Contacts of the helix formed by residues 505 - 513 (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 ILE 505 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481C LEU* 5.4 12.6 - - + -
496C TYR* 4.4 18.4 - - + +
499C GLU* 4.2 16.6 - - + -
500C ILE* 3.9 27.5 - - + +
504C ASP* 1.3 78.1 + - - +
506C HIS* 1.3 101.7 + - + +
507C THR 3.4 1.8 - - - -
508C LYS* 3.1 25.3 + - + +
509C ASN* 3.0 29.9 + - - +
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Residues in contact with HIS 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C LEU* 6.0 5.8 - - + -
504C ASP* 3.6 0.8 + - - -
505C ILE* 1.3 96.8 - - + +
507C THR* 1.3 53.3 + - - +
509C ASN* 2.7 18.6 + - + +
510C GLN* 2.5 36.6 + - - +
518C ARG* 3.4 47.6 - - + +
521C ALA* 4.1 3.5 - - - +
522C LYS* 4.2 29.4 - - + +
525C ILE* 4.3 11.0 - - + +
526C TYR* 6.5 0.2 - - + -
4005C DAD 3.6 37.2 + - - -
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Residues in contact with THR 507 (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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504C ASP* 2.5 42.9 + - - +
506C HIS* 1.3 72.6 - - - +
508C LYS* 1.3 55.9 + - - +
510C GLN* 3.4 19.1 - - - +
511C ILE* 2.7 47.1 + - - +
518C ARG* 4.0 19.5 - - - +
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Residues in contact with LYS 508 (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 GLU* 5.3 7.5 - - - +
496C TYR* 5.3 9.4 - - + +
499C GLU* 4.0 26.2 - - + -
504C ASP 4.6 6.3 - - - +
505C ILE* 3.1 21.8 + - + +
507C THR* 1.3 81.9 + - - +
509C ASN* 1.3 54.6 + - - +
511C ILE* 3.5 9.3 - - - +
512C ALA* 2.5 38.9 + - + +
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Residues in contact with ASN 509 (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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505C ILE* 3.0 40.0 + - - +
506C HIS* 2.7 21.9 + - - +
508C LYS* 1.3 76.8 - - - +
510C GLN* 1.3 59.0 + - - +
511C ILE 2.9 1.6 - - - -
512C ALA* 2.7 25.6 + - - +
513C ALA* 2.8 16.5 + - - +
521C ALA* 4.3 13.9 - - - +
524C PHE* 6.3 2.5 - - + -
525C ILE* 4.8 17.8 - - + +
555C PHE* 3.5 27.1 - - + -
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Residues in contact with GLN 510 (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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506C HIS 2.5 15.8 + - - +
507C THR* 3.4 23.1 + - - +
509C ASN* 1.3 72.4 - - - +
511C ILE* 1.3 58.2 + - - +
513C ALA 2.5 21.2 - - - +
514C GLU* 4.6 0.2 - - - -
515C LEU* 3.4 22.5 + - + +
516C PRO 2.5 26.3 - - - +
517C THR 3.6 18.6 - - - +
518C ARG* 3.9 19.7 + - - +
521C ALA* 3.5 15.6 + - - +
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Residues in contact with ILE 511 (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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507C THR* 2.7 26.7 + - - +
508C LYS* 3.6 7.2 - - - +
510C GLN* 1.3 81.8 - - - +
512C ALA* 1.3 74.2 + - - +
513C ALA 3.3 5.8 + - - +
514C GLU* 4.1 8.8 + - - +
558C ASN* 5.2 1.3 - - + +
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Residues in contact with ALA 512 (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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508C LYS* 2.5 23.9 + - + +
509C ASN* 2.7 13.5 + - - +
511C ILE* 1.3 75.5 - - - +
513C ALA* 1.3 59.1 + - - +
514C GLU* 3.7 4.9 + - - +
554C LYS* 3.2 18.8 - - - +
555C PHE* 3.1 32.8 - - + +
558C ASN* 3.6 18.4 - - + +
559C THR* 4.8 7.4 - - - -
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Residues in contact with ALA 513 (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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509C ASN 2.8 8.9 + - - +
510C GLN 2.5 29.8 - - - +
511C ILE 3.4 1.4 - - - +
512C ALA* 1.3 75.3 - - - +
514C GLU* 1.3 54.4 + - - +
515C LEU* 2.5 17.2 + - + +
524C PHE* 3.2 40.2 - - + -
551C LEU* 4.4 7.2 - - + +
555C PHE* 3.5 19.5 - - + +
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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