Contacts of the helix formed by residues 547 - 559 (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 547 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538C GLY* 4.5 3.4 - - - +
541C VAL* 5.8 6.3 - - + -
543C ALA* 3.8 26.2 - - + +
545C LYS 3.4 0.6 - - - -
546C GLU* 1.3 86.2 - - + +
548C GLY* 1.3 63.1 + - - +
550C GLU* 3.5 6.4 - - - +
551C LEU* 3.0 24.8 + - - +
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Residues in contact with GLY 548 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537C ILE* 4.3 11.7 - - - +
538C GLY* 3.3 35.0 - - - -
545C LYS 3.0 6.2 + - - +
547C ARG* 1.3 75.5 - - - +
549C LYS* 1.3 55.7 + - - +
550C GLU 2.8 10.8 + - - -
551C LEU* 3.1 15.1 + - - +
552C LYS* 3.4 12.3 + - - +
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Residues in contact with LYS 549 (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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545C LYS 2.7 19.6 + - - +
546C GLU* 3.1 10.2 - - - +
548C GLY* 1.3 68.4 - - - +
550C GLU* 1.3 54.5 + - - +
552C LYS* 4.9 6.5 - - - -
553C LYS* 5.0 4.3 - - - +
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Residues in contact with GLU 550 (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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546C GLU* 3.0 32.8 - - - +
547C ARG* 3.5 9.2 - - - +
548C GLY 2.8 0.4 + - - -
549C LYS* 1.3 74.6 - - - +
551C LEU* 1.3 63.6 + - - +
552C LYS 3.4 0.7 - - - -
553C LYS* 2.9 28.1 - - - +
554C LYS* 3.1 10.9 + - - +
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Residues in contact with LEU 551 (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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513C ALA* 4.4 5.9 - - + +
514C GLU* 5.7 4.0 - - - +
515C LEU* 5.6 8.1 - - + -
524C PHE* 4.3 18.8 - - + -
537C ILE* 6.3 1.1 - - + -
547C ARG 3.0 15.8 + - - +
548C GLY* 3.6 7.4 - - - +
550C GLU* 1.3 74.1 - - - +
552C LYS* 1.3 54.3 + - - +
553C LYS 2.8 5.0 + - - -
554C LYS* 3.0 6.7 + - - +
555C PHE* 2.6 38.9 + - - +
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Residues in contact with LYS 552 (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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524C PHE* 4.2 15.8 - - + -
528C PHE* 6.2 4.5 - - + -
548C GLY 3.4 10.2 + - - +
549C LYS* 5.2 4.3 - - - -
550C GLU 5.2 1.6 - - - +
551C LEU* 1.3 77.6 - - - +
553C LYS* 1.3 53.0 + - - +
555C PHE* 4.4 2.2 - - - -
556C LEU* 2.7 40.8 + - + +
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Residues in contact with LYS 553 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549C LYS 5.0 2.4 - - - +
550C GLU* 2.9 25.4 + - - +
551C LEU 2.8 0.6 - - - -
552C LYS* 1.3 79.1 - - - +
554C LYS* 1.3 50.8 + - - +
555C PHE 3.1 0.2 + - - -
556C LEU* 3.2 3.1 - - - +
557C GLU* 2.7 39.1 + - - +
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Residues in contact with LYS 554 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512C ALA 3.2 12.4 - - - +
514C GLU* 3.4 41.3 - - + +
550C GLU 3.1 7.1 + - - +
551C LEU* 3.0 7.0 + - - +
553C LYS* 1.3 80.4 - - - +
555C PHE* 1.3 57.8 + - - +
557C GLU* 3.5 6.8 - - - +
558C ASN* 3.0 23.9 + - - +
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Residues in contact with PHE 555 (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* 3.5 28.3 - - + -
512C ALA* 3.1 33.9 - - + -
513C ALA* 3.5 21.5 - - + +
524C PHE* 3.7 24.0 - + + -
525C ILE* 4.5 13.7 - - + -
528C PHE* 3.6 35.9 - + - -
551C LEU 2.6 20.5 + - - +
552C LYS* 4.0 2.2 - - - +
554C LYS* 1.3 71.3 - - - +
556C LEU* 1.3 61.4 + - + +
557C GLU 2.9 9.8 + - - -
558C ASN 4.1 0.5 - - - -
559C THR* 3.2 32.5 + - - -
562C ILE* 4.7 20.2 - - + -
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Residues in contact with LEU 556 (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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528C PHE* 5.9 3.4 - - + -
552C LYS* 2.7 24.2 + - + +
553C LYS* 3.2 4.9 - - - +
555C PHE* 1.3 77.3 - - + +
557C GLU* 1.3 54.7 + - - +
559C THR 4.1 12.6 - - - -
560C PRO* 5.1 0.5 - - - +
562C ILE* 5.8 6.3 - - + -
563C ALA* 4.0 23.9 - - + +
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Residues in contact with GLU 557 (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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553C LYS 2.7 20.9 - - - +
554C LYS* 3.5 9.0 - - - +
555C PHE 3.0 0.2 + - - -
556C LEU* 1.3 77.7 - - - +
558C ASN* 1.3 62.2 + - - +
559C THR 3.1 5.5 + - - -
560C PRO* 4.2 10.8 - - - +
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Residues in contact with ASN 558 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511C ILE 5.2 0.9 - - - +
512C ALA* 3.6 23.9 - - - +
554C LYS 3.0 17.5 + - - +
557C GLU* 1.3 73.8 - - - +
559C THR* 1.3 58.9 + - - +
560C PRO* 3.6 7.5 - - - +
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Residues in contact with THR 559 (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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512C ALA* 4.8 4.7 - - - -
555C PHE* 3.2 30.7 + - - +
556C LEU* 4.1 3.5 - - - -
557C GLU 4.5 2.7 - - - -
558C ASN* 1.3 79.5 - - - +
560C PRO* 1.3 67.0 - - - +
561C ALA* 3.2 4.7 + - - +
562C ILE* 3.4 33.7 + - - +
563C ALA* 3.7 7.3 + - - +
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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