Contacts of the helix formed by residues 461 - 467 (chain A) in PDB entry 3KSS
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 PHE 461 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457A ILE* 5.1 4.9 - - + -
458A THR* 3.0 16.2 + - - +
459A LEU 3.0 0.6 + - - -
460A SER* 1.3 81.1 + - - +
462A ILE* 1.3 65.8 + - - +
463A PRO* 3.3 0.4 - - - -
464A ILE* 2.9 42.9 + - + +
465A PHE* 3.8 3.7 + + - -
475A PHE* 5.5 0.9 - + - -
478A LEU* 5.4 0.9 - - + -
479A ALA* 3.5 37.2 - - + -
482A LYS* 4.9 23.8 - - + -
483A THR* 3.7 16.2 - - - +
928A THR* 3.3 40.4 - - + -
931A ILE* 3.6 23.1 - - + -
932A ALA* 4.8 9.0 - - + -
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Residues in contact with ILE 462 (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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458A THR 4.6 0.4 + - - -
459A LEU* 2.7 28.6 + - + +
461A PHE* 1.3 77.0 - - - +
463A PRO* 1.3 66.1 - - + +
465A PHE* 2.7 44.9 + - + +
466A THR* 3.1 9.3 + - - +
875A MET* 3.2 46.9 - - + +
878A MET* 6.3 0.7 - - + -
879A THR* 4.3 10.3 - - - +
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Residues in contact with PRO 463 (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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460A SER 2.9 29.6 - - - +
461A PHE 3.3 1.3 - - - -
462A ILE* 1.3 94.8 - - + +
464A ILE* 1.3 61.8 + - + +
466A THR* 2.9 25.0 + - - +
467A LEU 3.5 0.7 + - - -
872A LEU* 2.9 46.0 - - + +
875A MET* 4.3 9.4 - - + -
876A VAL* 5.2 3.8 - - + -
879A THR* 4.6 15.0 - - + +
931A ILE* 5.8 5.2 - - + -
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Residues in contact with ILE 464 (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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461A PHE* 2.9 46.8 + - + +
463A PRO* 1.3 82.6 - - + +
465A PHE* 1.3 62.4 + - - +
466A THR 3.3 0.3 + - - -
467A LEU* 3.6 18.0 + - - +
472A GLY* 5.0 6.2 - - - +
475A PHE* 4.6 11.2 - - + +
476A GLY* 5.9 1.7 + - - +
479A ALA* 4.4 10.8 - - + -
872A LEU* 5.1 2.5 - - + -
924A VAL* 4.3 26.9 - - + +
927A GLY 4.9 4.5 - - - +
928A THR* 4.6 10.1 - - - +
931A ILE* 4.1 26.7 - - + -
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Residues in contact with PHE 465 (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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461A PHE* 4.7 1.6 - + - -
462A ILE* 2.7 37.6 + - + +
464A ILE* 1.3 74.8 - - - +
466A THR* 1.3 59.9 + - - +
467A LEU 3.0 9.2 - - - +
473A ARG* 3.4 21.9 + - - +
476A GLY* 3.9 8.1 - - - -
479A ALA* 3.2 41.3 - - + -
480A PHE* 3.6 36.6 - + + -
483A THR* 3.3 39.5 - - + -
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Residues in contact with THR 466 (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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462A ILE* 3.1 8.8 + - - +
463A PRO* 2.9 15.7 + - - +
465A PHE* 1.3 76.2 - - - +
467A LEU* 1.3 65.6 + - - +
468A GLU* 3.3 11.6 + - - +
473A ARG* 5.0 0.5 + - - -
868A ALA* 4.1 6.9 - - - +
871A LYS* 3.3 22.9 - - + +
872A LEU* 3.3 34.5 - - - +
875A MET* 2.9 35.6 - - + +
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Residues in contact with LEU 467 (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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463A PRO 3.5 5.4 + - - +
464A ILE* 3.8 13.8 - - - +
465A PHE 3.0 15.6 - - - +
466A THR* 1.3 76.1 - - - +
468A GLU* 1.3 68.9 + - - +
469A GLY* 3.6 15.3 - - - +
471A GLU* 4.6 13.9 - - - +
472A GLY* 4.1 23.3 - - - +
473A ARG* 4.0 5.9 + - - -
865A LEU* 5.5 7.9 - - + -
868A ALA* 3.8 24.5 - - + -
872A LEU* 4.3 8.6 - - + +
924A VAL* 3.9 33.0 - - + -
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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