Contacts of the helix formed by residues 559 - 571 (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 THR 559 (chain C).
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Specific contacts
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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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Residues in contact with PRO 560 (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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556C LEU 5.1 1.1 - - - +
557C GLU* 4.2 9.4 - - - +
558C ASN 3.6 7.9 - - - +
559C THR* 1.3 87.1 - - - +
561C ALA* 1.3 55.5 + - + +
563C ALA* 3.1 13.5 + - + +
564C ALA* 2.5 36.0 + - - +
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Residues in contact with ALA 561 (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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488C MET* 3.9 43.8 - - + +
491C PHE* 4.2 4.2 - - + -
492C ASP* 4.1 16.8 - - + +
559C THR* 3.2 1.7 - - - -
560C PRO* 1.3 81.0 - - + +
562C ILE* 1.3 62.0 + - + +
564C ALA* 3.0 9.2 + - - +
565C LEU* 2.8 28.8 + - - +
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Residues in contact with ILE 562 (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* 4.3 15.3 - - + -
488C MET* 3.4 33.7 - - + -
528C PHE* 3.9 25.1 - - + -
555C PHE* 4.7 17.3 - - + -
556C LEU* 5.8 7.0 - - + -
559C THR* 3.4 33.4 - - - +
561C ALA* 1.3 76.9 - - + +
563C ALA* 1.3 61.5 + - - +
565C LEU* 3.7 5.7 - - - +
566C ARG* 3.1 23.8 + - + +
610C LEU* 4.5 16.4 - - + -
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Residues in contact with ALA 563 (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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556C LEU* 4.0 24.6 - - + +
559C THR 3.7 1.7 + - - +
560C PRO* 3.1 23.0 - - + +
562C ILE* 1.3 78.9 - - - +
564C ALA* 1.3 60.0 + - - +
566C ARG* 3.7 3.9 + - - +
567C GLU* 2.3 42.8 + - - +
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Residues in contact with ALA 564 (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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491C PHE* 3.3 38.9 - - + -
560C PRO 2.5 17.1 + - - +
561C ALA* 3.0 10.7 + - - +
563C ALA* 1.3 70.4 - - - +
565C LEU* 1.3 70.0 + - - +
567C GLU* 3.1 8.1 + - - +
568C SER* 2.9 20.3 + - - -
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Residues in contact with LEU 565 (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* 3.3 27.4 - - + -
487C PHE* 3.1 48.7 - - + +
488C MET* 3.8 5.4 - - + +
490C ARG* 6.5 0.4 - - - -
491C PHE* 3.5 8.2 - - + -
561C ALA 2.8 17.7 + - - +
562C ILE* 3.7 5.4 - - - +
564C ALA* 1.3 70.6 - - - +
566C ARG* 1.3 64.1 + - - +
568C SER* 2.4 30.2 + - - +
569C ILE* 3.1 13.3 + - + +
610C LEU* 3.2 36.8 - - + -
613C LEU* 5.1 4.9 - - + -
614C LEU* 5.1 0.4 - - + -
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Residues in contact with ARG 566 (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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562C ILE* 3.1 16.6 + - + +
563C ALA* 3.8 7.2 - - - +
565C LEU* 1.3 80.9 - - - +
567C GLU* 1.3 67.2 + - - +
569C ILE* 3.5 9.6 + - - +
570C GLN* 3.3 28.4 + - + +
610C LEU* 4.9 14.8 - - + -
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Residues in contact with GLU 567 (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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563C ALA* 2.3 38.6 + - - +
564C ALA* 3.1 9.7 + - - +
565C LEU 3.0 1.0 + - - -
566C ARG* 1.3 80.0 - - - +
568C SER* 1.3 66.1 + - - +
569C ILE 3.1 0.2 + - - -
570C GLN* 3.3 8.0 + - - +
571C GLN* 3.0 22.7 + - - +
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Residues in contact with SER 568 (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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195A GLU* 4.6 12.5 - - - +
490C ARG* 4.4 16.3 + - - -
491C PHE* 3.7 20.4 - - - -
564C ALA 2.9 10.4 + - - -
565C LEU* 2.4 33.8 + - - +
567C GLU* 1.3 75.6 - - - +
569C ILE* 1.3 62.7 + - - +
571C GLN* 3.3 17.7 - - - +
572C THR* 3.3 14.6 + - - -
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Residues in contact with ILE 569 (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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565C LEU* 3.1 15.2 + - + +
566C ARG* 3.7 8.3 - - - +
567C GLU 3.1 0.6 - - - -
568C SER* 1.3 79.5 + - - +
570C GLN* 1.3 64.7 + - - +
571C GLN 2.8 1.1 - - - -
572C THR* 2.5 38.9 + - - +
573C LEU* 3.6 4.9 + - + +
593C ILE* 5.0 15.5 - - + -
609C ALA* 3.6 27.4 - - + -
610C LEU* 3.9 30.7 - - + +
613C LEU* 3.8 32.1 - - + -
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Residues in contact with GLN 570 (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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566C ARG* 3.3 15.0 + - + +
567C GLU* 3.8 8.3 - - - +
569C ILE* 1.3 80.8 - - - +
571C GLN* 1.3 57.1 + - - +
573C LEU* 5.0 2.6 - - - +
574C VAL* 2.8 55.4 + - + +
606C PRO* 2.8 49.3 + - - +
609C ALA* 4.0 10.1 - - - +
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Residues in contact with GLN 571 (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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195A GLU* 6.2 2.7 - - - +
567C GLU 3.0 13.3 + - - +
568C SER* 3.3 16.2 - - - +
569C ILE 2.8 0.2 - - - -
570C GLN* 1.3 78.6 - - - +
572C THR* 1.3 58.8 + - - +
573C LEU 3.5 2.3 + - - -
574C VAL 3.9 10.2 - - - +
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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