Contacts of the helix formed by residues 484 - 499 (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 LYS 484 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482C ASP* 3.1 25.4 + - - +
483C ARG* 1.3 78.1 - - + +
485C SER* 1.3 58.3 + - - +
487C GLU* 3.3 10.1 + - - +
488C PHE* 2.9 28.8 + - - +
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Residues in contact with SER 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C GLU* 3.9 19.6 + - - -
415C LEU* 4.4 0.5 - - - +
417C ALA* 5.4 4.8 - - - +
418C PHE* 3.8 9.3 - - - -
481C ILE* 3.7 17.3 - - - +
482C ASP* 2.9 20.7 + - - +
484C LYS* 1.3 76.7 - - - +
486C LYS* 1.3 57.5 + - - +
487C GLU 3.1 0.2 - - - -
488C PHE* 3.3 6.9 + - - +
489C LEU* 3.0 32.4 + - - +
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Residues in contact with LYS 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C PHE* 4.1 11.9 - - + -
460C LEU* 4.0 27.7 - - + +
463C GLU* 3.4 36.6 + - + -
476C PHE* 2.3 53.0 + - + +
477C SER 3.2 6.7 + - - -
478C GLN* 3.8 1.8 - - - +
481C ILE* 2.3 48.2 + - + -
482C ASP 3.2 0.6 + - - -
483C ARG* 3.1 12.0 + - - +
485C SER* 1.3 75.9 - - - +
487C GLU* 1.3 59.1 + - + +
489C LEU 4.5 1.1 - - - +
490C SER* 2.8 20.2 + - - -
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Residues in contact with GLU 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C ARG* 3.0 43.6 + - + +
484C LYS* 3.8 9.0 - - - +
485C SER 3.1 0.4 - - - -
486C LYS* 1.3 78.1 - - - +
488C PHE* 1.3 67.3 + - - +
489C LEU 3.3 0.7 - - - -
490C SER* 3.3 5.4 + - - -
491C LYS* 3.0 53.6 + - - +
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Residues in contact with PHE 488 (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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412C PHE* 3.5 44.9 - + + -
414C GLU* 3.7 34.8 - - + -
415C LEU* 3.5 20.0 - - + -
484C LYS 2.9 17.7 + - - +
485C SER* 3.5 8.3 - - - +
487C GLU* 1.3 76.2 - - - +
489C LEU* 1.3 62.0 + - - +
491C LYS* 3.1 14.9 + - + +
492C LYS* 3.0 54.1 + - + +
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Residues in contact with LEU 489 (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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405C LEU* 4.4 15.5 - - + -
408C LEU* 4.1 17.0 - - + -
415C LEU* 3.7 22.2 - - + -
418C PHE* 3.5 37.5 - - + -
456C PHE* 3.6 24.5 - - + -
460C LEU* 4.0 8.5 - - + -
485C SER 3.0 17.2 + - - +
488C PHE* 1.3 78.9 - - - +
490C SER* 1.3 56.3 + - - +
492C LYS* 3.3 3.5 + - + +
493C ILE* 2.9 54.3 + - + +
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Residues in contact with SER 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C LEU* 3.7 22.6 - - - +
460C LEU* 3.3 17.5 - - - +
486C LYS 2.8 25.5 + - - -
487C GLU* 3.3 8.8 + - - -
488C PHE 3.3 0.6 - - - -
489C LEU* 1.3 77.6 - - - +
491C LYS* 1.3 60.4 + - - +
493C ILE* 3.3 1.4 + - - +
494C GLU* 2.9 37.0 + - - +
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Residues in contact with LYS 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C GLU* 3.0 44.0 + - - +
488C PHE* 3.1 12.9 + - + +
490C SER* 1.3 77.8 - - - +
492C LYS* 1.3 62.7 + - + +
494C GLU* 3.9 5.0 - - - +
495C TYR* 3.0 28.6 + - - +
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Residues in contact with LYS 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C LEU* 3.9 24.0 - - + -
412C PHE* 3.4 43.0 - - + -
415C LEU* 5.0 2.2 - - + -
488C PHE* 3.0 46.6 + - + +
489C LEU* 3.7 6.1 - - + +
491C LYS* 1.3 80.8 - - + +
493C ILE* 1.3 57.6 + - - +
495C TYR* 3.3 12.7 + - + +
496C GLU* 2.9 34.9 + - - +
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Residues in contact with ILE 493 (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* 5.1 4.5 - - + -
404C LEU* 4.7 9.4 - - + +
405C LEU* 6.3 0.2 - - + -
408C LEU* 4.3 10.1 - - + -
453C LEU* 4.1 24.4 - - + +
456C PHE* 3.5 39.0 - - + -
457C LEU* 3.7 24.2 - - + -
460C LEU* 4.1 5.4 - - + -
489C LEU* 2.9 36.8 + - + +
490C SER 3.6 3.6 - - - +
492C LYS* 1.3 74.2 - - - +
494C GLU* 1.3 61.6 + - - +
496C GLU* 3.3 6.0 + - - +
497C ARG* 2.9 29.9 + - + +
501C PHE* 5.5 0.5 - - - -
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Residues in contact with GLU 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C LEU* 3.9 22.3 - - + +
490C SER* 2.9 22.1 + - - +
491C LYS* 3.9 4.9 - - - +
493C ILE* 1.3 75.6 - - - +
495C TYR* 1.3 63.2 + - - +
497C ARG* 3.2 29.1 + - - +
498C ASN* 3.0 43.1 + - - +
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Residues in contact with TYR 495 (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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491C LYS 3.0 15.5 + - - +
492C LYS* 3.3 17.9 - - + +
494C GLU* 1.3 79.7 - - - +
496C GLU* 1.3 87.1 + - + +
497C ARG 3.2 0.2 + - - -
498C ASN* 4.9 1.3 - - - +
499C ASN* 2.7 58.6 + - + +
502C PRO* 4.1 17.9 - - + +
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Residues in contact with GLU 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C LEU* 4.2 23.3 - - + -
408C LEU* 4.3 10.5 - - + +
492C LYS* 2.9 22.6 + - - +
493C ILE* 3.9 3.8 - - - +
495C TYR* 1.3 90.6 - - + +
497C ARG* 1.3 59.5 + - - +
499C ASN 3.5 2.9 + - - -
501C PHE* 2.7 38.7 + - + +
502C PRO* 3.1 19.4 - - - +
503C ILE* 3.0 54.8 + - - +
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Residues in contact with ARG 497 (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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450C ASP* 2.4 43.8 + - - +
453C LEU* 3.6 24.7 - - + +
454C ALA* 3.7 27.9 - - - +
457C LEU* 3.8 17.0 - - - +
493C ILE 2.9 18.3 + - - +
494C GLU* 3.4 30.9 + - - +
495C TYR 3.1 0.2 - - - -
496C GLU* 1.3 79.5 - - - +
498C ASN* 1.3 68.2 + - - +
499C ASN 3.6 0.3 + - - -
500C GLY 4.1 4.2 + - - -
501C PHE* 3.8 19.7 - - + -
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Residues in contact with ASN 498 (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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494C GLU* 3.0 35.3 + - - +
495C TYR* 4.9 1.0 - - - +
497C ARG* 1.3 86.6 - - - +
499C ASN* 1.3 68.3 + - - +
500C GLY 3.5 1.9 + - - -
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Residues in contact with ASN 499 (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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495C TYR* 2.7 55.8 + - + +
496C GLU 3.5 0.2 + - - -
497C ARG 3.4 0.4 - - - -
498C ASN* 1.3 88.7 + - - +
500C GLY* 1.3 61.1 + - - +
501C PHE 3.3 2.2 - - - -
502C PRO* 3.4 20.0 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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