Contacts of the helix formed by residues 687 - 699 (chain A) in PDB entry 1Y8B
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 687 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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682A GLY 4.7 0.4 - - - -
683A ASN* 3.0 35.0 + - - +
684A PHE* 4.2 11.6 + - - -
685A ALA 3.8 1.0 - - - -
686A ASN* 1.3 74.5 - - - +
688A CYS* 1.3 53.5 + - - +
689A ALA* 2.7 25.8 + - - +
690A PHE* 2.9 23.0 + - - +
691A LYS* 4.1 0.7 + - - +
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Residues in contact with CYS 688 (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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686A ASN* 2.9 17.3 + - - -
687A SER* 1.3 70.9 - - - +
689A ALA* 1.3 52.9 + - - +
690A PHE 3.1 0.4 - - - -
691A LYS* 3.0 15.9 + - + +
692A ALA* 2.4 40.1 + - + +
715A TRP* 4.7 17.9 - - + -
719A GLU* 5.7 3.8 - - + +
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Residues in contact with ALA 689 (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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607A VAL* 4.8 2.6 - - + +
608A VAL* 5.6 9.0 - - + -
611A VAL* 3.6 36.8 - - + -
612A GLU* 6.4 0.9 - - + -
687A SER* 2.7 15.7 + - - +
688A CYS* 1.3 74.4 - - - +
690A PHE* 1.3 54.8 + - - +
692A ALA* 4.0 7.2 - - - -
693A ALA* 2.5 39.0 + - - +
719A GLU* 4.9 4.9 + - - -
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Residues in contact with PHE 690 (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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604A LEU* 5.6 0.5 - - - +
657A GLN* 5.2 9.9 - - - -
660A LEU* 4.8 5.8 - - + -
661A GLU* 3.2 31.9 - - + -
664A ALA* 3.6 31.0 - - + -
687A SER* 2.9 19.0 + - - +
689A ALA* 1.3 80.9 - - - +
691A LYS* 1.3 73.0 + - + +
693A ALA* 3.9 4.6 - - - +
694A SER* 3.0 25.2 + - - -
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Residues in contact with LYS 691 (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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687A SER 4.1 0.4 + - - -
688A CYS* 3.0 19.5 + - + +
690A PHE* 1.3 89.2 - - + +
692A ALA* 1.3 51.9 + - - +
694A SER* 2.7 20.0 + - - +
695A ASP* 2.7 41.1 + - - +
715A TRP* 5.4 5.8 - - + -
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Residues in contact with ALA 692 (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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607A VAL* 6.2 0.7 - - + -
688A CYS* 2.4 30.9 + - + +
689A ALA* 3.6 6.7 - - - +
691A LYS* 1.3 70.5 - - - +
693A ALA* 1.3 67.6 + - - +
694A SER 3.0 1.3 - - - -
695A ASP* 2.7 24.4 + - - +
696A LEU* 3.1 16.3 + - + +
715A TRP* 3.3 37.2 - - + -
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Residues in contact with ALA 693 (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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603A ILE* 4.5 4.0 - - - +
604A LEU* 3.5 29.6 - - + +
607A VAL* 3.4 26.3 - - + +
608A VAL* 5.5 1.6 - - + +
689A ALA 2.5 24.4 + - - +
690A PHE* 3.9 4.7 - - - +
692A ALA* 1.3 71.7 - - - +
694A SER* 1.3 60.3 + - - +
696A LEU* 3.2 30.1 - - - +
697A ILE* 4.5 3.8 + - - +
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Residues in contact with SER 694 (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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604A LEU* 4.6 4.0 - - - +
657A GLN* 5.2 5.7 + - - -
660A LEU* 3.4 34.0 - - - +
690A PHE* 3.0 18.6 + - - -
691A LYS* 2.7 27.7 + - - +
693A ALA* 1.3 74.7 - - - +
695A ASP* 1.3 67.4 + - - +
696A LEU 3.0 2.2 - - - -
697A ILE* 2.8 24.8 + - - +
698A PHE* 3.9 1.6 + - - +
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Residues in contact with ASP 695 (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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691A LYS* 2.7 40.6 + - - +
692A ALA* 2.7 16.8 + - - +
694A SER* 1.3 74.9 + - - +
696A LEU* 1.3 57.9 + - + +
697A ILE 3.0 0.7 + - - -
698A PHE* 3.0 7.3 + - - +
699A LEU* 2.7 42.7 + - + +
715A TRP* 2.9 41.0 - - + +
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Residues in contact with LEU 696 (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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603A ILE* 4.0 22.7 - - + -
607A VAL* 4.0 3.8 - - + -
635A LEU* 4.5 6.1 - - + -
639A SER* 5.1 10.4 + - - +
692A ALA* 3.1 12.3 + - + +
693A ALA* 3.2 27.1 - - - +
694A SER 2.9 0.2 + - - -
695A ASP* 1.3 79.5 - - + +
697A ILE* 1.3 57.4 + - + +
699A LEU* 4.9 1.8 - - - -
700A GLY* 2.9 30.3 + - - +
708A THR* 5.4 3.6 - - - +
711A LEU* 4.0 28.0 - - + -
712A LEU* 3.8 38.8 - - + +
715A TRP* 5.3 4.9 - - + -
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Residues in contact with ILE 697 (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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600A VAL* 4.2 32.8 - - + -
603A ILE* 4.5 15.5 - - + -
639A SER* 5.7 0.2 - - - +
642A ILE* 4.6 14.1 - - + +
646A LEU* 4.8 22.5 - - + +
656A VAL* 4.2 20.0 - - + -
660A LEU* 4.4 11.2 - - + -
693A ALA 4.6 3.4 - - - +
694A SER* 2.8 24.5 + - - +
696A LEU* 1.3 80.4 - - - +
698A PHE* 1.3 63.5 + - - +
700A GLY* 3.7 4.3 + - - -
701A VAL* 4.5 5.4 + - - +
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Residues in contact with PHE 698 (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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653A LYS* 4.0 45.8 - - + -
694A SER 3.9 0.8 + - - +
695A ASP* 3.0 10.0 + - - +
697A ILE* 1.3 77.8 - - - +
699A LEU* 1.3 58.5 + - + +
700A GLY 2.6 15.4 + - - -
701A VAL* 3.2 31.6 + - + +
702A LYS* 4.0 15.6 + - + +
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Residues in contact with LEU 699 (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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695A ASP* 2.7 27.3 + - + +
696A LEU 3.9 0.7 - - - -
698A PHE* 1.3 76.5 - - + +
700A GLY* 1.3 61.9 + - - +
701A VAL 3.3 0.9 - - - -
702A LYS* 3.9 33.9 - - + +
703A GLN* 3.2 20.1 + - - -
711A LEU* 3.7 30.8 - - + +
715A TRP* 4.2 31.9 - - + +
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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