Contacts of the helix formed by residues 391 - 411 (chain B) in PDB entry 3U0Z
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 SER 391 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B ASP* 1.3 76.4 - - - +
392B SER* 1.3 57.1 - - - +
394B ARG* 3.2 10.8 - - - +
395B GLN* 3.2 30.5 + - - +
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Residues in contact with SER 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ASP 4.2 9.5 + - - -
391B SER* 1.3 77.2 - - - +
393B ARG* 1.3 59.1 + - - +
394B ARG 3.0 4.9 - - - -
395B GLN* 3.6 3.7 + - - +
396B TYR* 3.1 24.4 + - - +
431B LYS* 4.5 13.5 - - - +
432B ILE 2.9 44.6 + - - -
433B PHE* 4.2 16.3 - - - +
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Residues in contact with ARG 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ASP* 3.0 41.0 + - - +
392B SER* 1.3 77.9 + - - +
394B ARG* 1.3 58.6 + - - +
396B TYR* 4.1 5.0 - - - +
397B GLN* 4.0 29.2 + - - +
430B GLY* 3.4 24.2 + - - +
431B LYS* 3.5 35.8 - - + +
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Residues in contact with ARG 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ASP 3.4 6.8 + - - +
391B SER* 3.2 17.0 + - - +
392B SER 3.0 1.6 - - - -
393B ARG* 1.3 75.5 - - - +
395B GLN* 1.3 69.7 + - + +
396B TYR 3.1 1.1 - - - -
397B GLN* 2.9 22.9 + - - +
398B GLU* 3.2 36.9 + - + +
401B LYS* 5.3 7.7 - - - +
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Residues in contact with GLN 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B SER* 3.2 15.1 + - - +
392B SER* 3.7 9.4 - - - +
394B ARG* 1.3 81.4 - - + +
396B TYR* 1.3 52.7 + - - +
398B GLU* 3.1 6.6 + - - +
399B LYS* 2.8 67.9 + - - +
432B ILE* 4.2 22.0 + - + +
433B PHE* 5.9 1.0 - - - +
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Residues in contact with TYR 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B SER 3.1 11.4 + - - +
393B ARG 4.1 3.6 - - - +
394B ARG 3.1 0.4 - - - -
395B GLN* 1.3 78.3 - - - +
397B GLN* 1.3 81.5 + - + +
399B LYS* 3.3 2.1 + - - +
400B TYR* 2.9 36.1 + + + +
421B HIS* 5.9 0.5 - - - -
424B TYR* 3.6 32.1 - + - -
425B GLU* 3.6 32.1 - - - +
428B TYR* 3.8 15.7 - - + -
430B GLY* 3.3 53.0 + - - +
431B LYS* 3.5 5.4 - - - +
432B ILE* 4.2 14.1 - - + +
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Residues in contact with GLN 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ARG* 4.0 24.9 + - - +
394B ARG* 2.9 15.1 + - - +
396B TYR* 1.3 98.9 - - + +
398B GLU* 1.3 63.0 + - + +
400B TYR* 4.0 4.6 - - + +
401B LYS* 3.1 32.6 + - - +
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Residues in contact with GLU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ARG* 3.2 37.0 + - + +
395B GLN* 3.1 9.8 + - - +
397B GLN* 1.3 78.1 - - - +
399B LYS* 1.3 61.5 + - - +
401B LYS* 3.1 19.5 + - + +
402B GLN* 2.8 29.3 + - - +
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Residues in contact with LYS 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B GLN* 2.8 46.0 + - - +
396B TYR 3.7 2.7 - - - +
398B GLU* 1.3 77.6 - - + +
400B TYR* 1.3 56.7 + - - +
402B GLN* 2.8 34.9 + - + +
403B VAL* 2.9 15.1 + - - +
424B TYR* 3.7 18.6 - - - +
432B ILE* 4.1 25.1 - - + +
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Residues in contact with TYR 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B TYR* 2.9 24.8 + + + +
397B GLN* 4.6 4.5 - - + +
399B LYS* 1.3 76.0 - - - +
401B LYS* 1.3 60.5 + - - +
403B VAL* 3.6 28.5 - - + -
404B GLU* 3.2 51.6 + - + +
407B MET* 4.2 11.7 - - + +
417B ARG* 4.6 0.3 + - - +
420B ILE* 4.9 1.1 - - + -
421B HIS* 2.9 60.1 + + - +
424B TYR* 3.9 31.9 + + + -
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Residues in contact with LYS 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ARG* 5.3 7.5 - - - +
397B GLN* 3.1 21.8 + - - +
398B GLU* 3.1 26.7 + - + +
400B TYR* 1.3 75.6 - - - +
402B GLN* 1.3 63.1 + - - +
404B GLU* 3.6 15.7 + - - +
405B GLN* 3.2 31.0 + - - +
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Residues in contact with GLN 402 (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 GLU 2.8 13.1 + - - +
399B LYS* 2.8 27.4 + - + +
401B LYS* 1.3 71.7 - - - +
403B VAL* 1.3 66.0 + - + +
405B GLN* 3.0 26.0 + - - +
406B TYR* 3.1 12.7 + - - +
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Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B LYS 2.9 14.5 + - - +
400B TYR* 3.6 31.6 - - + +
401B LYS 3.3 0.2 - - - -
402B GLN* 1.3 74.9 - - + +
404B GLU* 1.3 64.8 + - - +
406B TYR* 3.0 20.0 + - - +
407B MET* 3.0 21.9 + - + +
420B ILE* 4.2 20.2 - - + -
424B TYR* 4.1 25.4 - - + +
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Residues in contact with GLU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B TYR* 3.2 48.9 + - + +
401B LYS* 3.6 17.9 - - - +
403B VAL* 1.3 77.5 - - - +
405B GLN* 1.3 63.9 + - + +
407B MET* 3.5 17.3 + - + +
408B SER* 3.1 25.8 + - - -
417B ARG* 4.9 1.0 + - - -
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Residues in contact with GLN 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LYS* 3.2 20.4 + - - +
402B GLN* 3.0 19.6 + - - +
404B GLU* 1.3 79.1 - - + +
406B TYR* 1.3 54.4 - - - +
408B SER* 3.1 8.6 + - - -
409B PHE* 2.8 35.0 + - - +
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Residues in contact with TYR 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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402B GLN 3.1 7.6 + - - +
403B VAL* 3.0 12.1 + - - +
405B GLN* 1.3 77.3 - - - +
407B MET* 1.3 73.7 + - + +
409B PHE* 3.2 5.6 + + - -
410B HIS* 2.9 65.2 + + + +
412B LEU* 4.8 10.1 - - + -
420B ILE* 6.5 0.2 - - + -
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Residues in contact with MET 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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400B TYR* 4.2 15.7 - - - +
403B VAL* 3.0 17.9 + - + +
404B GLU* 3.6 29.2 - - + +
405B GLN 3.2 0.2 - - - -
406B TYR* 1.3 80.8 - - + +
408B SER* 1.3 52.8 + - - +
410B HIS* 3.0 2.8 + - - +
411B LYS 2.8 30.5 + - - -
412B LEU* 3.5 26.1 + - + -
417B ARG* 3.4 55.8 + - + +
420B ILE* 4.1 26.7 - - + -
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Residues in contact with SER 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 GLU 3.1 15.2 + - - -
405B GLN* 3.3 10.4 - - - -
407B MET* 1.3 72.7 - - - +
409B PHE* 1.3 66.8 + - - +
411B LYS* 2.9 21.5 + - - +
417B ARG* 3.7 21.2 + - - +
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Residues in contact with PHE 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLN 2.8 18.2 + - - +
406B TYR* 3.2 6.0 + - - +
408B SER* 1.3 73.8 - - - +
410B HIS* 1.3 87.9 + + + +
411B LYS* 3.7 16.8 + - - -
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Residues in contact with HIS 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B TYR* 2.9 66.6 + + + +
409B PHE* 1.3 103.1 + + - +
411B LYS* 1.3 72.0 + - - +
412B LEU* 3.3 25.6 + - + +
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Residues in contact with LYS 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B MET 2.8 6.7 + - - -
408B SER 2.9 13.6 + - - +
409B PHE* 3.9 17.0 - - - -
410B HIS* 1.3 80.1 - - - +
412B LEU* 1.3 63.9 + - - +
413B PRO* 3.6 5.0 - - - +
417B ARG* 3.5 11.9 - - - +
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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
------------------------------------------------------------
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