Contacts of the helix formed by residues 395 - 409 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A SER* 4.5 8.2 + - - +
390A GLN 3.5 6.1 - - - +
391A ILE* 3.3 32.7 + - + +
394A GLY* 1.3 74.7 - - - -
396A ASN* 1.3 60.7 + - - +
397A GLU* 3.1 5.7 + - - -
398A ILE* 3.1 22.9 + - - +
399A GLN* 2.9 24.7 + - - +
420A FAD 2.7 52.4 + - - +
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Residues in contact with ASN 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A LYS* 3.0 34.7 + - - +
351A ALA* 3.5 10.7 + - + -
354A SER* 2.9 22.8 + - - -
355A GLU* 3.4 28.1 + - - +
390A GLN* 3.1 28.1 + - - +
395A THR* 1.3 74.3 - - - +
397A GLU* 1.3 64.7 + - - +
399A GLN* 3.4 7.7 - - - +
400A ARG* 3.0 36.8 + - - +
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Residues in contact with GLU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A GLN 5.2 0.9 - - - +
395A THR* 3.0 8.3 - - - +
396A ASN* 1.3 82.1 + - - +
398A ILE* 1.3 58.9 + - - +
400A ARG* 3.2 9.7 + - - +
401A LEU* 2.9 30.3 + - - +
420A FAD 2.8 61.5 + - + +
313B PHE* 3.5 21.0 - - + -
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Residues in contact with ILE 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A SER* 3.8 32.3 - - - +
273A ARG* 4.1 7.0 - - - +
394A GLY* 3.9 8.1 - - - -
395A THR* 3.1 33.6 + - - +
397A GLU* 1.3 74.3 - - - +
399A GLN* 1.3 73.7 + - - +
400A ARG 3.1 0.2 - - - -
401A LEU* 3.0 21.4 + - + +
402A ILE* 2.8 53.8 + - + +
420A FAD 4.5 11.4 - - + +
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Residues in contact with GLN 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ARG* 3.3 27.8 + - - +
347A ALA* 3.4 33.2 - - + +
350A LYS* 4.1 13.4 - - + +
351A ALA* 4.0 5.6 - - + -
393A GLU 3.2 9.9 + - - -
394A GLY* 2.8 39.0 + - - -
395A THR 2.9 19.1 + - - +
396A ASN* 3.4 23.1 - - - +
398A ILE* 1.3 81.8 - - - +
400A ARG* 1.3 57.5 + - - +
402A ILE* 3.1 6.3 + - - +
403A ILE* 3.0 32.0 + - - +
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Residues in contact with ARG 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A ALA* 4.5 5.4 - - + +
355A GLU* 3.0 40.8 + - - -
396A ASN* 3.0 26.2 + - - +
397A GLU* 3.3 12.0 + - - +
398A ILE 3.1 0.2 - - - -
399A GLN* 1.3 75.8 - - + +
401A LEU* 1.3 60.8 + - - +
403A ILE* 3.3 2.1 + - + -
404A ALA* 2.8 25.3 + - - +
313B PHE* 3.5 39.7 - - + -
316B VAL* 3.2 31.9 - - + +
317B ASP* 3.1 30.4 + - - -
320B ILE* 4.0 17.1 - - + +
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Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A GLU 2.9 10.9 + - - +
398A ILE* 3.3 25.1 - - + +
400A ARG* 1.3 76.0 - - - +
402A ILE* 1.3 62.7 + - + +
404A ALA* 3.4 5.8 + - + +
405A ARG* 3.1 43.2 + - - +
420A FAD 3.5 36.8 - - + +
309B GLN* 3.9 16.6 - - + +
312B GLN* 4.8 7.6 - - - +
313B PHE* 3.2 33.0 - - + -
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Residues in contact with ILE 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A MET* 6.5 0.7 - - - -
270A ASN* 5.5 1.3 - - - +
273A ARG* 3.3 32.1 - - - +
343A ALA* 4.2 21.8 - - + +
344A HIS* 4.7 2.0 - - + +
347A ALA* 4.1 13.2 - - + -
398A ILE* 2.8 36.1 + - + +
399A GLN* 3.3 13.2 - - - +
401A LEU* 1.3 78.3 - - + +
403A ILE* 1.3 63.0 + - - +
405A ARG* 3.3 14.2 + - - +
406A HIS* 3.2 19.3 + - + +
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Residues in contact with ILE 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A HIS* 4.1 6.3 - - + +
347A ALA* 3.9 12.6 - - + +
348A ILE* 3.1 43.5 - - + +
351A ALA* 5.3 0.9 - - + -
399A GLN* 3.0 17.4 + - + +
400A ARG* 3.3 6.7 + - + +
402A ILE* 1.3 73.4 - - - +
404A ALA* 1.3 60.5 + - - +
406A HIS* 3.0 10.0 + - + +
407A ILE* 2.9 36.2 + - + +
316B VAL* 3.8 28.0 - - + +
319B LEU* 3.7 28.3 - - + -
320B ILE* 4.2 8.1 - - + -
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Residues in contact with ALA 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A ARG 2.8 18.6 + - - +
401A LEU* 3.5 11.4 - - + +
402A ILE 3.3 0.2 - - - -
403A ILE* 1.3 76.5 - - - +
405A ARG* 1.3 57.1 + - + +
407A ILE* 3.2 6.3 + - - +
408A LEU* 2.9 37.2 + - + +
312B GLN* 4.1 32.1 - - + +
313B PHE* 5.7 0.2 - - + -
316B VAL* 3.6 16.1 - - + +
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Residues in contact with ARG 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A LEU* 3.1 29.6 + - - +
402A ILE* 3.6 11.2 - - - +
404A ALA* 1.3 73.6 - - + +
406A HIS* 1.3 60.9 + - - +
408A LEU* 3.8 3.1 - - - -
409A ALA* 2.8 34.2 + - - +
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Residues in contact with HIS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A HIS* 3.4 55.0 + + + +
402A ILE* 3.2 9.6 + - + +
403A ILE 3.0 8.9 + - - +
405A ARG* 1.3 81.5 - - - +
407A ILE* 1.3 62.9 - - - +
409A ALA* 3.7 14.4 + - - +
292B ARG* 5.2 0.3 + - - -
319B LEU* 4.1 19.8 - - + +
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Residues in contact with ILE 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A ILE* 2.9 20.7 + - + +
404A ALA* 3.6 7.4 - - - +
405A ARG 3.2 0.2 - - - -
406A HIS* 1.3 81.4 - - - +
408A LEU* 1.3 67.5 + - + +
409A ALA 3.7 2.6 + - - +
288B LEU* 4.5 13.2 - - + -
292B ARG* 3.0 56.0 + - + +
296B LYS* 5.0 0.2 - - - -
315B LEU* 3.4 39.7 - - + +
316B VAL* 3.8 13.9 - - + +
319B LEU* 3.6 29.6 - - + -
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Residues in contact with LEU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A ALA* 2.9 26.1 + - + +
405A ARG* 4.4 2.7 - - - +
407A ILE* 1.3 92.1 - - + +
409A ALA* 1.3 66.3 + - - +
410A ALA* 2.9 3.3 + - - +
292B ARG* 4.0 15.7 - - + -
296B LYS* 2.8 35.5 + - - +
306B ALA* 4.1 21.3 - - + +
312B GLN* 3.7 32.5 - - + +
315B LEU* 4.1 16.8 - - + -
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Residues in contact with ALA 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A ARG 2.8 19.7 + - - +
406A HIS* 3.7 12.9 - - - +
407A ILE 3.4 4.0 - - - +
408A LEU* 1.3 73.8 - - - +
410A ALA* 1.3 70.0 + - - +
296B LYS* 5.5 0.9 - - - -
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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