Contacts of the helix formed by residues 395 - 409 (chain B) in PDB entry 1UKW
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 395 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162B SER* 4.9 4.8 + - - +
390B GLN 3.5 9.2 - - - -
391B ILE* 3.5 28.7 - - + +
394B GLY* 1.3 72.7 - - - -
396B ASN* 1.3 59.2 + - - +
397B GLU* 3.0 7.4 + - - -
398B ILE* 3.1 19.8 + - - +
399B GLN* 2.9 28.3 + - - +
421B FAD 2.6 57.6 + - - +
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Residues in contact with ASN 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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350B LYS* 3.2 21.1 + - - +
351B ALA* 3.6 19.5 + - + -
354B SER* 3.1 21.9 + - - -
355B GLU* 3.1 28.9 + - - +
390B GLN* 3.1 27.8 + - - +
395B THR* 1.3 72.7 - - - +
397B GLU* 1.3 64.9 + - - +
399B GLN* 3.4 8.2 - - - +
400B ARG* 3.0 38.9 + - - +
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Residues in contact with GLU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PHE* 3.8 25.4 - - + -
390B GLN 5.1 0.7 - - - +
395B THR* 3.0 9.9 + - - -
396B ASN* 1.3 83.7 + - - +
398B ILE* 1.3 59.9 + - - +
400B ARG* 3.1 7.2 + - - +
401B LEU* 2.8 30.4 + - - +
421B FAD 2.9 54.8 + - + +
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Residues in contact with ILE 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B SER* 4.3 28.7 - - - +
273B ARG* 5.4 4.7 - - - +
394B GLY* 3.7 10.1 - - - -
395B THR* 3.1 30.7 + - - +
397B GLU* 1.3 73.2 - - - +
399B GLN* 1.3 82.8 + - - +
401B LEU* 3.4 22.4 - - + +
402B ILE* 2.7 44.2 + - + +
421B FAD 4.6 14.6 - - + +
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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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273B ARG* 3.1 36.5 + - - +
347B ALA* 3.3 23.4 - - - +
350B LYS* 4.1 10.4 - - + +
351B ALA* 4.1 5.6 - - + -
393B GLU 3.2 16.8 + - - -
394B GLY* 3.0 29.1 + - - +
395B THR 2.9 19.0 + - - +
396B ASN* 3.4 24.2 - - - +
398B ILE* 1.3 86.9 - - - +
400B ARG* 1.3 62.7 + - - +
402B ILE* 3.0 8.3 + - - +
403B ILE* 3.0 26.5 + - - +
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Residues in contact with ARG 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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313A PHE* 3.6 42.6 - - + -
316A VAL* 3.4 25.5 - - + +
317A ASP* 3.0 31.8 + - - -
320A ILE* 3.9 15.5 - - + +
351B ALA* 4.4 5.5 - - + +
355B GLU* 3.0 40.0 + - - -
396B ASN* 3.0 32.7 + - - +
397B GLU* 3.1 10.1 + - - +
399B GLN* 1.3 78.9 - - + +
401B LEU* 1.3 51.7 + - - +
403B ILE* 3.1 4.7 + - + -
404B ALA* 2.7 36.5 + - - +
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Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLN* 4.0 17.3 - - + +
312A GLN* 4.0 19.5 - - - +
313A PHE* 4.1 14.1 - - + -
397B GLU 2.8 16.0 + - - +
398B ILE* 3.1 23.1 + - + +
400B ARG* 1.3 75.6 - - - +
402B ILE* 1.3 65.0 + - + +
404B ALA* 3.4 4.6 + - + +
405B ARG* 3.1 32.4 + - + +
421B FAD 3.5 37.7 - - + +
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Residues in contact with ILE 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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266B MET* 6.4 1.8 - - - -
273B ARG* 4.7 15.5 - - - +
343B ALA* 4.0 22.2 - - + +
344B HIS* 4.6 2.7 - - - -
347B ALA* 4.0 16.6 - - + -
398B ILE* 2.7 35.5 + - + +
399B GLN* 3.0 10.5 + - - +
401B LEU* 1.3 76.5 - - + +
403B ILE* 1.3 62.5 + - - +
405B ARG* 3.4 19.5 + - - +
406B HIS* 3.3 19.5 + - + +
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Residues in contact with ILE 403 (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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316A VAL* 3.6 33.0 - - + +
319A LEU* 3.8 27.8 - - + -
320A ILE* 4.2 8.7 - - + -
344B HIS* 4.2 5.6 - - + +
347B ALA* 3.9 12.8 - - + +
348B ILE* 3.5 42.6 - - + +
351B ALA* 5.2 1.1 - - + -
399B GLN* 3.0 18.4 + - + +
400B ARG* 3.6 8.3 - - + +
402B ILE* 1.3 74.5 - - - +
404B ALA* 1.3 66.3 + - - +
406B HIS* 3.1 9.2 + - + +
407B ILE* 2.9 23.7 + - + +
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Residues in contact with ALA 404 (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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312A GLN* 3.9 31.9 - - + +
313A PHE* 5.9 0.2 - - + -
315A LEU* 6.3 0.2 - - - -
316A VAL* 3.5 17.9 - - + +
400B ARG 2.7 21.6 + - - +
401B LEU* 3.6 8.3 - - + +
403B ILE* 1.3 72.7 - - - +
405B ARG* 1.3 52.2 + - + +
407B ILE* 3.1 4.6 + - - +
408B LEU* 2.7 48.6 + - + +
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Residues in contact with ARG 405 (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 LEU* 3.1 18.2 + - - +
402B ILE* 3.5 21.3 - - - +
403B ILE 3.2 0.2 - - - -
404B ALA* 1.3 75.8 - - + +
406B HIS* 1.3 60.1 - - - +
408B LEU* 5.0 2.9 - - - -
409B ALA* 2.8 34.4 + - - +
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Residues in contact with HIS 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.1 18.5 - - + +
344B HIS* 3.6 54.1 + + + +
402B ILE 3.3 9.6 + - - +
403B ILE 3.1 8.9 + - - +
405B ARG* 1.3 79.8 - - - +
407B ILE* 1.3 65.5 + - + +
409B ALA* 3.8 13.3 - - - +
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Residues in contact with ILE 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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288A LEU* 4.4 9.4 - - + -
292A ARG* 3.3 42.7 + - + +
315A LEU* 3.5 44.0 - - + +
316A VAL* 3.9 9.9 - - + +
319A LEU* 3.6 33.7 - - + -
403B ILE* 2.9 16.6 + - + +
404B ALA* 3.3 8.1 - - - +
406B HIS* 1.3 81.3 - - + +
408B LEU* 1.3 78.5 + - + +
409B ALA 3.5 4.7 + - - +
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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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292A ARG* 4.4 7.2 - - + +
296A LYS* 2.8 39.8 + - + +
306A ALA* 4.3 24.2 - - + +
312A GLN* 4.2 20.0 - - + +
315A LEU* 4.0 20.9 - - + -
404B ALA* 2.7 47.6 + - + +
405B ARG* 4.4 3.1 - - - +
407B ILE* 1.3 86.1 - - + +
409B ALA* 1.3 69.6 + - - +
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Residues in contact with ALA 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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292A ARG* 5.6 0.5 - - - -
296A LYS* 4.3 4.5 - - - -
405B ARG 2.8 19.4 + - - +
406B HIS* 3.8 12.7 - - - +
407B ILE 3.3 7.1 - - - +
408B LEU* 1.3 87.8 - - - +
410B ALA* 1.3 63.1 + - - +
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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