Contacts of the helix formed by residues 415 - 433 (chain B) in PDB entry 5T0I
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 THR 415 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B GLU* 3.9 15.6 + - - -
413B LYS* 4.9 2.3 - - - +
414B VAL* 1.3 73.8 - - - +
416B ASN* 1.3 58.6 + - - +
417B GLU* 3.6 30.7 - - + +
418B ASP* 3.7 20.0 - - + +
419B PHE* 2.7 39.5 + - - +
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Residues in contact with ASN 416 (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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414B VAL* 4.0 13.7 + - - +
415B THR* 1.3 75.6 - - - +
417B GLU* 1.3 60.2 + - - +
419B PHE* 4.8 3.4 - - - -
420B LYS* 2.5 46.8 + - - +
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Residues in contact with GLU 417 (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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415B THR* 3.6 17.5 - - + +
416B ASN* 1.3 79.3 - - - +
418B ASP* 1.3 62.9 + - + +
420B LYS* 4.5 4.1 - - - +
421B LYS* 3.3 26.0 + - - +
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Residues in contact with ASP 418 (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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405B MET* 3.3 44.5 - - - +
415B THR* 3.2 23.6 + - + -
417B GLU* 1.3 82.1 - - + +
419B PHE* 1.3 57.1 + - - +
421B LYS* 3.1 29.8 + - - +
422B SER* 2.7 38.4 + - - -
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Residues in contact with PHE 419 (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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383B LEU* 6.2 3.8 - - + -
398B ILE 5.5 2.5 - - - -
402B ALA* 4.4 26.2 - - + -
414B VAL* 4.4 20.4 - - + -
415B THR 2.7 24.1 + - - +
416B ASN* 4.5 2.9 - - - +
418B ASP* 1.3 75.0 + - - +
420B LYS* 1.3 68.8 + - + +
422B SER* 2.8 12.7 + - - -
423B LYS* 2.8 47.0 + - + +
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Residues in contact with LYS 420 (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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416B ASN* 2.5 48.9 + - - +
417B GLU* 4.7 3.6 - - - +
418B ASP 3.4 0.4 - - - -
419B PHE* 1.3 89.2 - - + +
421B LYS* 1.3 57.4 + - - +
423B LYS* 3.8 7.7 - - + +
424B GLU* 3.1 23.9 + - - +
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Residues in contact with LYS 421 (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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417B GLU 3.3 17.8 + - - +
418B ASP* 3.1 31.5 + - - +
420B LYS* 1.3 77.7 - - - +
422B SER* 1.3 66.1 + - - +
424B GLU* 3.2 27.5 + - + +
425B ASN* 3.8 2.3 + - - +
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Residues in contact with SER 422 (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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401B GLU* 4.0 24.5 - - - +
405B MET* 5.4 10.1 - - - +
418B ASP* 2.7 26.8 + - - -
419B PHE* 2.8 29.1 + - - -
421B LYS* 1.3 73.8 - - - +
423B LYS* 1.3 64.1 + - - +
424B GLU 3.4 0.2 + - - -
425B ASN* 3.4 18.4 + - - +
426B VAL 4.1 0.9 + - - -
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Residues in contact with LYS 423 (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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386B ALA* 5.7 5.6 - - - +
387B LYS* 4.2 27.8 - - - +
398B ILE* 3.7 44.1 - - + +
401B GLU* 5.1 2.9 - - - +
419B PHE* 2.8 34.3 + - + +
420B LYS* 3.9 9.9 - - + +
422B SER* 1.3 75.9 + - - +
424B GLU* 1.3 60.1 + - - +
425B ASN 3.3 0.2 + - - -
426B VAL* 3.3 4.3 + - + +
427B LEU* 2.8 50.0 + - + +
430B LYS* 5.5 1.6 - - - +
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Residues in contact with GLU 424 (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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420B LYS 3.1 13.9 + - - +
421B LYS* 3.2 20.3 - - + +
422B SER 3.2 0.6 - - - -
423B LYS* 1.3 76.6 - - - +
425B ASN* 1.3 63.9 + - - +
427B LEU* 4.0 12.8 - - + -
428B TYR* 2.8 44.7 + - + +
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Residues in contact with ASN 425 (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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401B GLU* 5.4 4.9 + - - +
421B LYS 3.8 2.6 + - - +
422B SER* 3.4 13.4 + - - +
423B LYS 3.2 0.2 - - - -
424B GLU* 1.3 89.5 + - - +
426B VAL* 1.3 63.5 + - + +
428B TYR* 4.0 7.4 - - - +
429B LYS* 3.1 25.1 + - - +
314C LYS* 4.7 20.8 - - - +
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Residues in contact with VAL 426 (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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394B ASP* 4.7 18.4 - - + +
397B ALA* 6.0 2.5 - - + -
398B ILE* 3.6 26.7 - - + +
401B GLU* 3.3 29.8 - - - +
422B SER 4.7 2.0 - - - +
423B LYS* 3.3 8.5 + - + +
425B ASN* 1.3 81.1 - - + +
427B LEU* 1.3 66.1 + - - +
429B LYS* 3.2 18.1 + - + +
430B LYS* 3.2 24.4 + - - +
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Residues in contact with LEU 427 (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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386B ALA 5.3 4.5 - - - +
387B LYS* 5.1 9.4 - - + -
423B LYS* 2.8 41.8 + - + +
424B GLU* 3.8 12.1 - - + +
426B VAL* 1.3 76.3 - - - +
428B TYR* 1.3 57.9 + - - +
430B LYS* 3.2 17.2 - - + +
431B GLN* 2.9 65.9 + - + +
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Residues in contact with TYR 428 (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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424B GLU* 2.8 36.0 + - + +
425B ASN* 4.2 7.4 - - - +
427B LEU* 1.3 70.6 - - - +
429B LYS* 1.3 63.9 + - + +
431B GLN* 3.8 13.7 - - + +
432B GLU* 2.7 76.4 + - + +
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Residues in contact with LYS 429 (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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394B ASP* 6.1 1.3 - - - +
425B ASN 3.1 17.6 + - - +
426B VAL* 3.2 19.2 + - + +
428B TYR* 1.3 82.4 - - + +
430B LYS* 1.3 59.2 + - - +
432B GLU* 3.8 11.9 + - + +
433B GLY 4.4 2.4 + - - -
301C LEU* 5.3 14.7 - - - +
304C ALA* 5.4 12.6 + - - +
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Residues in contact with LYS 430 (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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387B LYS* 3.3 47.6 - - + +
388B ASP 5.4 1.8 - - - +
389B ASP 4.6 8.5 - - - +
390B LEU* 3.4 56.8 - - + +
394B ASP* 5.5 1.9 - - - +
423B LYS* 5.6 1.1 - - - +
426B VAL* 3.2 19.5 + - - +
427B LEU* 3.2 22.9 - - + +
429B LYS* 1.3 78.8 - - - +
431B GLN* 1.3 63.6 + - + +
432B GLU 3.3 1.3 - - - -
433B GLY* 3.8 3.4 + - - +
434B THR* 3.5 20.1 + - - +
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Residues in contact with GLN 431 (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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427B LEU* 2.9 56.0 + - + +
428B TYR* 2.9 17.5 + - + +
430B LYS* 1.3 79.9 - - + +
432B GLU* 1.3 61.2 + - - +
434B THR* 3.0 23.7 + - + +
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Residues in contact with GLU 432 (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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428B TYR* 2.7 60.7 + - + +
429B LYS* 4.1 7.6 - - + +
430B LYS 3.3 0.6 - - - -
431B GLN* 1.3 76.5 - - - +
433B GLY* 1.3 58.7 + - - +
434B THR 3.4 1.9 + - - -
435B PRO* 4.5 5.7 - - - +
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Residues in contact with GLY 433 (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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429B LYS 4.4 2.6 + - - -
430B LYS* 3.8 8.2 + - - +
432B GLU* 1.3 79.8 - - - +
434B THR* 1.3 64.0 + - - +
435B PRO* 3.1 15.5 - - - +
436B GLU* 5.1 1.9 - - - +
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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