Contacts of the helix formed by residues 478 - 488 (chain C) in PDB entry 1SL0
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 GLY 478 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476C ALA 3.4 4.2 + - - -
477C SER* 1.3 69.8 - - - +
479C LEU* 1.3 53.2 + - - +
480C GLU* 2.6 19.4 + - - -
481C LEU* 3.1 9.4 + - - +
482C ARG* 3.0 27.1 + - - +
4005C DAD 5.0 30.0 + - - +
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Residues in contact with LEU 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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476C ALA* 3.9 26.8 + - + +
477C SER 2.9 6.7 + - - -
478C GLY* 1.3 74.6 - - - +
480C GLU* 1.3 65.7 + - - +
482C ARG* 4.0 4.5 - - - +
483C CYS* 2.9 40.0 + - - -
618C GLY* 3.4 18.6 - - - +
621C ILE* 3.6 26.0 - - + -
622C CYS* 3.3 35.2 - - - -
654C ASP* 4.9 7.2 - - + -
677C MET* 5.2 1.3 - - + -
690C LEU* 4.0 22.4 - - + -
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Residues in contact with GLU 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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429C ARG* 5.3 8.3 + - - -
478C GLY* 2.6 6.9 + - - -
479C LEU* 1.3 80.4 - - - +
481C LEU* 1.3 69.0 + - - +
482C ARG 2.9 0.7 - - - -
483C CYS* 2.8 20.2 + - - +
484C LEU* 3.4 7.8 + - - +
614C LEU* 4.7 10.9 - - + +
615C GLN* 5.4 8.2 - - - +
618C GLY* 5.2 7.1 - - - -
654C ASP* 5.7 6.8 - - - +
4005C DAD 5.6 11.1 + - + +
21Q 2DT 5.5 6.8 - - - +
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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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478C GLY* 3.1 9.1 + - - +
480C GLU* 1.3 78.7 - - - +
482C ARG* 1.3 57.7 + - + +
484C LEU* 3.2 13.4 + - - +
485C ALA* 3.0 23.9 + - - +
500C ILE* 5.8 6.5 - - + -
505C ILE* 5.4 14.6 - - + -
506C HIS* 6.0 5.6 - - + -
525C ILE* 5.6 10.3 - - + -
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Residues in contact with ARG 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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477C SER* 3.1 37.7 + - - -
478C GLY* 3.0 18.3 + - - +
479C LEU 3.8 4.5 - - - +
480C GLU 2.9 0.8 - - - -
481C LEU* 1.3 74.3 - - + +
483C CYS* 1.3 66.2 + - - +
484C LEU 3.0 1.6 - - - -
485C ALA* 3.0 9.1 + - - +
486C HIS* 3.0 26.5 + - - +
500C ILE* 5.1 20.2 + - + +
501C LEU* 5.4 8.9 - - - +
686C PHE* 4.2 2.6 - - - -
688C CYS* 3.7 23.6 - - - +
689C LEU* 2.6 32.1 + - - +
690C LEU* 3.8 23.8 - - + +
691C ASP* 3.3 23.7 + - - +
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Residues in contact with CYS 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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479C LEU* 2.9 27.8 + - - -
480C GLU* 2.8 13.8 + - - +
482C ARG* 1.3 72.7 - - - +
484C LEU* 1.3 59.7 + - - +
486C HIS* 3.9 1.0 - - - +
487C PHE* 3.1 32.4 + - - -
614C LEU* 3.6 22.2 - - + +
617C ALA* 3.8 12.1 - - + -
618C GLY* 3.3 36.8 - - - -
621C ILE* 4.1 9.9 - - - -
686C PHE* 4.2 10.7 - - - -
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Residues in contact with LEU 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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480C GLU 3.4 3.2 + - - +
481C LEU* 3.2 16.3 + - - +
482C ARG 3.0 0.6 - - - -
483C CYS* 1.3 78.2 - - - +
485C ALA* 1.3 67.5 + - - +
487C PHE* 3.3 1.5 + - - +
488C MET* 2.7 43.8 + - + +
525C ILE* 4.7 18.8 - - + -
528C PHE* 4.8 8.3 - - + -
562C ILE* 4.3 20.0 - - + -
565C LEU* 3.3 32.3 - - + -
610C LEU* 4.4 5.6 - - + -
614C LEU* 3.4 28.0 - - + +
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Residues in contact with ALA 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 3.0 12.9 + - - +
482C ARG* 3.0 14.5 + - - +
484C LEU* 1.3 77.2 - - - +
486C HIS* 1.3 67.3 + - - +
488C MET* 2.9 17.9 + - - +
489C ALA* 3.0 13.2 + - - +
496C TYR* 4.2 14.9 - - + +
497C ALA* 3.8 31.5 + - - +
500C ILE* 5.4 3.4 - - + -
688C CYS* 4.2 7.2 - - + -
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Residues in contact with HIS 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 ARG 3.0 11.4 + - - +
483C CYS 3.9 1.1 - - - +
485C ALA* 1.3 77.8 - - - +
487C PHE* 1.3 101.4 + + - +
489C ALA* 2.9 20.9 + - - +
490C ARG* 4.2 1.6 + - - +
497C ALA* 5.8 0.4 - - - -
596C LEU* 4.5 4.6 - - - +
684C TRP 4.6 3.1 - - - -
685C ASN 3.7 9.2 - - - -
686C PHE* 3.5 58.6 - + + -
687C ARG* 2.9 34.7 + - + +
688C CYS* 4.3 5.7 - - + +
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Residues in contact with PHE 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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483C CYS 3.1 22.5 + - - +
484C LEU* 3.8 3.1 - - - +
486C HIS* 1.3 105.1 - + - +
488C MET* 1.3 57.1 + - - +
489C ALA 3.3 2.5 + - - -
490C ARG* 4.1 17.5 + - - +
565C LEU* 3.1 30.5 - - + +
596C LEU* 4.7 13.2 - - + -
613C LEU* 3.6 44.2 - - + -
614C LEU* 4.2 7.0 - - + -
617C ALA* 3.5 32.1 - - + -
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Residues in contact with MET 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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484C LEU* 2.7 44.9 + - + +
485C ALA* 3.3 4.7 - - - +
487C PHE* 1.3 71.9 - - - +
489C ALA* 1.3 58.9 + - - +
490C ARG 3.4 1.6 - - - +
491C PHE* 3.6 8.9 + - - +
492C ASP* 2.9 30.8 + - + +
495C GLU* 5.7 0.4 - - + -
496C TYR* 3.3 34.3 - - + +
561C ALA* 3.9 28.3 - - + +
562C ILE* 3.4 45.8 - - + -
565C LEU* 3.9 12.3 - - + -
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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