Contacts of the helix formed by residues 405 - 416 (chain B) in PDB entry 6UZA
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 405 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398B LEU* 5.0 6.3 - - + -
401B GLN* 3.7 30.3 - - + +
402B THR* 3.7 31.2 - - + +
403B MET 3.1 1.6 - - - +
404B ALA* 1.3 82.6 - - - +
406B LYS* 1.3 58.2 + - - +
407B PHE 3.3 1.3 - - - -
408B LEU* 3.2 12.5 + - + +
409B VAL* 3.1 25.3 + - + +
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Residues in contact with LYS 406 (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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392B TYR* 3.4 22.6 + - - -
398B LEU* 3.4 35.1 + - + -
399B ARG 4.5 4.2 + - - -
401B GLN* 4.0 22.0 + - + -
402B THR 4.1 11.0 + - - +
403B MET* 4.4 14.1 - - - +
404B ALA 4.4 0.6 - - - +
405B VAL* 1.3 74.5 - - - +
407B PHE* 1.3 60.6 + - - +
409B VAL* 3.3 12.5 - - + +
410B VAL* 3.0 33.0 + - + +
440B PHE* 4.2 17.7 - - + -
444B VAL* 6.2 0.2 - - + -
1005B Y01 4.0 37.3 + - + +
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Residues in contact with PHE 407 (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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403B MET* 4.9 10.6 - - + +
404B ALA* 4.4 16.9 - - + +
405B VAL 3.3 1.0 - - - +
406B LYS* 1.3 79.1 - - - +
408B LEU* 1.3 71.2 + - + +
410B VAL* 3.3 6.7 + - + +
411B LEU* 3.0 61.5 + - + +
1005B Y01 3.7 53.2 - - + +
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Residues in contact with LEU 408 (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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404B ALA* 3.3 24.9 - - + +
405B VAL* 3.2 14.6 + - + +
407B PHE* 1.3 98.2 - - + +
409B VAL* 1.3 56.1 + - - +
411B LEU* 3.4 10.8 + - + +
412B ALA* 2.9 27.4 + - - +
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Residues in contact with VAL 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LEU* 4.5 29.8 - - + -
405B VAL* 3.1 10.8 + - + +
406B LYS* 3.3 27.1 - - + +
408B LEU* 1.3 73.1 - - - +
410B VAL* 1.3 60.0 + - - +
412B ALA* 3.9 9.4 - - + -
413B VAL* 2.9 46.4 + - + +
440B PHE* 5.6 0.7 - - + -
441B MET* 5.4 6.7 - - + -
444B VAL* 4.5 14.6 - - + -
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Residues in contact with VAL 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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406B LYS 3.0 18.7 + - - +
407B PHE* 3.5 10.1 - - - +
408B LEU 3.3 0.2 - - - -
409B VAL* 1.3 77.2 - - - +
411B LEU* 1.3 61.2 + - + +
413B VAL 3.4 0.3 + - - -
414B ALA* 2.9 26.2 + - - +
443B PHE* 6.3 0.2 - - + -
444B VAL* 4.0 34.8 - - + +
447B ALA* 4.8 3.1 - - + -
448B ALA* 3.6 17.8 - - - +
451B THR* 4.4 14.4 - - - +
1005B Y01 4.1 44.4 - - + -
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Residues in contact with LEU 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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407B PHE* 3.0 55.9 + - + +
408B LEU* 3.7 12.8 - - + +
410B VAL* 1.3 80.4 - - + +
412B ALA* 1.3 56.4 + - - +
414B ALA* 3.2 6.6 + - + +
415B ILE* 2.9 36.9 + - + +
451B THR* 4.3 23.6 - - + -
1005B Y01 5.2 3.1 - - + -
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Residues in contact with ALA 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 LEU 2.9 17.0 + - - +
409B VAL* 3.2 15.2 + - + +
411B LEU* 1.3 75.6 - - - +
413B VAL* 1.3 62.1 + - + +
415B ILE* 3.3 9.5 + - - +
416B GLY* 3.0 24.8 + - - -
420B LEU* 5.6 0.3 - - - +
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Residues in contact with VAL 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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409B VAL* 2.9 24.5 + - + +
410B VAL 4.0 3.1 - - - +
412B ALA* 1.3 74.0 - - + +
414B ALA* 1.3 62.9 + - - +
416B GLY 4.6 0.7 - - - +
417B LEU* 3.3 40.1 + - + +
420B LEU* 3.8 30.7 - - + -
441B MET* 4.4 16.2 - - + -
444B VAL* 3.9 16.8 - - + -
445B ALA* 4.2 20.4 - - + -
448B ALA* 3.9 4.5 - - + -
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Residues in contact with ALA 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 VAL 2.9 15.5 + - - +
411B LEU* 3.3 15.7 - - + +
412B ALA 3.2 0.4 - - - -
413B VAL* 1.3 79.1 - - - +
415B ILE* 1.3 64.4 + - + +
417B LEU* 4.3 1.4 + - - +
448B ALA* 3.6 22.6 - - + +
451B THR* 4.8 12.8 - - + -
452B ILE* 3.3 30.5 - - + +
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Residues in contact with ILE 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 LEU* 2.9 24.3 + - + +
412B ALA* 3.3 8.0 + - - +
414B ALA* 1.3 81.1 - - + +
416B GLY* 1.3 59.8 + - - +
417B LEU 3.3 4.5 + - - -
418B PRO* 4.3 7.3 - - - +
419B PHE* 4.8 6.0 - - + -
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Residues in contact with GLY 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 ALA 3.0 13.0 + - - -
413B VAL 3.7 3.6 - - - -
415B ILE* 1.3 78.7 - - - +
417B LEU* 1.3 59.1 + - - -
418B PRO* 3.7 1.6 - - - -
419B PHE* 3.7 24.8 + - - +
420B LEU* 3.3 31.4 + - - +
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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