Contacts of the helix formed by residues 398 - 411 (chain B) in PDB entry 1U0C
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 LYS 398 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ARG* 6.4 0.2 - - - -
317B VAL* 3.4 20.0 - - + +
318B ASP* 3.1 24.0 + - - +
319B GLY 5.5 1.1 - - - -
321B GLY 3.1 21.8 + - - +
322B SER* 4.6 1.1 - - - -
323B ILE* 3.6 26.6 - - + +
395B LEU* 3.8 7.4 - - + +
397B LEU* 1.3 89.5 - - + +
399B GLN* 1.3 63.4 + - - +
401B GLN* 3.0 26.2 - - + +
402B ALA* 3.2 23.4 + - - +
436B ASN* 4.7 2.4 + - - +
565D G 4.2 3.0 + - - -
566D A 3.1 34.5 + - - +
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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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392B GLN* 2.6 47.6 + - + +
393B PRO* 3.5 13.7 + - - +
395B LEU* 3.6 35.3 + - + +
396B LYS* 4.5 5.5 + - - +
397B LEU 3.7 1.2 - - - -
398B LYS* 1.3 77.6 - - - +
400B LYS* 1.3 64.8 + - + +
402B ALA* 3.2 4.0 + - - +
403B ASN* 3.0 32.9 + - - +
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Residues in contact with LYS 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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398B LYS 3.3 0.6 - - - -
399B GLN* 1.3 78.9 - - + +
401B GLN* 1.3 67.0 + - - +
403B ASN* 3.0 8.0 + - - +
404B LEU* 2.8 27.0 + - + +
435B LEU* 3.5 38.6 - - + -
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Residues in contact with GLN 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ILE* 3.9 16.2 - - + -
397B LEU 3.6 11.5 + - - +
398B LYS* 3.0 46.8 - - + +
400B LYS* 1.3 80.7 + - - +
402B ALA* 1.3 56.4 + - - +
404B LEU* 3.2 8.8 + - - +
405B VAL* 2.8 34.8 + - - +
432B ILE* 3.9 26.2 - - + +
435B LEU* 3.7 29.2 + - + +
436B ASN* 2.9 25.9 + - - +
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Residues in contact with ALA 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ILE* 4.2 6.7 - - + -
388B LEU* 3.8 22.2 - - + +
392B GLN* 4.5 12.1 - - + -
395B LEU* 3.7 21.1 - - + -
398B LYS 3.2 15.0 + - - +
399B GLN* 3.3 9.9 - - - +
400B LYS 3.1 0.6 - - - -
401B GLN* 1.3 77.5 - - - +
403B ASN* 1.3 57.1 + - - +
405B VAL* 3.1 4.9 + - - +
406B LEU* 3.0 31.8 + - - +
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Residues in contact with ASN 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B GLN* 2.9 45.5 - - - +
399B GLN* 3.0 28.7 + - - +
400B LYS* 3.0 5.7 + - - +
402B ALA* 1.3 73.9 - - - +
404B LEU* 1.3 65.1 + - - +
405B VAL 3.2 0.2 - - - -
406B LEU* 3.5 15.4 - - - +
407B LYS* 3.1 24.9 + - - +
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Residues in contact with LEU 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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400B LYS* 2.8 18.6 + - + +
401B GLN 3.5 0.9 - - - +
403B ASN* 1.3 78.4 - - - +
405B VAL* 1.3 59.3 + - - +
407B LYS* 3.5 28.3 + - + +
408B ILE* 2.9 32.6 + - - +
428B TRP* 3.8 8.7 - - + +
431B GLN* 3.4 47.1 - - + +
432B ILE* 3.5 32.8 - - + +
435B LEU* 4.4 11.9 - - + -
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Residues in contact with VAL 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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323B ILE* 3.3 21.8 - - + -
324B ILE 4.4 4.9 - - - +
341B LEU* 4.0 33.2 - - + -
342B THR 5.7 1.6 - - - +
384B LEU* 4.6 4.5 - - + -
388B LEU* 3.5 21.3 - - + -
401B GLN 2.8 16.6 + - - +
402B ALA 3.5 7.6 - - - +
404B LEU* 1.3 75.8 - - - +
406B LEU* 1.3 66.3 + - - +
408B ILE* 3.1 8.2 + - - +
409B ILE* 3.0 30.7 + - + +
432B ILE* 3.8 15.9 - - + -
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Residues in contact with LEU 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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385B HIS* 3.5 36.3 - - + +
388B LEU* 3.7 12.3 - - + -
389B THR* 3.3 42.8 - - + +
392B GLN* 4.4 8.1 - - + +
402B ALA 3.0 17.2 + - - +
403B ASN* 3.5 29.2 - - - +
405B VAL* 1.3 74.6 - - - +
407B LYS* 1.3 65.8 + - - +
409B ILE* 2.8 17.7 + - + +
410B GLU* 3.0 22.5 + - - +
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Residues in contact with LYS 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 ASN 3.1 15.7 + - - +
404B LEU* 3.5 26.8 - - + +
406B LEU* 1.3 78.6 - - - +
408B ILE* 1.3 63.8 + - - +
410B GLU* 3.5 14.2 + - - +
411B GLN* 3.1 28.8 + - + +
428B TRP* 3.5 52.6 - - + +
431B GLN* 4.8 2.0 + - - -
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Residues in contact with ILE 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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325B ALA* 4.4 5.4 - - + -
339B LEU* 4.6 13.0 - - + -
341B LEU* 3.6 22.9 - - + -
404B LEU 2.9 16.4 + - - +
405B VAL 3.4 7.6 - - - +
407B LYS* 1.3 77.7 - - - +
409B ILE* 1.3 62.4 + - - +
411B GLN* 3.2 5.2 + - - +
412B LEU* 3.2 22.9 + - + +
425B VAL* 3.9 16.1 - - + +
428B TRP* 3.2 43.5 - - + -
429B VAL* 3.7 22.0 - - + +
432B ILE* 3.9 15.9 - - + -
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Residues in contact with ILE 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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341B LEU* 3.2 27.4 - - + -
381B ILE* 3.6 46.9 - - + +
382B LYS* 4.3 17.5 - - - +
384B LEU* 4.3 9.0 - - + -
385B HIS* 4.1 22.9 - - + +
405B VAL* 3.0 19.0 + - + +
406B LEU* 2.8 14.6 + - + +
408B ILE* 1.3 71.6 - - - +
410B GLU* 1.3 62.2 + - - +
412B LEU* 3.1 26.5 + - + +
413B PRO* 4.0 2.4 - - - +
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Residues in contact with GLU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LYS* 5.9 1.6 - - - +
385B HIS* 3.2 29.4 + - + +
406B LEU* 3.0 16.2 + - - +
407B LYS* 3.5 20.4 + - - +
409B ILE* 1.3 76.3 - - - +
411B GLN* 1.3 71.8 + - - +
412B LEU 3.2 3.5 + - - -
413B PRO* 3.5 15.0 - - - +
414B SER* 5.9 0.2 - - - -
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Residues in contact with GLN 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 LYS* 3.1 23.3 + - + +
408B ILE 3.4 5.2 - - - +
409B ILE 3.2 0.2 - - - -
410B GLU* 1.3 88.8 + - - +
412B LEU* 1.3 62.2 + - - +
413B PRO* 3.7 1.3 - - - -
414B SER* 3.2 13.1 + - - -
415B ALA* 3.2 22.7 + - - +
421B LYS* 2.6 40.0 + - - +
425B VAL* 3.9 11.1 - - + +
428B TRP* 4.4 11.2 - - + +
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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