Contacts of the helix formed by residues 687 - 696 (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 LYS 687 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A TYR* 3.7 46.2 - - + +
576A GLY* 2.8 30.9 + - - +
577A ASN 3.9 0.9 - - - +
578A TYR* 3.7 29.8 + - + -
685A ALA 3.2 1.8 + - - -
686A SER* 1.3 72.3 - - - +
688A LYS* 1.3 63.9 + - - +
691A ASP* 2.7 57.2 + - - +
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Residues in contact with LYS 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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572A ASP* 4.3 7.6 - - - +
574A VAL* 3.1 41.1 - - + +
576A GLY* 5.5 1.3 - - - +
686A SER* 3.0 19.3 - - - +
687A LYS* 1.3 76.2 - - - +
689A GLU* 1.3 65.3 + - + +
691A ASP* 3.5 6.6 - - - +
692A LYS* 3.1 24.3 + - - +
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Residues in contact with GLU 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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568A LYS 4.6 0.9 - - - +
569A ILE* 3.4 31.9 - - + +
570A ASP* 3.9 17.5 + - - +
572A ASP* 4.8 1.4 - - - +
686A SER* 3.0 33.3 + - - +
688A LYS* 1.3 84.6 - - + +
690A VAL* 1.3 61.9 + - - +
692A LYS* 3.3 8.4 + - - +
693A LEU* 3.0 22.9 + - - +
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Residues in contact with VAL 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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547A LEU* 4.6 6.5 - - + -
566A LEU* 4.4 16.6 - - + -
569A ILE* 4.7 8.7 - - + +
578A TYR* 3.4 31.0 - - + -
685A ALA* 4.5 13.2 - - + -
686A SER 3.2 17.5 + - - +
689A GLU* 1.3 71.4 - - - +
691A ASP* 1.3 63.1 + - - +
693A LEU* 2.7 32.4 + - + +
694A VAL* 2.9 13.2 + - + +
699A LEU* 3.9 23.6 - - + -
701A MSE 4.6 8.7 - - - -
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Residues in contact with ASP 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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578A TYR* 2.5 31.3 + - - -
687A LYS* 2.7 47.1 + - - +
688A LYS* 3.5 7.4 - - - +
690A VAL* 1.3 76.5 - - - +
692A LYS* 1.3 56.7 + - - +
694A VAL* 3.1 29.1 + - - +
695A GLU* 3.2 19.4 + - - +
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Residues in contact with LYS 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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688A LYS 3.1 10.6 + - - +
689A GLU* 3.4 11.0 - - - +
690A VAL 3.1 0.2 - - - -
691A ASP* 1.3 74.4 - - - +
693A LEU* 1.3 60.9 + - + +
694A VAL 3.0 2.0 - - - -
695A GLU* 3.0 20.9 + - + +
696A GLU* 2.9 59.0 + - + +
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Residues in contact with LEU 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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565A CYS* 3.8 42.2 - - + +
566A LEU* 4.5 7.6 - - + -
569A ILE* 4.7 7.2 - - + -
689A GLU 3.0 18.4 + - - +
690A VAL* 2.7 28.3 + - + +
692A LYS* 1.3 73.0 - - + +
694A VAL* 1.3 58.5 + - - +
696A GLU* 3.6 6.7 + - - +
697A GLY 3.1 2.4 + - - -
698A LYS* 2.9 62.0 + - + +
699A LEU* 3.1 15.7 + - + -
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Residues in contact with VAL 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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24A VAL* 3.7 14.6 - - + +
25A GLY* 4.9 1.3 - - - -
26A LYS* 4.2 5.8 - - - +
27A THR* 3.5 34.0 + - + +
30A ASN* 3.3 13.2 - - - +
690A VAL 2.9 17.9 + - - +
691A ASP* 3.1 14.8 - - - +
692A LYS 3.0 0.2 - - - -
693A LEU* 1.3 74.7 - - - +
695A GLU* 1.3 66.5 + - + +
697A GLY* 2.9 13.0 + - - -
699A LEU* 3.2 23.8 - - + +
701A MSE 4.0 26.2 - - + -
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Residues in contact with GLU 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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26A LYS* 4.4 36.2 + - + +
30A ASN* 3.8 11.3 + - - +
691A ASP* 3.5 18.2 - - - +
692A LYS* 3.0 23.6 + - + +
694A VAL* 1.3 78.3 - - + +
696A GLU* 1.3 62.9 + - + +
697A GLY 3.3 0.9 + - - -
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Residues in contact with GLU 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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30A ASN* 4.3 3.8 + - - -
34A LYS* 4.0 5.9 + - - -
692A LYS* 2.9 55.8 + - + +
693A LEU* 4.2 6.8 - - - +
695A GLU* 1.3 74.5 - - + +
697A GLY* 1.3 62.2 + - - +
698A LYS* 3.1 42.8 + - + +
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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