Contacts of the helix formed by residues 460 - 473 (chain A) in PDB entry 1S11
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 460 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A PRO* 2.5 37.1 + - + +
416A PHE* 3.9 17.9 - + - -
458A LYS 2.7 5.1 + - - -
459A GLY* 1.3 68.5 - - - +
461A CYS* 1.4 69.2 + - - +
462A ILE 3.1 1.2 + - - -
464A ILE* 3.2 45.8 + - + +
529A PHE* 3.3 45.8 - + - -
789B MET* 3.8 7.9 - - + -
793B GLU* 3.1 48.5 - - + -
796B TRP* 3.7 32.0 + + + -
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Residues in contact with CYS 461 (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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416A PHE* 2.8 43.2 + - - +
417A VAL* 3.5 14.4 - - + -
459A GLY 2.8 2.2 + - - -
460A PHE* 1.4 80.8 - - - +
462A ILE* 1.3 68.0 + - + +
464A ILE* 2.9 9.3 + - - +
465A LEU* 2.7 39.2 + - + +
478A LEU* 5.6 0.9 - - + -
510A VAL* 2.7 37.5 - - - -
529A PHE* 6.6 0.2 - - - -
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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
----------------------------------------------------------
416A PHE 5.9 0.2 - - - +
417A VAL* 5.9 2.5 - - + -
447A ASP* 4.3 15.0 - - + +
448A GLU* 3.8 31.2 - - + +
451A GLY 4.2 3.4 - - - -
452A TYR* 3.7 43.5 - - + +
459A GLY* 2.8 28.8 + - - +
461A CYS* 1.3 73.0 - - + +
463A ASP* 1.3 70.9 + - - +
465A LEU* 3.3 11.2 + - - +
466A LYS* 2.9 29.4 + - - +
476A TYR* 4.0 1.4 + - - -
478A LEU* 5.1 7.6 - - + -
796B TRP* 3.7 19.1 - - + -
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Residues in contact with ASP 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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452A TYR* 2.4 24.9 + - - -
460A PHE 4.1 2.0 + - - -
461A CYS 3.0 0.4 + - - -
462A ILE* 1.3 80.2 - - - +
464A ILE* 1.4 58.4 + - - +
465A LEU 3.1 0.7 - - - -
466A LYS* 2.2 42.3 + - + +
467A LYS* 2.7 43.6 + - + +
792B LEU* 4.0 19.6 - - + +
796B TRP* 3.6 18.0 - - + +
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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
----------------------------------------------------------
460A PHE* 3.2 57.9 + - + +
461A CYS* 2.9 10.1 + - - +
463A ASP* 1.4 73.1 - - - +
465A LEU* 1.4 60.3 + - + +
468A ILE* 2.7 56.9 + - + +
510A VAL* 6.5 0.2 - - + -
529A PHE* 5.5 7.2 - - + -
764B ILE* 4.1 16.6 - - + -
780B ILE* 6.1 0.4 - - + -
783B LEU* 4.6 3.8 - - + -
789B MET* 3.9 26.5 - - + -
792B LEU* 3.7 26.6 - - + +
796B TRP* 4.6 0.4 - - + -
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Residues in contact with LEU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ILE* 4.2 9.0 - - + -
461A CYS* 2.7 34.3 + - + +
462A ILE* 3.4 7.6 - - - +
464A ILE* 1.4 79.2 - - + +
466A LYS* 1.4 66.0 + - - +
468A ILE* 4.7 2.5 - - + -
469A SER* 2.6 31.9 + - - +
476A TYR* 3.5 29.4 - - + -
478A LEU* 3.7 36.1 - - + -
510A VAL* 3.8 41.7 - - + -
764B ILE* 5.7 0.9 - - + -
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Residues in contact with LYS 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A GLU* 2.4 35.3 + - - -
452A TYR* 2.8 17.6 + - - +
462A ILE* 2.9 19.4 + - - +
463A ASP* 2.2 42.5 + - + +
465A LEU* 1.4 72.1 - - - +
467A LYS* 1.3 57.7 + - + +
469A SER* 3.9 0.2 - - - -
470A LYS* 2.7 60.3 + - + +
476A TYR* 3.3 24.6 + - + +
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Residues in contact with LYS 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ASP* 2.7 33.6 + - + +
466A LYS* 1.3 72.9 - - + +
468A ILE* 1.4 54.6 + - - +
470A LYS* 4.0 6.7 - - + +
471A SER* 2.7 39.6 + - - +
783B LEU* 3.7 24.2 - - + -
788B GLU* 2.4 47.7 + - - +
791B GLU* 5.8 1.6 + - - -
792B LEU* 4.6 4.7 - - + +
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Residues in contact with ILE 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ILE* 2.7 40.1 + - + +
465A LEU* 4.0 2.9 - - + +
467A LYS* 1.4 70.6 - - - +
469A SER* 1.3 57.9 + - - +
471A SER* 4.7 0.2 - - - -
472A VAL* 2.6 50.4 + - + +
474A PHE* 4.6 8.7 - - + -
508A MET* 5.4 4.9 - - + -
764B ILE* 4.0 11.7 - - + -
776B VAL* 4.4 15.5 - - + +
779B ALA* 4.0 5.6 - - + -
780B ILE* 3.7 40.8 - - + +
783B LEU* 3.5 23.5 - - + +
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Residues in contact with SER 469 (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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408A ILE* 5.3 2.6 - - - +
465A LEU* 2.6 28.9 + - - +
466A LYS 3.9 0.7 - - - -
468A ILE* 1.3 72.8 - - - +
470A LYS* 1.4 51.5 + - - +
473A LYS 2.6 28.4 + - - -
474A PHE* 2.7 47.6 + - - -
476A TYR* 3.3 37.1 - - - +
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Residues in contact with LYS 470 (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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466A LYS* 2.7 41.8 + - + +
467A LYS* 4.0 7.4 - - + +
469A SER* 1.4 71.1 - - - +
471A SER* 1.4 67.1 + - - +
473A LYS* 3.0 21.4 + - - +
474A PHE 5.7 1.6 - - - +
476A TYR* 6.4 0.9 - - + -
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Residues in contact with SER 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A LYS* 2.7 24.2 + - - +
470A LYS* 1.4 73.1 - - - +
472A VAL* 1.4 60.7 + - - +
473A LYS* 3.6 17.2 - - - +
779B ALA* 4.0 16.8 - - - -
782B GLN* 2.6 33.1 + - - -
783B LEU* 4.1 5.8 - - - +
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Residues in contact with VAL 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ILE* 2.6 36.4 + - + +
471A SER* 1.4 70.0 - - - +
473A LYS* 1.4 74.7 + - - +
474A PHE* 3.5 20.9 - - + -
772B TRP* 3.4 42.5 - - + -
775B GLN* 4.0 13.7 - - + +
776B VAL* 3.9 19.3 - - + -
779B ALA* 3.4 24.5 - - + -
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Residues in contact with LYS 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A SER 2.6 15.4 + - - -
470A LYS* 3.0 16.1 + - - +
471A SER 3.6 12.3 - - - -
472A VAL* 1.4 77.6 - - - +
474A PHE* 1.4 61.3 + - - +
772B TRP* 5.3 6.5 - - + -
775B GLN* 5.7 3.5 + - - +
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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