Contacts of the helix formed by residues 472 - 486 (chain B) in PDB entry 1T9A
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 LYS 472 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B TYR* 4.2 2.7 - - + -
463B MET* 3.2 42.1 + - + +
464B GLU* 3.9 12.6 - - - -
465B GLU* 3.2 32.7 + - + +
466B THR* 6.0 0.2 - - - -
469B SER* 4.6 9.8 + - - -
470B LYS 4.2 8.7 + - - -
471B ILE* 1.3 76.1 - - - +
473B PRO* 1.3 73.9 - - + +
474B GLN* 3.9 9.9 - - - +
475B THR* 3.2 16.3 + - - +
476B VAL* 3.3 14.7 + - - +
646B ASP* 2.7 37.9 + - + +
649B VAL* 5.3 5.1 - - + +
672B GLU* 4.8 3.2 + - - -
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Residues in contact with PRO 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ILE 3.8 4.7 - - - +
472B LYS* 1.3 83.5 - - + +
474B GLN* 1.3 79.0 + - - +
476B VAL* 3.0 16.8 + - + +
477B ILE* 3.2 17.0 + - - +
503B TRP* 3.4 44.0 - - + -
575B LEU* 4.2 12.5 - - + +
645B VAL* 4.0 26.7 - - + -
646B ASP 4.4 9.9 - - - +
649B VAL* 4.5 10.5 - - + -
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Residues in contact with GLN 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B TYR* 3.3 54.4 - - + +
463B MET 5.2 0.4 - - - +
472B LYS* 3.9 3.1 - - - +
473B PRO* 1.3 92.5 - - - +
475B THR* 1.3 62.3 + - - +
477B ILE* 3.2 8.4 + - - +
478B LYS* 3.1 26.6 + - - +
503B TRP* 3.5 32.7 - - + +
507B HIS* 3.5 27.7 - - - +
649B VAL* 3.7 20.4 - - - +
650B PRO 4.5 4.4 + - - -
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Residues in contact with THR 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B TYR* 2.9 24.0 + - - +
464B GLU* 5.2 0.2 - - - +
465B GLU* 2.6 42.7 + - - +
472B LYS* 3.2 6.0 + - - +
473B PRO 3.1 0.2 - - - -
474B GLN* 1.3 79.8 - - - +
476B VAL* 1.3 63.0 + - - +
478B LYS* 3.2 6.5 + - + +
479B LYS* 2.9 51.8 + - + +
625B LEU* 4.5 2.7 - - + -
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Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ILE* 3.5 21.3 - - + -
472B LYS 3.4 15.7 - - - +
473B PRO* 3.0 12.1 + - + +
475B THR* 1.3 76.4 - - - +
477B ILE* 1.3 57.9 + - - +
479B LYS* 3.4 1.8 + - - +
480B LEU* 2.9 30.0 + - + +
573B LEU* 4.2 15.9 - - + -
575B LEU* 3.8 21.8 - - + -
625B LEU* 4.1 22.4 - - + -
629B LEU* 4.5 7.3 - - + +
643B VAL* 4.0 20.0 - - + -
645B VAL* 4.3 0.9 - - + -
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Residues in contact with ILE 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B PRO 3.2 13.7 + - - +
474B GLN 3.5 6.5 - - - +
475B THR 3.2 0.4 - - - -
476B VAL* 1.3 78.3 - - - +
478B LYS* 1.3 57.5 + - - +
480B LEU* 3.9 3.0 - - - -
481B SER* 2.9 31.6 + - - -
500B HIS 4.7 0.7 - - - +
503B TRP* 3.5 33.4 - - + +
504B ALA* 3.8 14.4 - - - +
507B HIS* 3.7 21.1 - - + -
508B TRP* 3.9 13.6 - - + +
547B ILE* 3.8 36.6 - - + -
573B LEU* 5.2 3.1 - - + -
575B LEU* 4.0 15.3 - - + -
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Residues in contact with LYS 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B TYR 5.8 0.8 + - - -
462B TYR* 3.8 27.0 + - + +
474B GLN 3.1 13.0 + - - +
475B THR* 3.2 6.5 + - + +
477B ILE* 1.3 76.6 - - - +
479B LYS* 1.3 63.3 + - + +
481B SER* 3.4 4.6 + - - -
482B LYS* 3.3 20.4 + - - +
507B HIS* 3.8 39.9 + - + +
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Residues in contact with LYS 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B THR* 2.9 35.9 + - + +
476B VAL 3.8 0.9 - - - +
478B LYS* 1.3 78.5 - - + +
480B LEU* 1.3 58.2 + - - +
482B LYS* 3.1 7.5 + - - +
483B VAL* 2.9 34.3 + - + +
622B GLN 5.9 1.3 - - - -
625B LEU* 3.4 31.2 - - + -
626B ASP* 2.9 39.6 + - - +
629B LEU* 3.6 12.8 - - + -
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Residues in contact with LEU 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B VAL* 2.9 18.8 + - + +
477B ILE* 4.0 3.4 - - - +
479B LYS* 1.3 77.5 - - - +
481B SER* 1.3 55.3 + - - +
483B VAL* 4.3 7.0 - - + -
484B ALA* 2.8 38.5 + - + +
508B TRP* 3.9 19.5 - - + -
545B ILE* 4.2 23.6 - - + -
547B ILE* 4.4 4.3 - - + -
573B LEU* 3.6 29.6 - - + -
629B LEU* 3.9 23.2 - - + +
632B PHE* 4.4 9.0 - - + -
633B VAL* 3.9 27.8 - - + -
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Residues in contact with SER 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B ILE 2.9 19.9 + - - -
478B LYS* 3.4 9.6 - - - -
480B LEU* 1.3 78.1 - - - +
482B LYS* 1.3 56.3 + - - +
484B ALA* 4.0 1.9 - - - +
485B ASN* 3.2 26.5 + - - +
507B HIS 4.4 0.9 - - - -
508B TRP* 3.6 33.8 + - - -
509B THR* 3.5 28.8 + - - -
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Residues in contact with LYS 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B LYS 3.3 7.7 + - - +
479B LYS* 3.1 10.4 + - - +
481B SER* 1.3 78.4 - - - +
483B VAL* 1.3 67.2 + - + +
485B ASN* 3.1 10.6 + - - +
486B ASP* 2.8 70.5 + - - +
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Residues in contact with VAL 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B LYS* 2.9 25.7 + - + +
480B LEU* 3.9 7.0 - - + +
482B LYS* 1.3 79.3 - - + +
484B ALA* 1.3 61.6 + - - +
486B ASP* 3.6 15.6 + - - +
487B THR* 3.3 15.4 + - - +
626B ASP* 5.3 5.2 - - - +
629B LEU* 4.1 20.4 - - + +
630B LYS* 4.0 34.5 - - + +
633B VAL* 3.8 24.2 - - + -
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Residues in contact with ALA 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B LEU* 2.8 23.3 + - + +
481B SER 4.0 3.4 - - - +
483B VAL* 1.3 71.1 - - - +
485B ASN* 1.3 62.7 + - - +
487B THR* 2.6 34.9 + - - +
489B ARG 4.9 0.2 - - - +
491B VAL* 3.9 16.7 - - + +
508B TRP* 4.0 20.2 - - + -
543B LEU* 4.5 3.8 - - + -
545B ILE* 4.1 17.7 - - + -
633B VAL* 4.8 3.4 - - + -
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Residues in contact with ASN 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B SER 3.2 16.9 + - - +
482B LYS* 3.1 11.1 + - - +
484B ALA* 1.3 74.4 - - - +
486B ASP* 1.3 68.1 + - - +
487B THR 2.8 11.2 + - - -
488B GLY* 2.8 18.4 + - - -
489B ARG 5.4 0.7 - - - +
491B VAL* 5.3 3.4 - - - -
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Residues in contact with ASP 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B LYS* 2.8 60.8 + - - +
483B VAL* 3.9 10.5 - - - +
484B ALA 3.4 0.4 - - - -
485B ASN* 1.3 82.9 + - - +
487B THR* 1.3 60.9 + - - +
488B GLY* 3.1 1.7 + - - -
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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
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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