Contacts of the helix formed by residues 419 - 434 (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 419 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C LEU* 3.3 17.4 - - - +
409C LYS* 4.9 3.8 - - - +
417C ALA 5.2 0.4 - - - +
418C PHE* 1.3 75.3 - - - +
420C SER* 1.3 66.2 + - - +
421C TYR* 3.0 30.0 + - + +
422C HIS* 3.1 39.3 + - - +
423C VAL 4.0 0.2 + - - -
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Residues in contact with SER 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C LYS* 3.9 36.5 + - - +
405C LEU* 4.1 9.1 - - - +
406C GLU* 6.4 2.2 - - - -
419C CYS* 1.3 74.0 - - - +
421C TYR* 1.3 58.0 + - - +
422C HIS 3.3 0.2 - - - -
423C VAL* 3.3 8.8 + - - +
424C LYS* 2.9 28.0 + - - +
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Residues in contact with TYR 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C GLU* 2.7 39.6 + - - -
419C CYS* 3.0 17.2 - - - +
420C SER* 1.3 78.6 + - - +
422C HIS* 1.3 57.3 + + - +
424C LYS* 4.0 19.3 - - + -
425C THR* 2.7 53.6 + - - -
428C PHE* 5.2 3.8 - + - -
467C HIS* 3.2 39.4 + + - -
468C TYR* 5.6 1.6 + - - +
469C PHE* 4.4 3.8 - - - -
475C LEU* 4.4 10.3 - - + -
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Residues in contact with HIS 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C LEU* 5.5 0.7 - - + -
417C ALA 3.3 27.1 - - - -
418C PHE* 3.5 11.6 - - + -
419C CYS* 3.1 39.0 + - - +
421C TYR* 1.3 78.1 - + + +
423C VAL* 1.3 57.7 + - + +
425C THR* 4.5 0.7 - - - -
426C ALA* 2.9 26.5 + - - +
456C PHE* 4.3 8.5 - - + -
465C LEU* 3.2 22.1 - - + +
475C LEU* 4.2 26.1 + - + +
476C PHE* 3.6 24.9 - + + -
481C ILE* 3.8 17.1 - - + +
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Residues in contact with VAL 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C LEU* 3.7 17.9 - - + -
401C MET* 3.5 42.0 - - + +
402C LYS* 4.1 8.5 - - + +
405C LEU* 3.7 35.2 - - + -
420C SER* 3.3 11.8 + - - +
421C TYR 3.2 0.2 - - - -
422C HIS* 1.3 74.8 - - - +
424C LYS* 1.3 60.5 + - - +
426C ALA* 3.1 8.3 + - - +
427C ILE* 2.9 28.1 + - - +
452C LEU* 5.1 2.1 - - + +
456C PHE* 4.5 13.9 - - + -
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Residues in contact with LYS 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C GLY* 5.6 3.2 - - - -
202C GLU* 2.9 37.1 + - - -
368C SER* 5.5 0.6 - - - +
371C GLU* 2.5 31.3 + - - +
375C LEU* 4.0 6.1 - - - -
398C LEU* 4.1 19.3 - - + -
420C SER 2.9 16.1 + - - +
421C TYR* 3.4 21.5 + - + +
423C VAL* 1.3 75.3 - - - +
425C THR* 1.3 57.9 + - - +
427C ILE* 3.2 11.8 - - + +
428C PHE* 2.9 56.0 + - + -
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Residues in contact with THR 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C TYR* 2.7 36.7 + - - -
422C HIS 3.6 4.0 - - - -
424C LYS* 1.3 75.5 - - - +
426C ALA* 1.3 64.3 + - - +
428C PHE* 3.0 15.4 + - - +
429C HIS* 3.0 30.4 + - + +
465C LEU* 3.8 11.0 - - + -
466C ASP 3.3 26.7 - - - +
468C TYR* 4.0 14.3 + - + +
475C LEU* 3.6 18.4 - - + +
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Residues in contact with ALA 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C MET* 6.5 0.4 - - + -
422C HIS 2.9 15.6 + - - +
423C VAL* 3.1 9.4 + - - +
425C THR* 1.3 76.0 - - - +
427C ILE* 1.3 57.1 + - - +
429C HIS* 3.3 2.0 + - - -
430C MET 2.9 21.5 + - - -
452C LEU* 4.1 9.0 - - + -
455C PHE* 3.1 30.1 - - + -
456C PHE* 3.9 24.7 - - + -
459C CYS* 5.2 0.7 - - - -
465C LEU* 4.2 11.6 - - + +
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Residues in contact with ILE 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ARG 3.6 3.8 - - - +
397C CYS* 4.1 4.9 - - + -
398C LEU* 3.6 46.4 - - + +
423C VAL 2.9 15.0 + - - +
424C LYS* 3.2 14.6 - - + +
426C ALA* 1.3 73.6 - - - +
428C PHE* 1.3 60.3 + - + +
430C MET* 3.9 4.5 - - + -
431C TRP* 2.9 79.5 + - + +
440C TRP* 4.6 3.8 - - + -
452C LEU* 3.7 31.1 - - + +
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Residues in contact with PHE 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C TRP* 4.5 1.9 - + - -
371C GLU* 3.8 37.9 - - + -
374C ILE* 3.8 18.6 - - + -
375C LEU* 3.8 13.2 - - + -
421C TYR* 5.2 2.9 - + - -
424C LYS* 2.9 43.2 + - + -
425C THR* 3.1 14.1 - - - +
427C ILE* 1.3 78.2 - - - +
429C HIS* 1.3 61.7 + - - +
431C TRP* 3.3 31.5 + + - +
432C THR* 2.9 29.6 + - - -
468C TYR* 3.7 40.6 + + + -
469C PHE* 4.5 5.8 - + - -
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Residues in contact with HIS 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C PRO* 5.2 6.2 - - + +
425C THR* 3.0 30.2 + - + +
426C ALA* 3.5 7.6 - - - +
428C PHE* 1.3 75.8 - - - +
430C MET* 1.3 57.7 + - - +
432C THR* 3.3 8.6 + - - +
433C GLN* 2.9 35.7 + - + +
455C PHE* 3.6 20.2 - + + -
465C LEU* 4.4 9.6 - - + -
466C ASP* 2.9 40.9 + - + +
467C HIS 4.8 0.9 - - - -
468C TYR* 3.8 26.9 - + - -
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Residues in contact with MET 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C ALA 2.9 8.0 + - - +
427C ILE* 3.6 11.7 - - - +
428C PHE 3.2 0.4 - - - -
429C HIS* 1.3 73.7 - - - +
431C TRP* 1.3 55.0 + - - +
433C GLN* 2.9 42.2 + - + +
434C ASP* 2.8 40.0 + - - +
440C TRP* 4.0 14.5 - - + -
451C LYS* 4.3 28.0 - - + +
452C LEU* 3.6 33.0 - - + -
455C PHE* 3.6 37.9 - - + -
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Residues in contact with TRP 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C TRP* 3.6 41.2 + + + -
374C ILE* 4.8 3.6 - - + -
375C LEU* 4.0 26.9 - - + -
378C HIS* 5.0 7.2 - - + -
394C ARG* 3.4 50.6 - - + +
395C LYS* 5.1 1.6 - - + -
398C LEU* 4.5 6.5 - - + -
427C ILE* 2.9 55.0 + - + +
428C PHE* 3.7 35.9 - + - +
430C MET* 1.3 72.0 - - - +
432C THR* 1.3 59.9 + - - +
434C ASP 3.0 24.8 - - - +
435C PRO* 3.3 7.8 - - - +
440C TRP* 3.3 26.5 - + - -
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Residues in contact with THR 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C PRO* 3.2 36.6 - - + +
328C ILE* 5.3 0.2 - - - -
331C TRP* 3.9 12.6 - - + +
428C PHE 2.9 11.8 + - - -
429C HIS* 3.4 13.0 - - - +
431C TRP* 1.3 75.4 - - - +
433C GLN* 1.3 65.7 + - + +
435C PRO* 3.6 13.5 - - - +
468C TYR* 2.6 28.8 + - - -
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Residues in contact with GLN 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C HIS* 2.9 18.4 + - + +
430C MET* 2.9 27.5 + - + +
432C THR* 1.3 78.2 - - + +
434C ASP* 1.3 69.7 - - - +
435C PRO* 3.1 10.4 - - - +
439C GLN* 4.7 1.2 + - - -
455C PHE* 3.6 30.5 - - - -
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Residues in contact with ASP 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ARG* 4.1 0.9 + - - -
430C MET* 2.8 19.6 + - - +
431C TRP* 3.0 9.3 - - - +
433C GLN* 1.3 87.7 - - - +
435C PRO* 1.3 62.1 - - - +
436C GLN 3.3 3.1 + - - -
439C GLN* 3.1 27.0 + - + +
440C TRP* 2.7 42.7 + - + +
451C LYS* 2.6 40.0 + - - +
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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