Contacts of the helix formed by residues 390 - 401 (chain B) in PDB entry 3Q36
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 390 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388B HIS 3.9 2.0 + - - -
389B SER* 1.3 72.3 - - - +
391B PRO* 1.3 62.7 - - + +
392B GLU* 3.1 14.6 + - - +
393B LEU* 2.7 48.8 + - - +
394B LEU 2.9 7.5 + - - -
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Residues in contact with PRO 391 (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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389B SER 3.6 5.1 - - - +
390B ASP* 1.3 84.6 - - + +
392B GLU* 1.3 57.4 + - - +
394B LEU* 3.7 5.9 - - + +
395B LYS* 2.8 31.6 + - - +
412B LEU* 4.0 26.3 - - + +
415B VAL* 5.0 13.0 - - + -
416B LYS* 5.5 15.5 - - + -
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Residues in contact with GLU 392 (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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390B ASP* 2.9 12.1 + - - +
391B PRO* 1.3 76.6 - - - +
393B LEU* 1.3 62.8 + - - +
395B LYS* 3.1 33.1 + - - +
396B GLN* 3.2 48.4 + - - +
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Residues in contact with LEU 393 (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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389B SER* 4.1 10.1 - - - -
390B ASP* 2.7 34.4 + - - +
392B GLU* 1.3 70.2 - - - +
394B LEU* 1.3 66.7 + - - +
396B GLN* 2.9 34.8 + - + +
397B LYS* 2.9 47.4 + - + +
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B PRO* 4.0 27.8 - - + +
386B PHE* 3.8 36.1 - - + +
389B SER* 4.0 10.9 - - - +
390B ASP 2.9 11.0 + - - +
391B PRO* 3.7 10.1 - - + +
393B LEU* 1.3 76.4 - - - +
395B LYS* 1.3 62.3 + - - +
397B LYS* 3.2 14.3 + - + +
398B LEU* 3.0 50.5 + - + +
411B ILE* 5.1 0.9 - - + -
412B LEU* 4.3 14.4 - - + -
415B VAL* 3.9 21.1 - - + -
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Residues in contact with LYS 395 (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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391B PRO 2.8 16.8 + - - +
392B GLU* 3.1 38.3 + - - +
393B LEU 3.1 0.2 - - - -
394B LEU* 1.3 74.7 - - - +
396B GLN* 1.3 66.1 + - - +
398B LEU* 3.5 8.8 + - - +
399B GLN* 3.1 42.8 + - - +
408B ILE* 3.9 20.6 - - + +
412B LEU* 4.2 18.5 - - + +
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Residues in contact with GLN 396 (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 GLU* 3.2 36.9 + - - +
393B LEU* 2.9 27.9 + - + +
395B LYS* 1.3 78.0 - - + +
397B LYS* 1.3 63.6 + - - +
399B GLN* 3.2 19.2 + - - +
400B SER* 3.1 22.6 + - - -
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Residues in contact with LYS 397 (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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290B GLN* 3.0 30.0 + - + +
385B PRO* 5.2 1.8 - - + -
389B SER* 2.8 26.5 + - - +
393B LEU* 2.9 54.9 + - + +
394B LEU* 3.4 14.1 - - + +
396B GLN* 1.3 76.3 - - - +
398B LEU* 1.3 63.0 - - + +
400B SER* 2.6 27.0 + - - +
401B TYR* 3.0 30.4 + - + +
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Residues in contact with LEU 398 (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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286B PRO* 5.7 0.4 - - + -
386B PHE* 4.5 14.1 - - + -
394B LEU* 3.0 36.2 + - + +
395B LYS* 4.0 2.0 - - - +
396B GLN 3.4 0.2 - - - -
397B LYS* 1.3 72.8 - - + +
399B GLN* 1.3 65.0 + - - +
401B TYR* 3.0 14.5 + - + -
402B LYS 3.1 0.2 + - - -
403B ILE* 3.0 34.5 + - + +
408B ILE* 4.0 30.5 - - + -
411B ILE* 3.8 28.9 - - + -
412B LEU* 5.4 1.8 - - + -
427B TYR* 4.0 30.5 - - + -
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Residues in contact with GLN 399 (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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395B LYS* 3.1 42.4 + - - +
396B GLN* 3.5 20.9 + - - +
397B LYS 3.2 0.2 - - - -
398B LEU* 1.3 70.7 - - - +
400B SER* 1.3 56.5 - - - +
401B TYR 2.9 3.8 - - - -
402B LYS* 2.5 28.8 + - - +
403B ILE 4.5 3.6 - - - +
408B ILE* 3.6 17.5 - - + +
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Residues in contact with SER 400 (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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289B ARG* 5.0 3.1 + - - -
396B GLN 3.1 8.6 + - - -
397B LYS* 2.6 24.2 + - - +
399B GLN* 1.3 79.2 - - - +
401B TYR* 1.3 69.8 + - - +
402B LYS* 3.1 8.9 + - - +
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Residues in contact with TYR 401 (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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286B PRO* 4.3 15.2 + - + -
289B ARG* 3.1 63.0 + - + +
290B GLN* 4.0 21.7 + - - +
293B LYS* 6.3 0.7 - - - -
397B LYS* 3.0 34.7 + - + +
398B LEU* 3.3 17.0 - - + +
399B GLN 2.9 1.6 - - - -
400B SER* 1.3 87.6 - - - +
402B LYS* 1.3 72.4 + - - +
403B ILE* 3.4 13.4 + - + +
427B TYR* 3.8 24.2 - + + -
431B ILE* 5.2 4.9 - - + +
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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