Contacts of the helix formed by residues 460 - 477 (chain A) in PDB entry 4KM5
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 LEU 460 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ALA* 3.6 23.0 - - + +
165A LEU* 4.0 18.6 - - + -
166A ARG* 3.3 31.2 - - - +
169A LEU* 4.1 10.3 - - + -
405A CYS* 3.7 29.8 - - + -
408A ASP* 4.0 16.4 - - + -
409A CYS* 4.1 11.2 - - - -
412A LEU* 4.4 8.7 - - + -
456A ASP 3.8 0.4 + - - -
457A ARG 3.7 12.9 + - - +
458A LYS 3.4 3.0 + - - -
459A ASP* 1.3 76.9 - - - +
461A GLY* 1.3 58.3 + - - +
463A CYS* 3.9 0.2 - - - +
464A PHE* 3.0 29.3 + - - +
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Residues in contact with GLY 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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161A GLY 4.1 22.2 - - - +
162A ALA* 3.5 7.8 - - - +
165A LEU* 3.7 18.0 - - - +
458A LYS 5.3 0.2 + - - -
459A ASP 3.2 0.4 - - - -
460A LEU* 1.3 78.4 - - - +
462A LEU* 1.3 60.2 - - - +
464A PHE* 3.7 2.3 + - - +
465A ASP* 3.2 22.9 + - - +
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Residues in contact with LEU 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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161A GLY 5.2 0.4 - - - +
459A ASP* 3.1 32.0 + - + +
461A GLY* 1.3 75.0 - - - +
463A CYS* 1.3 64.8 + - - +
465A ASP* 3.4 9.2 + - + +
466A ASN* 3.3 37.1 + - - +
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Residues in contact with CYS 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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405A CYS* 3.7 19.3 - - - -
409A CYS* 3.7 19.1 - - - -
454A GLN 3.2 27.8 - - - -
455A TRP* 3.7 14.1 - - + -
459A ASP* 2.7 38.1 + - - +
460A LEU 3.9 0.7 - - - +
462A LEU* 1.3 73.6 - - - +
464A PHE* 1.3 62.3 + - - +
466A ASN* 3.3 13.3 + - - +
467A CYS* 3.3 24.3 + - - -
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Residues in contact with PHE 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 4.0 19.7 - - + -
409A CYS* 3.7 15.2 - - - -
412A LEU* 3.5 31.0 - - + -
413A MET* 3.6 32.8 - - + -
416A LEU* 4.5 3.8 - - + -
460A LEU 3.0 18.8 + - - +
461A GLY 4.1 4.0 - - - +
462A LEU 3.4 0.2 - - - -
463A CYS* 1.3 74.7 - - - +
465A ASP* 1.3 65.6 + - - +
467A CYS* 3.2 3.9 + - + +
468A VAL* 3.0 32.5 + - + +
516A PHE* 3.5 39.7 - + - -
519A PHE* 3.8 28.3 - + - -
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Residues in contact with ASP 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A GLY 3.2 16.6 + - - +
462A LEU* 3.6 12.4 - - + +
463A CYS 3.3 0.4 - - - -
464A PHE* 1.3 80.4 - - + +
466A ASN* 1.3 62.5 + - - +
468A VAL* 3.3 6.8 + - - +
469A THR* 3.0 39.5 + - - +
512A ARG* 3.1 37.4 + - - +
516A PHE* 5.3 5.6 - - + -
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Residues in contact with ASN 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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445A VAL* 4.8 11.5 - - + +
449A ASN* 5.3 11.3 + - - +
454A GLN 5.7 1.4 + - - -
455A TRP* 6.4 0.2 - - + -
462A LEU* 3.3 32.5 + - - +
463A CYS* 3.5 13.1 - - - +
464A PHE 3.2 0.4 - - - -
465A ASP* 1.3 81.4 - - - +
467A CYS* 1.3 59.0 + - - +
469A THR* 3.1 8.3 + - - -
470A TYR* 3.0 31.2 + - - +
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Residues in contact with CYS 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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409A CYS* 3.9 23.6 - - - -
413A MET* 3.8 24.2 - - + +
441A ALA* 5.7 0.9 - - - +
442A PHE* 4.4 12.3 - - + -
445A VAL* 4.3 18.2 - - + +
455A TRP* 4.0 19.5 - - - -
463A CYS 3.3 15.3 - - - -
464A PHE* 3.2 8.4 + - - +
466A ASN* 1.3 78.2 - - - +
468A VAL* 1.3 62.4 + - - +
470A TYR* 3.6 2.3 + - - +
471A PHE* 3.1 23.2 + - - +
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Residues in contact with VAL 468 (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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413A MET* 3.7 14.4 - - - -
416A LEU* 4.7 3.1 - - + -
464A PHE* 3.0 44.9 + - + +
465A ASP* 3.6 9.2 - - - +
466A ASN 3.3 0.2 - - - -
467A CYS* 1.3 77.4 - - - +
469A THR* 1.3 58.7 + - - +
471A PHE* 3.2 5.0 + - - +
472A LEU* 2.9 28.4 + - + +
508A ILE* 3.7 27.2 - - + +
512A ARG* 4.2 26.2 - - + -
516A PHE* 4.0 11.2 - - + -
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Residues in contact with THR 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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465A ASP* 3.0 23.8 + - - +
466A ASN* 3.1 19.6 + - - -
468A VAL* 1.3 74.9 - - - +
470A TYR* 1.3 56.6 + - - +
472A LEU* 3.3 12.9 + - + +
473A GLN* 3.0 26.2 + - - +
476A ARG* 4.8 2.1 + - - -
512A ARG* 3.4 39.0 - - - +
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Residues in contact with TYR 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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441A ALA* 3.7 14.6 - - + -
444A HIS* 3.2 41.6 - + + +
445A VAL* 3.6 25.1 - - + -
448A GLN* 3.6 36.4 + - - -
466A ASN 3.0 19.7 + - - +
467A CYS 3.9 1.8 - - - +
469A THR* 1.3 75.0 + - - +
471A PHE* 1.3 66.5 + - - +
473A GLN* 3.3 28.0 + - - +
474A CYS* 3.1 44.2 + - - -
480A LEU* 5.3 0.8 - - + +
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Residues in contact with PHE 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A MET* 3.9 19.3 - - + -
417A LEU* 5.7 5.2 - - + -
433A PHE* 5.2 1.8 - + + -
437A HIS* 3.7 31.0 - - + -
438A VAL* 4.0 15.9 - - + -
441A ALA* 3.6 20.0 - - + -
467A CYS 3.1 18.6 + - - +
468A VAL* 3.2 4.7 + - - +
470A TYR* 1.3 75.8 - - - +
472A LEU* 1.3 64.9 + - - +
474A CYS* 3.4 8.0 + - + +
475A LEU* 3.2 33.6 + - + +
480A LEU* 4.7 0.4 - - + -
491A PHE* 3.8 24.0 - + - -
504A LEU* 3.9 27.1 - - + -
508A ILE* 3.8 22.2 - - + -
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Residues in contact with LEU 472 (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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468A VAL* 2.9 26.7 + - + +
469A THR* 3.4 18.2 - - + +
471A PHE* 1.3 74.7 - - - +
473A GLN* 1.3 59.4 + - - +
475A LEU* 3.1 10.0 + - + +
476A ARG* 3.0 58.1 + - - +
505A THR* 3.8 37.0 - - + +
508A ILE* 3.7 25.6 - - + -
509A GLU* 4.0 11.7 - - + -
512A ARG* 4.5 14.8 - - - +
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Residues in contact with GLN 473 (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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448A GLN* 6.0 0.2 - - - +
469A THR 3.0 13.1 + - - +
470A TYR* 3.3 31.9 + - - +
472A LEU* 1.3 75.4 - - - +
474A CYS* 1.3 56.7 + - - +
476A ARG* 4.1 12.5 - - - +
477A THR* 2.7 56.0 + - + +
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Residues in contact with CYS 474 (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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441A ALA* 4.9 1.3 - - - -
470A TYR* 3.1 52.3 + - - -
471A PHE* 3.5 12.1 - - + +
472A LEU 3.2 0.2 - - - -
473A GLN* 1.3 80.5 - - - +
475A LEU* 1.3 58.2 + - - +
477A THR* 3.8 1.8 - - - -
478A GLU 3.1 4.3 + - - -
479A LYS 3.0 45.9 + - - +
480A LEU* 3.9 15.7 - - + -
491A PHE* 3.2 24.2 - - + -
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Residues in contact with LEU 475 (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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433A PHE* 4.2 0.2 - - + -
471A PHE* 3.2 30.5 + - + +
472A LEU* 3.1 11.9 + - - +
474A CYS* 1.3 75.7 - - - +
476A ARG* 1.3 67.2 + - - +
478A GLU* 3.2 19.1 + - - +
491A PHE* 3.5 26.7 - - + -
501A LYS* 3.6 32.4 - - + +
502A GLU* 6.1 0.7 - - - +
504A LEU* 3.9 17.7 - - + -
505A THR* 3.2 41.7 - - - +
508A ILE* 4.0 11.4 - - + -
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Residues in contact with ARG 476 (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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469A THR 4.8 1.8 + - - -
472A LEU* 3.0 52.5 + - - +
473A GLN* 4.0 11.0 - - - +
475A LEU* 1.3 78.0 - - - +
477A THR* 1.3 62.2 + - + +
478A GLU* 3.1 4.7 + - - +
498A LYS* 5.7 1.9 + - - -
505A THR* 4.1 14.4 - - + +
509A GLU* 2.9 29.7 + - - +
512A ARG* 6.2 0.2 - - - +
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Residues in contact with THR 477 (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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473A GLN* 2.7 42.9 + - + +
474A CYS* 3.8 1.7 - - - -
476A ARG* 1.3 78.3 - - + +
478A GLU* 1.3 69.0 + - - +
479A LYS* 3.2 34.7 + - - +
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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
------------------------------------------------------------
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