Contacts of the helix formed by residues 602 - 607 (chain J) in PDB entry 6GYS
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 602 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509J TYR* 3.5 9.7 + - - -
598J GLN 3.3 12.7 - - - +
599J SER* 3.7 15.2 + - - +
600J GLU 2.9 8.1 + - - +
601J TYR* 1.3 69.4 - - - +
603J ILE* 1.3 68.6 + - - +
604J SER* 3.6 17.1 + - - -
605J ASP* 2.8 51.9 + - - +
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Residues in contact with ILE 603 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J TYR* 5.1 7.6 - - - +
72J ILE* 5.5 2.0 - - + -
509J TYR* 5.2 3.6 - - + -
513J ARG* 3.4 32.5 - - - +
543J ASN* 4.7 12.6 - - + +
544J ASP* 3.3 32.5 - - + +
547J ILE* 5.2 9.2 - - + -
548J ILE* 4.0 24.9 - - + +
598J GLN* 4.2 7.9 + - + +
601J TYR 3.2 3.8 + - - -
602J ASN* 1.3 75.5 + - - +
604J SER* 1.3 65.0 + - - +
605J ASP 3.1 4.9 + - - -
606J ILE* 3.4 26.0 + - + +
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Residues in contact with SER 604 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547J ILE* 4.5 12.3 - - - +
548J ILE* 5.9 3.6 - - - +
551J LYS* 4.0 22.5 + - - +
602J ASN* 3.2 14.8 + - - -
603J ILE* 1.3 80.8 - - - +
605J ASP* 1.3 60.6 + - - +
606J ILE* 3.1 8.3 + - - -
607J LEU* 3.4 23.7 + - - +
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Residues in contact with ASP 605 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506J LYS* 3.3 13.9 + - - +
509J TYR* 4.5 17.6 + - + -
600J GLU 4.8 1.4 - - - +
602J ASN* 2.8 49.5 + - - +
603J ILE 3.1 2.0 - - - -
604J SER* 1.3 75.9 - - - +
606J ILE* 1.3 57.1 + - - +
607J LEU 3.2 7.1 + - - +
608J SER* 4.1 3.6 + - - -
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Residues in contact with ILE 606 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72J ILE* 5.0 6.3 - - + -
76J GLY* 3.4 32.4 - - - +
77J LEU* 3.8 30.9 - - + +
80J THR 5.0 1.6 - - - +
506J LYS* 2.9 34.6 + - + +
509J TYR* 4.2 24.0 - - + -
548J ILE* 3.8 27.4 - - + -
603J ILE* 3.4 19.5 - - + +
604J SER* 4.7 1.3 - - - -
605J ASP* 1.3 77.0 - - - +
607J LEU* 1.3 65.6 + - + +
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Residues in contact with LEU 607 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76J GLY 5.2 1.3 - - - +
80J THR* 3.3 42.4 - - + +
82J GLN* 4.2 30.5 - - + +
506J LYS* 3.5 1.1 - - - -
548J ILE* 6.4 1.3 - - + -
551J LYS* 3.4 49.1 - - + +
604J SER* 3.4 17.5 + - - +
605J ASP* 3.2 3.8 - - - +
606J ILE* 1.3 83.9 - - + +
608J SER* 1.3 60.5 + - - +
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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