Contacts of the helix formed by residues 518 - 527 (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 ARG 518 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504C ASP* 3.4 18.2 + - - -
506C HIS* 3.4 44.9 - - + +
507C THR* 4.0 23.4 - - + +
510C GLN* 3.9 23.1 - - - +
517C THR* 1.3 71.7 + - - +
519C ASP* 1.3 64.4 + - - +
520C ASN 2.9 4.5 - - - -
521C ALA* 2.6 28.4 + - - +
522C LYS* 2.9 11.5 + - + +
4005C DAD 3.6 18.6 + - - -
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Residues in contact with ASP 519 (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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517C THR* 3.5 9.4 + - + +
518C ARG* 1.3 88.7 + - - +
520C ASN* 1.3 60.4 + - - +
522C LYS* 3.4 22.2 + - - +
523C THR* 3.3 17.7 + - - -
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Residues in contact with ASN 520 (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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515C LEU* 3.9 14.3 - - + +
516C PRO* 4.2 14.1 - - + +
517C THR* 3.0 37.8 + - + +
518C ARG 2.9 0.6 - - - -
519C ASP* 1.3 76.9 - - - +
521C ALA 1.3 51.6 + - - +
523C THR* 3.0 9.7 + - - -
524C PHE* 2.8 33.4 + - - +
540C ILE 3.6 22.8 + - - +
541C VAL* 3.9 17.2 + - - +
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Residues in contact with ALA 521 (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* 4.1 8.3 - - - +
509C ASN* 4.3 6.1 - - - +
510C GLN* 3.5 41.5 + - - +
515C LEU* 3.5 11.2 - - - +
517C THR 3.4 1.4 + - - +
518C ARG* 2.6 16.9 + - - +
520C ASN* 1.3 74.1 + - - +
522C LYS* 1.3 54.1 + - - +
524C PHE* 3.7 4.3 - - - +
525C ILE* 2.9 34.2 - - - -
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Residues in contact with LYS 522 (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* 4.2 24.8 + - + +
518C ARG* 2.9 9.7 + - + +
519C ASP* 3.5 27.1 - - - +
520C ASN 3.2 0.4 - - - -
521C ALA* 1.3 76.8 + - - +
523C THR* 1.3 59.5 + - - +
525C ILE* 3.4 16.5 - - - +
526C TYR* 3.4 14.9 - - - +
4005C DAD 4.5 7.6 + - + -
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Residues in contact with THR 523 (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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519C ASP 3.3 11.5 + - - -
520C ASN* 3.0 10.4 + - - -
522C LYS* 1.3 76.9 - - - +
524C PHE* 1.3 68.2 + - - +
525C ILE 3.0 2.6 + - - -
526C TYR* 3.5 2.1 + - - -
527C GLY* 3.1 22.1 + - - +
540C ILE* 4.8 17.7 - - + -
4005C DAD 5.6 9.6 - - - +
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Residues in contact with PHE 524 (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* 5.8 2.2 - - + -
513C ALA* 3.2 34.8 - - + -
515C LEU* 4.1 19.7 - - + -
520C ASN 2.8 15.0 + - - +
521C ALA* 3.7 5.8 - - - -
523C THR* 1.3 79.1 - - - +
525C ILE* 1.3 64.6 + - + +
527C GLY 3.4 13.5 - - - +
528C PHE* 3.7 18.6 - + + +
537C ILE* 5.3 14.8 - - + -
540C ILE* 6.0 4.2 - - + +
548C GLY 6.1 0.2 - - - -
551C LEU* 4.3 9.6 - - + -
552C LYS* 4.2 21.1 - - + -
555C PHE* 3.7 32.5 - + + -
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Residues in contact with ILE 525 (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* 5.6 10.3 - - + -
484C LEU* 4.7 13.5 - - + -
506C HIS* 4.3 17.0 - - + +
509C ASN* 4.8 19.3 - - + +
521C ALA 2.9 19.9 - - - -
522C LYS* 3.4 15.0 - - - +
524C PHE* 1.3 75.5 - - + +
526C TYR* 1.3 65.7 + - + +
527C GLY 2.4 18.2 + - - -
528C PHE* 3.1 53.8 + - + -
555C PHE* 4.5 16.2 - - + -
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Residues in contact with TYR 526 (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* 6.5 0.2 - - + -
522C LYS 3.4 17.5 - - - +
523C THR* 3.5 3.4 + - - +
525C ILE* 1.3 83.8 - - + +
527C GLY* 1.3 54.3 + - - +
528C PHE 3.7 1.7 + - - -
4005C DAD 3.7 46.4 + - + +
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Residues in contact with GLY 527 (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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523C THR* 3.1 12.4 + - - +
524C PHE* 3.4 7.6 - - - +
525C ILE 2.4 11.1 + - - -
526C TYR* 1.3 74.4 - - - +
528C PHE* 1.3 64.3 + - - +
4005C DAD 6.0 1.3 - - - -
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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