Contacts of the helix formed by residues 408 - 421 (chain B) in PDB entry 2Y4T
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 GLN 408 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406B LYS 3.3 2.4 + - - -
407B LYS* 1.3 79.6 - - + +
409B GLU* 1.3 66.3 + - - +
410B ILE 3.2 2.5 - - - -
411B ILE* 3.2 35.2 + - + +
412B LYS* 3.7 10.0 + - - +
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Residues in contact with GLU 409 (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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399B LEU 5.3 2.6 - - - +
401B VAL* 3.5 41.5 + - - +
405B ALA* 5.3 2.2 - - + -
406B LYS* 3.2 31.2 + - - +
407B LYS 3.0 1.0 + - - -
408B GLN* 1.3 79.5 - - - +
410B ILE* 1.3 64.8 + - + +
412B LYS* 3.3 44.1 + - - +
413B ALA* 3.3 11.6 + - - +
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Residues in contact with ILE 410 (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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396B TYR* 5.6 0.9 - - + -
405B ALA* 4.2 27.8 - - + +
407B LYS* 3.4 18.4 - - - +
409B GLU* 1.3 77.2 - - - +
411B ILE* 1.3 62.2 + - + +
413B ALA* 3.4 6.9 + - + +
414B TYR* 3.0 29.8 + - + +
446B LYS* 5.1 11.4 - - + -
449B LEU* 3.9 42.6 - - + +
454B MET* 4.4 22.4 - - + -
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Residues in contact with ILE 411 (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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408B GLN* 3.2 32.6 + - + +
410B ILE* 1.3 79.2 - - + +
412B LYS* 1.3 64.2 + - - +
414B TYR* 3.5 1.7 + - - +
415B ARG* 3.3 39.6 + - + +
446B LYS* 3.5 28.0 - - - +
450B SER* 6.0 1.1 - - - +
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Residues in contact with LYS 412 (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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408B GLN* 3.7 7.7 + - - +
409B GLU* 3.3 44.6 + - - +
411B ILE* 1.3 78.9 - - - +
413B ALA* 1.3 62.2 + - - +
415B ARG* 4.3 4.2 - - - +
416B LYS* 3.5 37.1 + - - +
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Residues in contact with ALA 413 (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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398B ILE 5.5 2.0 - - - +
399B LEU* 5.1 22.2 - - + +
409B GLU* 3.3 19.7 + - + +
410B ILE* 3.6 9.0 - - + +
411B ILE 3.2 0.6 - - - -
412B LYS* 1.3 80.4 - - + +
414B TYR* 1.3 63.6 + - - +
416B LYS* 4.2 2.2 - - - +
417B LEU* 3.2 34.7 + - + +
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Residues in contact with TYR 414 (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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410B ILE* 3.0 18.1 + - + +
411B ILE* 4.1 2.2 - - + +
413B ALA* 1.3 75.0 - - - +
415B ARG* 1.3 90.9 + - + +
417B LEU* 3.1 4.6 + - - -
418B ALA* 2.7 58.9 + - + +
442B ILE* 3.8 24.2 - - + -
443B ALA* 4.1 16.1 - - - +
446B LYS* 3.4 50.7 - - + -
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Residues in contact with ARG 415 (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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411B ILE* 3.3 29.1 + - + +
412B LYS* 4.3 5.6 - - - +
414B TYR* 1.3 113.1 - - + +
416B LYS* 1.3 60.7 + - - +
418B ALA* 4.3 2.9 - - - +
419B LEU* 3.4 24.3 + - - +
446B LYS* 5.5 4.9 - - - +
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Residues in contact with LYS 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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412B LYS* 3.5 25.7 + - - +
413B ALA* 4.2 2.7 - - - +
414B TYR 3.2 0.6 - - - -
415B ARG* 1.3 76.7 - - - +
417B LEU* 1.3 62.1 + - + +
419B LEU* 3.5 7.7 + - - +
420B GLN* 2.9 49.6 + - - +
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Residues in contact with LEU 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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398B ILE* 4.3 10.8 - - + +
399B LEU* 3.5 43.7 - - + -
413B ALA* 3.2 21.7 + - + +
414B TYR* 3.1 4.1 + - - +
416B LYS* 1.3 81.0 - - + +
418B ALA* 1.3 54.7 + - - +
420B GLN* 3.1 16.7 + - - +
421B TRP* 2.7 60.1 + - + +
442B ILE* 4.2 25.8 - - + -
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Residues in contact with ALA 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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414B TYR* 2.7 53.9 + - + +
415B ARG* 4.3 2.7 - - - +
417B LEU* 1.3 73.6 - - - +
419B LEU* 1.3 59.9 + - - +
422B HIS* 3.6 11.1 + - - +
439B PHE* 3.5 23.7 - - + -
442B ILE* 3.6 16.7 - - + +
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Residues in contact with LEU 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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415B ARG 3.4 17.8 + - - +
416B LYS* 3.8 5.6 - - - +
417B LEU 3.3 0.4 - - - -
418B ALA* 1.3 77.6 - - - +
420B GLN* 1.3 62.0 + - - +
422B HIS* 4.0 3.7 + - + +
425B ASN* 3.2 19.9 + - - +
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Residues in contact with GLN 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 LYS* 2.9 39.1 + - - +
417B LEU* 3.1 23.2 + - - +
419B LEU* 1.3 78.0 - - - +
421B TRP* 1.3 64.4 + - + +
422B HIS 3.3 0.4 - - - -
425B ASN* 3.3 22.5 + - - +
426B PHE* 4.6 4.3 - - - -
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Residues in contact with TRP 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 LEU* 2.7 49.5 + - + +
419B LEU 3.5 0.2 - - - -
420B GLN* 1.3 76.0 + - + +
422B HIS* 1.3 61.4 + - - +
423B PRO* 3.5 7.4 - - - +
426B PHE* 3.6 33.2 - + - -
434B LYS 5.9 0.2 - - - -
435B ALA* 3.7 26.6 - - + +
438B LYS* 3.5 45.6 - - + +
439B PHE* 3.6 22.4 - - + +
442B ILE* 4.9 15.7 - - + -
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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