Contacts of the helix formed by residues 453 - 477 (chain A) in PDB entry 4KTQ
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 VAL 453 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A LEU* 3.0 16.7 + - + +
452A ASP* 1.3 65.6 + - - +
454A ALA* 1.3 73.1 + - + +
455A TYR 2.9 2.5 + - - -
456A LEU* 3.0 11.1 + - - +
457A ARG* 2.9 38.3 + - + +
550A PRO* 4.0 37.2 - - + +
553A ILE* 4.4 15.9 - - + -
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Residues in contact with ALA 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ASP* 3.6 6.6 + - - +
453A VAL* 1.3 82.7 - - + +
455A TYR* 1.3 65.4 + - - +
457A ARG* 3.2 11.3 - - - +
458A ALA* 3.1 16.1 + - - +
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Residues in contact with TYR 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ASP* 3.0 30.6 + - - +
453A VAL 3.0 0.4 - - - -
454A ALA* 1.3 77.7 - - - +
456A LEU* 1.3 61.9 + - - +
458A ALA* 2.5 43.1 + - + +
459A LEU* 3.1 19.6 + - + -
593A ARG* 2.8 58.2 + - - +
596A ARG* 3.4 24.5 + - + +
597A ALA* 3.4 33.4 - - + -
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Residues in contact with LEU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LEU* 3.4 45.3 - - + -
452A ASP 3.2 5.8 + - - +
453A VAL 3.0 7.1 + - - +
455A TYR* 1.3 83.6 - - + +
457A ARG* 1.3 61.2 + - - +
459A LEU* 3.5 12.9 + - + -
460A SER* 3.0 19.9 + - - -
545A TYR 5.2 1.1 - - - +
546A ILE* 3.4 35.4 - - + +
549A LEU* 4.4 6.1 - - + -
550A PRO* 4.0 23.8 - - + -
594A ILE* 4.7 12.6 - - + +
597A ALA* 3.5 22.9 - - + -
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Residues in contact with ARG 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A VAL* 2.9 29.2 + - + +
454A ALA* 3.2 13.0 - - - +
456A LEU* 1.3 73.6 - - - +
458A ALA* 1.3 69.5 + - - +
460A SER* 3.2 23.8 + - - -
461A LEU* 3.4 11.1 + - - +
546A ILE 5.2 1.6 + - - -
547A ASP* 4.4 5.9 + - - +
550A PRO* 3.1 35.4 - - - +
551A ASP* 3.4 21.0 + - - -
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Residues in contact with ALA 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ALA 3.1 10.1 + - - +
455A TYR* 2.5 27.2 + - + +
457A ARG* 1.3 73.1 - - - +
459A LEU* 1.3 63.4 + - - +
461A LEU* 3.1 12.1 + - - +
462A GLU* 3.3 11.3 + - - +
593A ARG* 6.3 0.4 - - - +
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Residues in contact with LEU 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A TYR* 3.1 26.2 + - + +
456A LEU* 3.5 14.8 - - + +
458A ALA* 1.3 78.7 - - - +
460A SER* 1.3 65.3 + - - +
462A GLU* 2.9 9.0 + - - +
463A VAL* 2.8 46.2 + - + +
546A ILE* 3.8 14.1 - - + -
590A LEU* 4.2 7.0 - - + -
593A ARG* 3.1 45.5 - - + +
594A ILE* 4.1 32.5 - - + +
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Residues in contact with SER 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LEU 3.0 10.2 + - - -
457A ARG* 3.3 16.3 + - - -
459A LEU* 1.3 79.0 - - - +
461A LEU* 1.3 71.7 + - - +
463A VAL* 4.6 1.6 - - - -
464A ALA* 3.0 28.8 + - - +
542A LYS* 3.4 12.9 + - - +
546A ILE* 3.5 11.6 - - - +
547A ASP* 3.5 23.6 + - - -
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Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A ARG 3.4 6.2 + - - +
458A ALA* 3.1 10.0 + - - +
460A SER* 1.3 92.0 + - - +
462A GLU* 1.3 61.7 + - - +
464A ALA* 3.6 7.5 - - + +
465A GLU* 2.9 29.4 + - - +
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Residues in contact with GLU 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 ALA 3.3 8.5 + - - +
459A LEU* 2.9 12.0 + - - +
461A LEU* 1.3 74.6 - - - +
463A VAL* 1.3 71.2 + - - +
465A GLU* 2.9 29.9 + - - +
466A GLU* 3.2 7.3 + - - +
593A ARG* 3.4 32.6 + - - -
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Residues in contact with VAL 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A LEU* 2.8 41.4 + - + +
460A SER* 4.1 2.7 - - - +
462A GLU* 1.3 76.2 - - - +
464A ALA* 1.3 56.1 + - - +
465A GLU 2.5 16.8 + - - -
466A GLU* 2.7 20.0 + - - +
467A ILE* 2.9 32.6 + - + +
538A LEU* 4.5 14.4 - - + +
542A LYS* 3.8 19.5 - - + -
546A ILE* 4.1 13.2 - - + -
590A LEU* 4.2 13.5 - - + -
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Residues in contact with ALA 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A SER 3.0 19.2 + - - +
461A LEU* 3.6 13.5 - - + +
463A VAL* 1.3 80.2 - - - +
465A GLU* 1.3 61.1 + - + +
467A ILE* 3.6 12.0 - - - +
468A ALA* 3.3 20.6 + - - +
542A LYS* 3.4 19.1 - - - +
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Residues in contact with GLU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A LEU 2.9 20.0 - - - +
462A GLU* 3.0 18.1 - - - +
463A VAL 2.5 4.6 + - - -
464A ALA* 1.3 71.7 - - + +
466A GLU* 1.3 63.7 + - - +
467A ILE 3.0 1.3 - - - -
468A ALA* 2.8 18.0 + - - +
469A ARG* 2.9 12.7 + - - +
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Residues in contact with GLU 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A GLU* 3.2 7.2 + - - +
463A VAL* 2.7 14.7 + - - +
465A GLU* 1.3 75.3 - - - +
467A ILE* 1.3 62.6 + - - +
469A ARG* 3.2 22.4 + - - +
470A LEU* 3.3 25.8 + - + +
534A GLN* 5.5 1.9 - - - +
538A LEU* 3.4 23.6 - - + -
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Residues in contact with ILE 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 VAL* 2.9 29.9 + - + +
464A ALA* 3.6 13.9 - - - +
466A GLU* 1.3 79.4 - - - +
468A ALA* 1.3 62.7 + - - +
470A LEU* 3.1 7.2 + - - +
471A GLU* 2.9 29.6 + - + +
535A TYR* 4.3 20.8 - - + +
538A LEU* 3.6 30.6 - - + +
539A THR* 4.2 24.9 - - + +
542A LYS* 4.2 14.6 - - + +
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Residues in contact with ALA 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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464A ALA 3.3 11.3 + - - +
465A GLU* 2.8 12.3 + - - +
467A ILE* 1.3 82.7 - - + +
469A ARG* 1.3 62.8 + - - +
471A GLU* 3.4 13.4 + - - +
472A ALA* 3.1 22.2 + - - +
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Residues in contact with ARG 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 GLU 2.9 10.0 + - - +
466A GLU* 3.2 20.6 + - - +
468A ALA* 1.3 76.1 - - - +
470A LEU* 1.3 60.7 + - + +
472A ALA* 3.4 7.9 + - - +
473A GLU* 3.1 28.0 + - - +
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Residues in contact with LEU 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 GLU* 3.3 29.2 - - + +
467A ILE 3.1 6.0 + - - +
469A ARG* 1.3 75.0 - - + +
471A GLU* 1.3 65.7 + - - +
472A ALA 3.1 1.6 - - - -
473A GLU* 3.1 8.0 + - + +
474A VAL* 2.9 33.3 + - + +
531A LYS* 4.1 31.6 - - + +
534A GLN* 4.1 22.4 - - + +
535A TYR* 4.0 31.9 - - + +
538A LEU* 4.1 17.5 - - + -
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Residues in contact with GLU 471 (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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467A ILE* 2.9 17.7 + - + +
468A ALA* 3.6 16.9 - - - +
470A LEU* 1.3 76.4 - - - +
472A ALA* 1.3 57.6 + - - +
474A VAL* 3.0 8.2 - - - +
475A PHE* 2.9 73.1 + - + -
484A LEU* 4.3 8.1 + - + +
535A TYR* 4.4 21.2 + - + -
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Residues in contact with ALA 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 ALA 3.1 12.8 + - - +
469A ARG* 3.4 11.4 - - - +
470A LEU 3.1 0.8 - - - -
471A GLU* 1.3 74.9 - - - +
473A GLU* 1.3 69.4 + - - +
475A PHE* 3.2 8.8 + - - +
476A ARG* 3.0 20.4 + - - +
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Residues in contact with GLU 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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469A ARG 3.1 13.2 + - - +
470A LEU* 3.1 14.6 + - + +
472A ALA* 1.3 80.4 - - - +
474A VAL* 1.3 66.8 + - + +
476A ARG* 2.7 59.2 + - - +
477A LEU* 3.0 25.6 + - + +
531A LYS* 4.8 15.6 - - + +
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Residues in contact with VAL 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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470A LEU* 2.9 17.7 + - + +
471A GLU 3.0 15.3 - - - +
473A GLU* 1.3 71.9 - - - +
475A PHE* 1.3 80.4 + - + +
477A LEU* 2.8 24.8 + - + +
478A ALA* 3.1 12.0 + - - +
482A PHE* 4.6 4.8 - - + -
484A LEU* 3.4 28.9 - - + -
528A ILE* 4.0 17.1 - - + +
531A LYS* 4.1 20.4 - - + +
532A ILE* 4.0 25.4 - - + +
535A TYR* 6.0 0.9 - - + -
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Residues in contact with PHE 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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471A GLU* 2.9 55.5 + - + +
472A ALA* 3.2 8.0 + - - +
474A VAL* 1.3 86.8 - - + +
476A ARG* 1.3 60.8 + - - +
478A ALA 3.5 1.2 + - - -
480A HIS 3.1 33.1 + - - +
481A PRO* 3.5 32.3 - - + -
482A PHE* 2.8 43.1 - + - -
483A ASN* 5.1 0.9 - - - -
484A LEU* 4.1 16.6 - - + -
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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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472A ALA 3.0 9.8 + - - +
473A GLU* 2.7 52.8 + - - +
475A PHE* 1.3 74.6 - - - +
477A LEU* 1.3 72.4 + - - +
478A ALA 2.6 5.9 + - - -
479A GLY* 2.4 30.8 + - - +
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Residues in contact with LEU 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A GLU* 3.0 42.3 + - + +
474A VAL* 2.8 14.2 + - + +
476A ARG* 1.3 98.5 - - - +
478A ALA* 1.3 56.6 + - - +
479A GLY 3.5 0.2 - - - -
498A LEU* 4.7 11.3 - - - +
526A HIS* 4.1 16.5 - - + -
527A PRO* 3.9 15.5 - - + -
528A ILE* 3.6 48.8 - - + +
531A LYS* 5.8 4.3 - - + -
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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