Contacts of the helix formed by residues 562 - 570 (chain C) in PDB entry 5Y7K
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 ASN 562 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C TYR* 3.9 6.1 - - - -
48C TYR* 3.5 19.9 - - + +
529C ILE* 5.9 0.2 - - - +
545C ASP* 5.7 2.6 + - - -
560C ARG* 3.7 32.7 - - + +
561C LEU* 1.3 75.5 - - - +
563C TRP* 1.3 65.5 + - - +
564C ALA* 3.2 22.1 + - - +
565C THR* 3.0 30.4 + - - -
566C TYR 3.5 2.9 + - - -
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Residues in contact with TRP 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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45C LEU* 3.9 12.6 - - + -
48C TYR* 3.7 15.1 - + + -
543C LEU* 4.3 1.3 - - + -
562C ASN* 1.3 75.4 - - - +
564C ALA* 1.3 65.1 + - - +
566C TYR* 3.1 21.9 + + - +
567C LEU* 3.0 54.2 + - + +
627C TRP* 3.6 51.6 - + + -
651C ILE* 4.6 3.8 - - + -
752C TYR* 3.4 38.6 + + + -
755C MET* 4.0 33.9 - - + -
756C SER* 3.1 21.0 + - - -
759C ILE* 4.0 17.9 - - + -
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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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529C ILE* 3.9 11.5 - - + +
545C ASP* 4.8 7.9 - - - +
562C ASN* 3.2 16.8 + - - +
563C TRP* 1.3 79.7 - - + +
565C THR* 1.3 62.1 + - - +
567C LEU* 3.3 9.6 + - - +
568C ALA* 3.1 24.1 + - - +
575C VAL* 3.5 37.6 - - + +
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Residues in contact with THR 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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43C TYR* 3.5 26.7 - - + -
509C MET* 4.0 13.5 - - + -
510C PRO* 3.7 31.6 - - + +
529C ILE* 4.6 3.0 - - - +
560C ARG 3.4 12.5 + - - +
561C LEU* 4.5 3.8 - - + -
562C ASN* 3.0 32.8 + - - -
564C ALA* 1.3 77.7 - - - +
566C TYR* 1.3 57.2 + - - +
568C ALA 3.4 0.2 + - - -
569C SER* 2.9 32.2 + - - -
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Residues in contact with TYR 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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43C TYR* 3.4 19.0 - - + +
44C THR 3.5 11.9 - - - +
45C LEU* 3.1 41.2 - - + +
48C TYR* 5.0 2.7 - - + -
562C ASN 3.5 2.0 + - - +
563C TRP* 3.1 26.7 + + + +
565C THR* 1.3 78.2 - - - +
567C LEU* 1.3 80.7 + - + +
570C THR* 2.9 45.0 + - + -
571C GLU* 2.9 33.1 + - + +
756C SER* 3.6 23.8 - - - -
760C LYS* 3.9 13.0 + - - +
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Residues in contact with LEU 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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543C LEU* 3.5 32.3 - - + -
563C TRP* 3.0 49.6 + - + +
564C ALA* 3.3 13.0 + - + +
566C TYR* 1.3 99.1 - - + +
568C ALA* 1.3 57.0 + - - +
571C GLU* 3.4 9.7 - - + +
572C ASN 3.2 8.7 + - - -
573C ILE* 2.8 53.3 + - + +
575C VAL* 5.1 3.8 - - + -
756C SER* 5.2 2.2 - - - +
759C ILE* 4.6 7.9 - - + -
760C LYS* 5.9 1.8 - - + -
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Residues in contact with ALA 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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510C PRO* 3.8 11.4 - - + -
529C ILE* 3.6 37.2 - - + +
531C PRO* 3.1 30.7 - - - +
532C PRO* 3.4 0.9 - - - +
564C ALA 3.1 8.1 + - - +
565C THR 4.0 0.2 - - - +
567C LEU* 1.3 77.9 - - - +
569C SER* 1.3 64.2 + - - +
572C ASN* 3.3 8.0 + - - +
573C ILE 3.3 19.1 - - - +
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Residues in contact with SER 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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42C THR* 3.2 15.5 - - - +
43C TYR* 2.8 34.6 + - - -
508C GLN 2.6 26.8 + - - -
510C PRO* 3.9 8.9 - - - +
532C PRO* 3.6 17.1 - - - +
565C THR 2.9 18.6 + - - -
568C ALA* 1.3 80.1 - - - +
570C THR* 1.3 59.9 + - - +
572C ASN* 4.0 5.7 - - - +
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Residues in contact with THR 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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42C THR* 2.7 22.1 + - - +
43C TYR 2.7 24.4 + - - -
44C THR* 3.6 9.1 - - + -
566C TYR* 2.9 24.6 + - + -
569C SER* 1.3 78.3 - - - +
571C GLU* 1.3 81.3 + - - +
572C ASN* 3.3 9.1 + - - -
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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