Contacts of the helix formed by residues 476 - 488 (chain C) in PDB entry 2DB3
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 ALA 476 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472C VAL* 3.9 11.0 - - + -
473C ASN* 2.9 16.1 + - + +
475C TYR* 1.3 100.8 - - + +
477C LYS* 1.3 63.3 + - - +
478C ARG 3.4 1.2 + - - -
479C SER* 3.5 10.5 + - - +
480C LYS* 3.1 21.5 + - + +
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Residues in contact with LYS 477 (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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472C VAL* 3.8 25.8 - - + -
473C ASN 3.3 6.9 + - - +
474C LYS* 3.2 32.9 + - + +
476C ALA* 1.3 75.5 - - - +
478C ARG* 1.3 65.7 + - - +
480C LYS* 3.3 3.5 + - - +
481C LEU* 3.0 24.8 + - - +
564C TYR* 2.8 55.7 + - + +
565C ASP* 3.0 22.6 + - - +
566C MET 4.6 1.4 - - - +
592C PHE* 3.7 21.6 + - + -
594C ASP* 4.4 16.5 + - - +
598C ASP* 5.0 0.8 + - - -
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Residues in contact with ARG 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C LYS 5.5 2.5 - - - -
475C TYR* 3.2 32.8 + - - +
476C ALA 3.4 0.8 - - - -
477C LYS* 1.3 78.0 - - - +
479C SER* 1.3 64.1 + - - +
481C LEU* 3.4 3.9 + - - +
482C ILE* 3.1 29.3 + - + +
504C PHE* 4.9 19.6 - - + -
505C LEU* 5.2 2.0 - - + -
508C PHE* 4.3 33.5 - - + -
564C TYR* 3.3 19.7 + - - +
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Residues in contact with SER 479 (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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475C TYR 5.2 1.4 + - - -
476C ALA* 3.5 11.9 + - - -
477C LYS 3.3 0.2 - - - -
478C ARG* 1.3 76.7 - - - +
480C LYS* 1.3 60.5 + - - +
482C ILE* 3.3 10.5 + - - +
483C GLU* 2.9 30.3 + - - +
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Residues in contact with LYS 480 (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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470C TYR* 4.0 34.5 - - - +
472C VAL* 4.3 18.4 - - + -
476C ALA 3.1 15.0 + - - +
477C LYS* 3.6 6.3 - - - +
479C SER* 1.3 78.4 - - - +
481C LEU* 1.3 63.1 + - - +
483C GLU* 3.2 31.3 + - - +
484C ILE* 3.0 30.6 + - + +
592C PHE* 3.6 27.1 - - + -
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Residues in contact with LEU 481 (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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477C LYS 3.0 11.7 + - - +
478C ARG 3.6 8.5 - - - +
480C LYS* 1.3 74.8 - - - +
482C ILE* 1.3 59.6 + - - +
484C ILE* 3.1 3.4 + - + -
485C LEU* 2.8 55.3 + - + +
494C VAL* 4.5 10.8 - - + -
505C LEU* 4.1 17.0 - - + -
508C PHE* 6.0 0.7 - - + -
509C LEU* 3.8 32.3 - - + -
562C ILE* 3.8 27.8 - - + -
564C TYR* 3.8 27.4 - - + -
592C PHE* 3.8 8.2 - - + -
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Residues in contact with ILE 482 (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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478C ARG* 3.1 17.0 + - + +
479C SER* 3.3 10.3 + - - +
481C LEU* 1.3 79.2 - - - +
483C GLU* 1.3 59.7 + - - +
485C LEU* 4.1 5.6 - - - +
486C SER* 2.7 41.9 + - - +
508C PHE* 3.2 30.3 - - + -
509C LEU* 4.2 12.3 - - + -
512C LYS* 3.0 45.1 - - + +
514C PHE* 4.6 9.3 - - + -
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Residues in contact with GLU 483 (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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226B SER* 4.8 14.9 + - - -
479C SER 2.9 12.8 + - - +
480C LYS* 3.2 37.4 + - - +
481C LEU 3.1 0.2 - - - -
482C ILE* 1.3 79.9 - - - +
484C ILE* 1.3 66.4 + - + +
486C SER* 3.3 6.2 + - - -
487C GLU* 3.3 18.2 + - - +
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Residues in contact with ILE 484 (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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470C TYR* 4.3 13.5 - - + +
480C LYS* 3.0 19.9 + - + +
481C LEU* 3.6 5.6 - - - +
483C GLU* 1.3 80.0 - - + +
485C LEU* 1.3 59.1 + - + +
487C GLU* 3.0 10.6 + - + +
488C GLN* 3.0 27.0 + - - +
560C HIS* 3.8 27.6 - - + +
562C ILE* 4.1 14.1 - - + -
588C ARG* 4.8 4.9 - - - +
590C THR* 4.2 15.3 - - + +
592C PHE* 3.6 33.9 - - + -
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Residues in contact with LEU 485 (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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481C LEU* 2.8 45.8 + - + +
482C ILE* 4.1 1.3 - - - +
484C ILE* 1.3 70.3 - - + +
486C SER* 1.3 65.0 + - - +
488C GLN 3.4 6.9 + - - +
489C ALA* 3.4 28.3 + - + +
492C THR* 4.1 32.1 - - + +
494C VAL* 5.1 0.4 - - + -
509C LEU* 3.7 38.1 - - + -
514C PHE* 3.4 23.8 - - + -
542C VAL* 4.4 13.5 - - + -
562C ILE* 4.3 6.3 - - + -
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Residues in contact with SER 486 (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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482C ILE* 2.7 34.7 + - - +
483C GLU* 3.5 7.6 - - - -
485C LEU* 1.3 78.0 - - - +
487C GLU* 1.3 65.5 + - - +
514C PHE* 4.0 12.8 - - - -
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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
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229B ASN* 4.3 18.2 + - - +
245B GLN* 4.1 11.8 - - - +
246B HIS* 3.3 15.0 + - - +
267B ILE* 3.5 51.8 - - + +
273B LYS* 4.5 6.5 + - - -
483C GLU 3.3 8.1 + - - +
484C ILE* 3.0 12.4 + - - +
486C SER* 1.3 82.0 - - - +
488C GLN* 1.3 63.8 + - + +
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Residues in contact with GLN 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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246B HIS* 3.5 46.2 + - + +
248B THR* 4.6 12.3 + - - +
484C ILE* 3.0 17.6 + - - +
485C LEU* 3.4 11.4 - - - +
486C SER 3.4 0.6 - - - -
487C GLU* 1.3 85.9 - - + +
489C ALA* 1.3 61.0 + - - +
490C ASP* 4.5 18.2 + - + +
492C THR* 4.4 4.2 - - - +
559C LYS* 6.2 2.3 - - - +
560C HIS* 5.0 4.5 + - - -
588C ARG* 3.1 28.8 + - - +
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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