
401C MET* 1.3 58.6 + - - +
403C TYR* 3.1 6.1 + - - +
404C LEU* 2.9 29.6 + - - +
445C LEU* 4.4 15.0 - - + -
449C PHE* 3.9 26.9 - - + -
504C PHE* 3.8 9.7 - - + -
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Residues in contact with MET 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C CYS 2.9 17.7 + - - +
398C LEU* 3.7 1.3 - - - +
400C LEU* 1.3 76.2 - - - +
402C LYS* 1.3 62.8 + - - +
404C LEU* 3.2 9.9 + - + +
405C LEU* 3.0 24.4 + - - +
423C VAL* 3.5 29.4 - - + -
426C ALA* 6.2 0.4 - - + -
449C PHE* 3.8 12.3 - - + -
452C LEU* 3.9 20.2 - - + -
453C LEU* 3.5 37.7 - - + -
456C PHE* 3.5 47.6 - - + -
493C ILE* 5.1 3.1 - - + -
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Residues in contact with LYS 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C SER* 3.1 22.4 + - - -
204C VAL* 3.6 29.1 - - + +
205C LYS* 5.4 0.7 - - - +
206C ILE* 4.4 13.9 - - + -
398C LEU* 2.9 46.8 + - + +
399C LYS* 3.6 5.6 - - - +
401C MET* 1.3 77.0 - - - +
403C TYR* 1.3 57.3 + - - +
405C LEU* 3.5 6.1 + - - +
406C GLU* 2.9 40.9 + - + +
420C SER* 3.9 33.0 + - - +
423C VAL* 4.2 9.9 - - + -
424C LYS* 6.4 0.4 - - + -
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Residues in contact with TYR 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C VAL* 3.9 16.6 - - + -
156C LYS* 3.1 35.4 + - - -
157C LEU* 3.5 27.4 - - + -
206C ILE* 3.8 13.0 - - + +
207C SER* 4.6 6.1 - - - -
399C LYS 2.9 17.5 + - - +
400C LEU 3.1 4.2 + - - +
402C LYS* 1.3 74.9 - - - +
404C LEU* 1.3 65.2 + - - +
406C GLU* 3.1 8.1 + - + +
407C GLN* 2.9 65.0 + - + +
504C PHE* 3.6 43.1 + + - -
506C LYS 3.9 1.4 + - - -
507C LEU* 5.4 2.9 - - - +
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Residues in contact with LEU 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400C LEU 2.9 10.8 + - - +
401C MET* 3.6 14.6 - - - +
403C TYR* 1.3 75.1 - - - +
405C LEU* 1.3 64.0 - - - +
407C GLN* 3.3 3.5 + - - +
408C LEU* 3.0 48.0 + - + +
449C PHE* 4.7 4.9 - - + -
453C LEU* 3.8 28.3 - - + -
493C ILE* 4.7 15.7 - - + +
496C GLU* 4.2 17.0 - - + -
501C PHE* 4.6 8.3 - - + -
503C ILE* 3.8 22.9 - - + -
504C PHE* 3.5 24.1 - - + -
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Residues in contact with LEU 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C MET 3.0 15.7 + - - +
402C LYS* 3.8 4.5 - - - +
404C LEU* 1.3 78.0 - - - +
406C GLU* 1.3 56.2 + - + +
408C LEU* 3.8 6.2 - - + -
409C LYS* 2.9 56.7 + - + +
415C LEU* 5.7 0.7 - - + -
418C PHE* 4.3 13.2 - - + -
419C CYS 3.3 37.5 - - - +
420C SER* 4.1 3.4 - - - +
422C HIS* 5.5 1.3 - - + -
423C VAL* 3.7 22.0 - - + -
456C PHE* 5.6 4.9 - - + -
489C LEU* 4.4 25.6 - - + -
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Residues in contact with GLU 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C LYS* 5.8 1.0 + - - -
206C ILE* 3.6 28.8 - - - +
207C SER* 5.5 2.3 + - - -
402C LYS* 2.9 30.6 + - + +
403C TYR* 3.1 12.8 + - + +
405C LEU* 1.3 75.6 - - + +
407C GLN* 1.3 61.2 + - - +
409C LYS* 3.5 8.6 + - + +
410C LYS* 2.9 31.3 + - + +
420C SER* 6.4 2.5 - - - -
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Residues in contact with GLN 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403C TYR* 2.9 53.5 + - + +
404C LEU 3.6 3.1 - - - +
406C GLU* 1.3 74.6 - - - +
408C LEU* 1.3 65.6 + - - +
410C LYS* 3.0 26.2 + - - +
411C GLU* 3.0 23.7 + - - +
503C ILE* 2.9 50.9 + - + +
506C LYS* 3.2 24.9 + - - +
507C LEU* 5.3 3.0 - - - +
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Residues in contact with LEU 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C LEU* 3.0 41.9 + - + +
405C LEU* 3.9 6.3 - - + +
407C GLN* 1.3 76.7 - - - +
409C LYS* 1.3 56.4 + - - +
411C GLU 3.2 0.9 + - - -
412C PHE* 2.8 43.2 + - + -
415C LEU* 3.5 16.3 - - + +
489C LEU* 4.1 22.4 - - + -
492C LYS* 3.9 26.7 - - + -
493C ILE* 4.3 12.6 - - + +
496C GLU* 4.3 13.9 - - + +
503C ILE* 3.6 20.4 - - + +
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Residues in contact with LYS 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C LEU* 2.9 45.3 + - + +
406C GLU* 3.8 7.6 - - + +
408C LEU* 1.3 75.9 - - - +
410C LYS* 1.3 60.3 + - - +
412C PHE 3.1 21.5 - - - +
415C LEU* 3.1 30.4 + - + +
416C ASP* 3.9 19.8 + - - +
418C PHE 3.0 28.5 + - - +
419C CYS* 4.9 3.4 - - - +
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Residues in contact with LYS 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C GLU* 2.9 18.4 + - + +
407C GLN* 3.0 26.1 + - - +
409C LYS* 1.3 76.7 - - - +
411C GLU* 1.3 60.2 + - - +
507C LEU* 4.0 24.5 - - - +
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Residues in contact with GLU 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C GLN 3.0 12.2 + - - +
408C LEU* 4.5 0.9 - - - -
410C LYS* 1.3 80.4 - - - +
412C PHE* 1.3 97.0 + - + +
413C GLN 4.1 0.7 + - - -
503C ILE* 3.8 10.5 - - - +
506C LYS* 2.9 36.9 + - - -
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Residues in contact with PHE 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C LEU* 2.8 33.7 + - + +
409C LYS* 3.1 21.3 - - - +
411C GLU* 1.3 111.2 - - + +
413C GLN* 1.3 62.5 + - - +
414C GLU* 3.2 14.3 + - - +
415C LEU* 3.8 14.0 + - + +
416C ASP* 4.1 2.8 - - - +
488C PHE* 3.5 27.8 - + + -
492C LYS* 3.4 39.3 - - - -
503C ILE* 5.5 0.4 - - + -
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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