Contacts of the helix formed by residues 679 - 688 (chain C) in PDB entry 5YDI
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 679 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484C THR 6.0 1.8 - - - -
535C TYR* 3.9 4.2 - - - -
553C LYS* 3.4 38.7 - - - +
557C ASP* 2.8 41.8 + - - +
561C THR* 4.6 11.4 - - + -
582C LEU* 6.2 2.7 - - + -
676C ARG 4.7 1.6 + - - -
677C GLY* 4.0 1.2 - - - -
678C PRO* 1.3 81.0 - - + +
680C LEU* 1.3 63.8 + - - +
681C ARG 3.3 2.9 - - - -
682C GLN* 3.3 41.5 + - + +
683C CYS* 3.2 27.4 + - - -
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Residues in contact with LEU 680 (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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538B TRP* 3.9 22.0 - - - +
539B THR* 3.7 36.6 - - + +
565C ASN* 5.5 0.7 - - - +
662C ARG* 3.2 44.0 - - + +
676C ARG* 3.2 35.1 + - + +
677C GLY* 3.8 9.0 - - - +
678C PRO 3.6 0.6 - - - -
679C ARG* 1.3 75.1 - - - +
681C ARG* 1.3 62.0 + - - +
683C CYS* 3.5 5.7 + - + +
684C ALA* 3.1 23.7 + - - +
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Residues in contact with ARG 681 (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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533B PHE* 3.5 30.1 + - + -
534B GLU* 3.4 24.4 + - - +
536B THR 3.8 10.1 + - - -
537B ASP* 5.5 0.2 - - - +
538B TRP* 3.3 45.0 - - + +
539B THR* 5.8 2.1 - - + +
681B ARG* 3.1 32.2 - - - +
534C GLU* 3.1 29.7 + - - +
679C ARG 3.3 0.4 - - - -
680C LEU* 1.3 78.6 - - - +
682C GLN* 1.3 72.1 + - - +
684C ALA* 3.3 5.4 + - - +
685C PHE* 3.1 23.9 + - - +
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Residues in contact with GLN 682 (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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534C GLU* 4.4 14.7 + - + +
535C TYR* 3.5 16.3 - - + +
557C ASP* 3.4 21.3 - - - +
562C CYS* 4.0 2.0 - - - -
679C ARG* 3.3 54.1 - - + +
680C LEU 3.4 0.4 - - - -
681C ARG* 1.3 92.2 - - - +
683C CYS* 1.3 61.9 + - - +
685C PHE* 3.1 19.6 + - - +
686C TRP* 3.1 22.2 + - - -
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Residues in contact with CYS 683 (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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561C THR* 4.4 0.9 - - - -
562C CYS* 2.0 58.8 - - + -
565C ASN* 3.6 20.6 - - + +
662C ARG* 5.6 2.2 - - - +
678C PRO 4.4 1.1 - - - -
679C ARG* 3.2 20.4 + - - +
680C LEU* 3.9 5.6 - - + +
681C ARG 3.4 0.2 - - - -
682C GLN* 1.3 73.0 - - - +
684C ALA* 1.3 60.5 + - - +
686C TRP 4.6 0.2 - - - +
687C LYS* 3.1 50.8 + - - +
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Residues in contact with ALA 684 (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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533B PHE* 4.0 2.2 - - + -
538B TRP* 3.7 41.5 - - + +
680C LEU 3.1 14.3 + - - +
681C ARG 3.4 10.1 - - - +
683C CYS* 1.3 76.0 - - - +
685C PHE* 1.3 59.2 + - - +
687C LYS* 5.2 0.2 - - - -
688C LYS* 3.0 33.0 + - + +
689C TYR* 3.0 11.3 + - - +
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Residues in contact with PHE 685 (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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533B PHE* 3.6 25.3 - + + -
530C ALA* 3.4 35.4 - - + -
531C ILE* 3.9 18.2 - - + -
534C GLU* 4.1 13.2 - - + -
535C TYR* 4.4 9.0 - + - -
681C ARG 3.1 8.6 + - - +
682C GLN* 3.1 12.8 + - - +
684C ALA* 1.3 78.9 - - - +
686C TRP* 1.3 88.7 + + - +
689C TYR* 3.5 34.5 + + - -
690C LEU* 2.8 56.5 + - + +
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Residues in contact with TRP 686 (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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520C ASN* 3.4 29.4 - - - -
523C VAL* 6.1 0.7 - - + -
531C ILE* 3.8 14.6 - - + -
535C TYR* 2.7 41.0 + + - -
554C MET* 3.6 20.2 - - + -
557C ASP* 3.7 14.9 - - + +
558C TYR* 3.5 48.5 - + + -
562C CYS* 4.4 6.7 - - + -
682C GLN 3.1 25.8 + - - +
683C CYS* 4.4 2.9 - - - +
685C PHE* 1.3 84.3 - + - +
687C LYS* 1.3 65.1 + - + +
690C LEU* 3.5 32.8 - - + +
691C PRO* 3.3 19.9 - - - +
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Residues in contact with LYS 687 (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 CYS* 3.6 34.7 + - + +
563C ASN* 5.7 2.9 - - - +
565C ASN* 4.6 3.4 - - - +
566C GLU* 3.7 41.9 - - - +
569C GLN* 4.6 9.4 + - - -
662C ARG* 5.2 4.4 - - - +
683C CYS* 3.1 30.8 + - - +
684C ALA* 5.2 0.4 - - - -
686C TRP* 1.3 80.8 - - + +
688C LYS* 1.3 65.6 + - + +
691C PRO* 3.3 14.9 - - - +
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Residues in contact with LYS 688 (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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538B TRP* 4.2 29.6 - - + -
684C ALA* 3.0 20.7 + - + +
687C LYS* 1.3 83.4 - - + +
689C TYR* 1.3 65.9 + - + +
691C PRO* 3.4 9.1 - - - +
692C GLN* 3.7 19.2 + - - +
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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