Contacts of the helix formed by residues 609 - 619 (chain A) in PDB entry 5ID6
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 SER 609 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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606A TYR* 5.4 1.0 - - - -
607A ASN* 4.8 4.0 - - - +
608A PRO* 1.3 78.7 - - - +
610A GLU* 1.3 59.5 + - - +
611A ASP* 2.8 23.9 + - - +
612A ILE* 3.1 31.2 + - - +
613A GLN* 3.5 23.7 + - - +
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Residues in contact with GLU 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608A PRO 5.6 0.9 - - - +
609A SER* 1.3 71.9 + - - +
611A ASP* 1.3 64.6 + - - +
612A ILE 3.2 1.1 - - - -
613A GLN* 3.1 37.8 - - - +
614A LYS* 2.4 64.9 + - + +
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Residues in contact with ASP 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A SER* 2.8 8.7 + - - +
610A GLU* 1.3 79.8 - - - +
612A ILE* 1.3 62.3 + - + +
614A LYS* 4.1 3.2 - - - +
615A ILE* 3.1 37.3 + - - +
631A ASP* 4.9 1.4 - - - +
634A LYS* 2.6 40.3 + - - +
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Residues in contact with ILE 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A PHE* 3.6 29.2 - - + -
608A PRO* 5.0 2.0 - - + -
609A SER* 3.1 43.0 + - - +
611A ASP* 1.3 77.8 - - + +
613A GLN* 1.3 67.1 + - - +
615A ILE* 3.2 9.6 + - - +
616A TYR* 3.1 20.6 + - - +
634A LYS* 4.4 21.8 - - + +
635A LEU* 4.3 7.9 - - + +
638A PHE* 3.8 42.6 - - + -
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Residues in contact with GLN 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A PHE* 4.6 11.7 - - + -
603A MSE 4.0 21.5 - - - +
608A PRO* 3.7 35.6 + - + +
609A SER 3.5 14.5 + - - +
610A GLU* 3.1 30.3 + - - +
611A ASP 3.5 0.2 - - - -
612A ILE* 1.3 77.6 - - - +
614A LYS* 1.3 57.5 + - - +
616A TYR* 3.2 4.9 + - - +
617A LYS* 3.0 41.1 + - - +
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Residues in contact with LYS 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A GLU* 2.4 62.7 + - + +
611A ASP* 4.1 4.5 - - - +
613A GLN* 1.3 76.4 - - - +
615A ILE* 1.3 63.1 + - + +
617A LYS* 3.2 31.8 - - + +
618A ASN* 2.8 43.1 + - - +
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Residues in contact with ILE 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A ASP* 3.1 28.7 + - - +
612A ILE* 3.2 10.8 + - - +
614A LYS* 1.3 76.5 - - + +
616A TYR* 1.3 53.1 + - - +
619A GLY* 2.7 28.6 + - - -
620A THR* 3.0 28.7 + - - +
621A PHE* 3.7 19.9 - - + -
631A ASP* 3.2 59.5 - - + +
634A LYS* 4.1 14.8 - - + -
635A LEU* 4.6 9.2 - - + +
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Residues in contact with TYR 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A PRO* 3.6 31.4 - - + +
598A PHE* 3.7 43.5 - + + -
612A ILE 3.1 12.8 + - - +
613A GLN* 3.2 8.0 + - - +
615A ILE* 1.3 75.4 - - - +
617A LYS* 1.3 70.9 + - + +
619A GLY* 3.1 12.3 + - - -
621A PHE* 3.5 30.8 - + + -
622A LYS* 5.3 3.6 - - - -
635A LEU* 4.8 6.3 - - + -
639A PHE* 5.9 0.4 - + - -
670A TYR* 6.2 0.2 - - - -
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Residues in contact with LYS 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A GLU* 4.8 1.6 + - - -
613A GLN* 3.0 26.4 + - - +
614A LYS* 3.2 57.1 - - + +
616A TYR* 1.3 83.1 - - + +
618A ASN* 1.3 74.6 + - - +
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Residues in contact with ASN 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A LYS* 2.8 36.2 + - - +
617A LYS* 1.3 90.2 - - - +
619A GLY* 1.3 64.0 + - - +
620A THR* 4.0 17.9 - - + +
622A LYS* 5.5 0.2 - - - -
626A MSE 5.5 4.3 - - - +
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Residues in contact with GLY 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A ILE 2.7 13.1 + - - -
616A TYR 3.1 11.7 + - - -
618A ASN* 1.3 80.9 - - - +
620A THR* 1.3 56.5 + - - -
621A PHE* 3.0 22.0 + - - -
622A LYS* 3.5 29.3 + - - +
623A LYS 5.1 1.0 - - - +
626A MSE 4.6 8.5 - - - +
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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