Contacts of the helix formed by residues 451 - 467 (chain A) in PDB entry 3TT9
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 ASP 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409A GLU* 4.1 22.2 + - + +
413A ARG* 3.2 35.1 + - - +
449A THR* 3.0 12.3 + - - +
450A ARG* 1.3 76.7 - - - +
452A LEU* 1.3 67.8 + - - +
453A GLU* 3.9 2.0 + - - +
454A THR* 2.8 43.1 + - - +
455A LYS* 3.3 17.9 + - - +
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Residues in contact with LEU 452 (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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450A ARG 3.8 2.8 + - - +
451A ASP* 1.3 73.9 + - - +
453A GLU* 1.3 64.3 + - - +
455A LYS* 3.1 7.6 + - - +
456A LYS* 3.1 32.0 + - - +
504A GLY 4.6 6.7 - - - +
505A LEU* 3.5 44.6 - - + +
506A LEU* 3.8 8.7 - - - +
507A ASP* 4.5 15.0 - - + +
510A ILE* 3.7 17.7 - - + +
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Residues in contact with GLU 453 (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 ARG* 3.4 29.8 - - + +
451A ASP* 3.3 2.4 + - - -
452A LEU* 1.3 80.2 - - - +
454A THR* 1.3 63.7 + - - +
456A LYS* 3.1 35.5 + - - +
457A GLN* 3.0 38.8 + - + +
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Residues in contact with THR 454 (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 GLU* 4.6 2.1 + - - +
412A GLN* 4.4 10.3 - - + +
413A ARG* 3.2 17.5 + - - +
416A CYS* 4.1 14.4 - - - -
445A VAL* 4.1 12.1 - - + -
449A THR* 3.9 15.2 + - + +
451A ASP* 2.8 33.1 + - - +
453A GLU* 1.3 76.0 - - - +
455A LYS* 1.3 57.1 + - - +
457A GLN* 3.2 12.9 + - - +
458A ILE* 3.0 45.8 + - + +
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Residues in contact with LYS 455 (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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446A LEU* 3.6 37.5 + - + +
447A LYS 5.3 3.0 + - - -
449A THR* 3.5 38.4 + - + -
450A ARG* 5.3 0.4 - - - +
451A ASP 3.6 9.0 - - - +
452A LEU* 3.1 9.5 + - - +
454A THR* 1.3 78.4 - - - +
456A LYS* 1.3 56.3 + - - +
458A ILE* 4.0 1.4 - - - +
459A THR* 3.0 34.5 + - - -
505A LEU* 2.8 45.8 + - - +
506A LEU* 4.3 11.4 - - + +
510A ILE* 3.6 17.5 - - + -
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Residues in contact with LYS 456 (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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1A GOL 3.7 13.5 - - - +
420A ARG* 3.7 3.8 + - - +
452A LEU* 3.1 20.8 + - - +
453A GLU* 3.1 37.9 + - - +
455A LYS* 1.3 72.7 - - - +
457A GLN* 1.3 62.9 + - + +
459A THR* 3.9 8.1 - - - -
460A GLY* 2.9 25.8 + - - -
507A ASP* 2.8 37.8 + - - -
509A ASP* 2.9 33.5 + - + +
510A ILE* 3.5 15.5 - - + +
513A ASN* 3.1 7.3 + - - -
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Residues in contact with GLN 457 (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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378A GLN* 4.0 9.3 + - - -
413A ARG* 3.2 44.1 + - - +
416A CYS* 3.6 18.5 - - + +
417A GLY* 3.4 20.2 + - - -
420A ARG* 3.8 17.6 - - - +
453A GLU* 3.0 26.1 + - + +
454A THR* 3.5 15.8 - - - +
456A LYS* 1.3 77.9 - - + +
458A ILE* 1.3 58.1 + - - +
460A GLY 3.8 0.2 - - - -
461A LEU* 2.9 30.2 + - - +
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Residues in contact with ILE 458 (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 CYS* 3.6 23.6 - - + -
442A LEU* 3.7 34.3 - - + +
445A VAL* 3.7 20.0 - - + -
446A LEU* 3.7 42.4 - - + +
449A THR* 5.3 0.2 - - + -
454A THR* 3.0 25.2 + - + +
455A LYS 4.0 3.4 - - - +
457A GLN* 1.3 75.2 - - - +
459A THR* 1.3 58.9 + - - +
461A LEU* 3.3 9.4 + - - +
462A LEU* 2.9 41.5 + - + +
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Residues in contact with THR 459 (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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446A LEU* 4.4 13.9 - - - +
455A LYS 3.0 21.2 + - - +
456A LYS* 3.5 4.3 - - - +
458A ILE* 1.3 80.2 - - - +
460A GLY* 1.3 54.5 + - - +
462A LEU* 3.4 6.6 + - - +
463A TRP* 2.9 28.8 + - - +
483A LEU* 4.6 1.6 - - - +
487A ILE* 4.7 0.2 - - - +
510A ILE* 3.8 18.6 - - + +
513A ASN* 2.9 48.2 - - + +
514A VAL* 3.0 25.4 - - - +
517A CYS* 3.7 6.7 - - - -
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Residues in contact with GLY 460 (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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420A ARG* 3.5 35.1 + - - -
456A LYS 2.9 12.9 + - - -
457A GLN 3.8 0.2 - - - -
459A THR* 1.3 76.4 - - - +
461A LEU* 1.4 58.3 + - - +
463A TRP* 3.3 7.1 + - - +
464A ASN* 3.0 32.7 + - - +
513A ASN* 3.8 7.9 - - - -
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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
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416A CYS* 4.3 5.6 - - - +
419A LEU* 3.5 33.4 - - + +
420A ARG* 3.8 25.1 - - - +
423A VAL* 4.1 7.2 - - + -
433A VAL* 4.6 5.8 - - + -
442A LEU* 3.7 42.0 - - + -
457A GLN 2.9 17.6 + - - +
458A ILE* 3.4 7.0 - - - +
460A GLY* 1.4 73.6 - - - +
462A LEU* 1.3 61.6 + - + +
464A ASN* 3.0 6.6 + - - +
465A LEU* 3.0 46.5 + - + +
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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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439A VAL* 4.2 17.7 - - + -
442A LEU* 4.5 11.2 - - + -
443A LEU* 3.8 27.6 - - + -
446A LEU* 4.9 0.9 - - + -
458A ILE* 2.9 34.4 + - + +
459A THR* 3.8 3.8 - - - +
461A LEU* 1.3 77.1 - - + +
463A TRP* 1.3 65.9 + - - +
465A LEU* 3.2 26.0 + - + +
466A SER* 2.9 24.1 + - - -
475A MET* 3.8 18.1 - - + +
483A LEU* 4.1 19.1 - - + -
517A CYS* 3.5 13.2 - - - -
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Residues in contact with TRP 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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1A GOL 4.2 8.5 - - - -
420A ARG* 4.8 7.4 - - - -
459A THR 2.9 16.9 + - - +
460A GLY* 3.4 4.9 - - - +
462A LEU* 1.3 76.1 - - - +
464A ASN* 1.3 65.3 + - - +
466A SER* 2.7 20.5 + - - -
467A SER* 3.6 5.0 + - - -
512A TYR* 3.6 38.8 - + - -
513A ASN* 3.6 35.7 - - - +
516A GLY* 3.3 39.0 + - - -
517A CYS* 3.2 15.1 - - - -
520A ASN* 3.6 14.2 + - - +
562A ASN* 4.8 3.6 - - - -
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Residues in contact with ASN 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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420A ARG* 3.3 40.2 + - - +
423A VAL* 3.6 17.4 - - + +
424A PHE* 3.8 29.3 - - - +
425A GLU 5.4 0.4 - - - -
430A LYS* 2.9 28.3 + - - +
460A GLY 3.0 18.4 + - - +
461A LEU 3.0 7.8 + - - +
463A TRP* 1.3 80.0 - - - +
465A LEU* 1.3 63.6 + - - +
467A SER* 3.1 7.5 + - - -
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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
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423A VAL* 4.1 16.4 - - + -
430A LYS* 3.6 42.4 - - + +
433A VAL* 4.2 10.3 - - + -
434A ALA* 5.2 1.8 - - + +
439A VAL* 3.7 30.5 - - + -
461A LEU* 3.0 27.3 + - + +
462A LEU* 3.2 22.0 + - + +
464A ASN* 1.3 75.1 - - - +
466A SER* 1.3 63.3 + - - +
468A ASN* 3.1 22.2 + - - +
471A LEU* 3.6 17.9 - - + +
475A MET* 4.3 10.1 - - - -
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Residues in contact with SER 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 LEU 2.9 12.2 + - - -
463A TRP* 2.7 24.5 + - - -
465A LEU* 1.3 76.6 - - - +
467A SER* 1.3 59.7 + - - +
468A ASN 3.2 1.9 + - - -
471A LEU* 5.3 0.4 - - - -
472A LYS* 3.4 21.1 - - - +
475A MET* 4.5 13.5 - - - -
517A CYS* 3.6 17.9 - - - -
520A ASN* 3.0 32.9 + - - +
521A MET* 4.3 11.4 - - - -
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Residues in contact with SER 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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430A LYS* 2.8 30.8 + - - -
463A TRP* 3.6 2.4 + - - -
464A ASN* 3.1 5.9 + - - -
465A LEU 3.1 0.2 + - - -
466A SER* 1.3 78.5 + - - +
468A ASN* 1.3 61.4 + - - +
469A ASP* 3.5 10.2 + - - +
472A LYS* 4.3 4.4 + - - +
520A ASN* 3.6 18.6 - - - -
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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