Contacts of the helix formed by residues 444 - 462 (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 ASN 444 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438C SER 5.1 3.6 + - - -
439C GLN 6.4 0.2 - - - -
441C ASP* 2.8 30.3 + - + +
443C ARG* 1.3 86.5 - - - +
445C LEU* 1.3 65.2 + - - +
446C SER* 3.3 2.9 - - - -
447C SER* 2.6 35.2 + - - +
448C CYS* 2.8 19.1 + - - -
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Residues in contact with LEU 445 (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* 4.2 23.3 - - + -
151C LYS* 4.4 19.5 - - + -
154C LEU* 3.7 26.0 - - + -
393C CYS* 3.8 22.9 - - + -
396C GLU* 4.2 11.4 - - + -
397C CYS* 3.8 22.0 - - - -
400C LEU* 4.4 9.4 - - + -
441C ASP 3.5 2.8 + - - -
442C PRO 3.9 16.2 - - - +
443C ARG 3.4 2.2 + - - -
444C ASN* 1.3 74.6 - - - +
446C SER* 1.3 54.8 + - - +
448C CYS* 2.9 4.5 + - - +
449C PHE* 2.6 36.0 + - + +
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Residues in contact with SER 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LYS* 3.2 31.1 - - - -
150C LEU* 3.6 21.5 - - - +
444C ASN 3.1 1.2 + - - -
445C LEU* 1.3 77.1 - - - +
447C SER* 1.3 58.5 + - - +
449C PHE* 3.0 4.3 + - - +
450C ASP* 2.9 31.6 + - - +
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Residues in contact with SER 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ASN* 2.6 38.2 + - - +
446C SER* 1.3 78.1 - - - +
448C CYS* 1.3 60.5 + - - +
450C ASP* 4.2 6.3 - - - +
451C LYS* 3.1 24.7 + - - +
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Residues in contact with CYS 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C CYS* 3.6 20.6 - - - -
397C CYS* 3.9 17.3 - - - -
439C GLN 3.5 24.7 - - - -
440C TRP* 3.9 16.4 - - + -
444C ASN* 2.8 26.5 + - - -
445C LEU 3.2 7.2 - - - +
447C SER* 1.3 76.3 + - - +
449C PHE* 1.3 67.1 + - - +
451C LYS* 3.0 25.1 + - - +
452C LEU* 3.0 12.6 + - - +
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Residues in contact with PHE 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C LEU* 4.0 21.8 - - + -
397C CYS* 3.9 21.1 - - + -
400C LEU* 3.9 24.9 - - + -
401C MET* 3.8 38.8 - - + -
404C LEU* 4.7 2.5 - - + -
445C LEU 2.6 16.7 + - - +
446C SER* 3.3 10.3 - - - +
448C CYS* 1.3 71.3 - - - +
450C ASP* 1.3 66.1 - - - +
452C LEU* 3.0 9.0 + - + +
453C LEU* 2.9 32.3 + - + +
501C PHE* 3.9 29.8 - + - -
504C PHE* 4.1 24.2 - + - -
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Residues in contact with ASP 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C SER 2.9 18.3 + - - +
447C SER* 4.2 5.6 - - - +
449C PHE* 1.3 74.3 - - + +
451C LYS* 1.3 53.8 + - - +
453C LEU* 3.0 13.2 + - + +
454C ALA* 2.7 32.6 + - - +
497C ARG* 2.4 53.6 + - - +
501C PHE* 5.5 2.8 - - + -
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Residues in contact with LYS 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C MET* 4.3 13.6 - - + +
434C ASP* 2.6 32.0 + - - +
439C GLN* 3.3 26.1 + - - +
440C TRP* 4.3 14.8 - - - -
447C SER 3.1 14.8 + - - +
448C CYS* 3.0 23.5 + - - +
450C ASP* 1.3 79.6 - - - +
452C LEU* 1.3 64.1 + - - +
454C ALA* 3.0 13.8 + - - +
455C PHE* 3.1 12.0 + - - +
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Residues in contact with LEU 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C CYS* 4.1 12.1 - - + +
401C MET* 3.9 37.2 - - + -
423C VAL* 5.1 1.1 - - + +
426C ALA* 4.1 11.2 - - + -
427C ILE* 3.7 50.3 - - + +
430C MET* 3.6 31.1 - - + -
440C TRP* 5.3 4.3 - - + -
448C CYS 3.0 6.5 + - - +
449C PHE* 3.0 10.4 + - + +
451C LYS* 1.3 78.0 - - - +
453C LEU* 1.3 65.5 + - - +
455C PHE* 3.0 7.0 + - + +
456C PHE* 2.9 20.0 + - + +
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Residues in contact with LEU 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C MET* 3.5 35.4 - - + -
404C LEU* 3.8 19.7 - - + -
449C PHE* 2.9 19.1 + - + +
450C ASP* 3.1 15.9 - - - +
452C LEU* 1.3 76.2 - - - +
454C ALA* 1.3 63.1 + - - +
456C PHE* 3.0 14.0 + - - +
457C LEU* 3.0 17.2 + - - +
493C ILE* 4.1 15.8 - - + +
497C ARG* 3.6 42.4 - - + +
501C PHE* 4.0 18.4 - - + -
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Residues in contact with ALA 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C ASP* 2.7 16.0 + - - +
451C LYS* 3.4 10.8 - - - +
453C LEU* 1.3 72.2 - - - +
455C PHE* 1.3 65.3 + - - +
457C LEU* 3.0 17.9 + - - +
458C GLU* 3.0 13.8 + - - +
497C ARG* 3.7 27.1 - - - +
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Residues in contact with PHE 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C ALA* 3.1 38.1 - - + -
429C HIS* 3.6 25.4 - + + -
430C MET* 3.6 31.0 - - + -
433C GLN* 3.6 24.9 - - - -
451C LYS 3.1 7.9 + - - +
452C LEU* 3.0 9.5 + - + +
454C ALA* 1.3 75.2 - - - +
456C PHE* 1.3 65.1 + - - +
458C GLU* 3.0 13.9 + - + +
459C CYS* 3.0 45.3 + - - -
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Residues in contact with PHE 456 (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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401C MET* 3.5 24.2 - - + -
405C LEU* 5.6 5.2 - - + -
418C PHE* 5.2 1.3 - + - -
422C HIS* 4.3 24.7 - - + -
423C VAL* 4.4 13.2 - - + -
426C ALA* 3.9 18.6 - - + -
452C LEU* 2.9 8.1 + - + +
453C LEU 3.0 10.1 + - - +
455C PHE* 1.3 78.4 - - - +
457C LEU* 1.3 62.1 + - - +
459C CYS* 2.9 12.9 + - + +
460C LEU* 2.9 41.4 + - + +
465C LEU* 5.0 0.4 - - + -
476C PHE* 4.0 27.6 - + - -
489C LEU* 3.6 15.7 - - + -
493C ILE* 3.5 28.5 - - + -
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Residues in contact with LEU 457 (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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453C LEU 3.0 15.7 + - - +
454C ALA* 3.0 8.9 + - - +
456C PHE* 1.3 75.6 - - - +
458C GLU* 1.3 50.5 + - - +
460C LEU* 2.9 17.4 + - + +
461C ARG* 2.7 35.0 + - - +
490C SER* 3.7 38.5 + - - +
493C ILE* 3.7 30.3 - - + -
494C GLU* 3.9 21.5 - - + +
497C ARG* 3.8 25.8 - - - +
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Residues in contact with GLU 458 (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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454C ALA 3.0 10.4 + - - +
455C PHE* 3.0 19.3 + - + +
457C LEU* 1.3 75.2 - - - +
459C CYS* 1.3 58.3 + - - +
461C ARG* 2.8 42.2 + - - +
462C THR* 2.8 55.7 + - - +
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Residues in contact with CYS 459 (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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426C ALA* 5.2 1.6 - - - -
455C PHE* 3.0 50.1 + - - -
456C PHE* 2.9 13.1 + - + +
458C GLU* 1.3 76.7 - - - +
460C LEU* 1.3 60.9 + - - +
462C THR* 3.9 2.5 - - - -
463C GLU 3.3 1.4 + - - -
464C LYS 3.0 46.7 + - - +
465C LEU* 4.0 16.2 - - + -
476C PHE* 3.3 19.6 - - + -
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Residues in contact with LEU 460 (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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418C PHE* 4.3 1.3 - - + -
456C PHE* 2.9 37.9 + - + +
457C LEU* 2.9 24.5 + - + +
459C CYS* 1.3 77.6 - - - +
461C ARG* 1.3 61.2 + - - +
463C GLU* 3.5 16.5 + - - +
476C PHE* 3.6 26.2 - - + -
486C LYS* 4.0 35.4 - - + +
489C LEU* 4.0 18.8 - - + -
490C SER* 3.3 34.3 - - - +
493C ILE* 4.1 0.4 - - + -
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Residues in contact with ARG 461 (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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457C LEU 2.7 16.0 + - - +
458C GLU* 2.8 39.0 + - - +
460C LEU* 1.3 76.3 - - - +
462C THR* 1.3 73.9 + - - +
463C GLU* 3.2 7.9 + - - +
490C SER* 5.9 0.2 - - - -
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Residues in contact with THR 462 (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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458C GLU* 2.8 47.5 + - - +
459C CYS* 3.8 6.6 + - - -
461C ARG* 1.3 90.5 - - - +
463C GLU* 1.3 69.8 + - - +
464C LYS* 3.4 21.4 + - - +
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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
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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