Contacts of the helix formed by residues 380 - 392 (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 GLU 380 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364B VAL* 3.2 26.5 - - - +
365B GLY* 4.3 5.9 + - - -
378B LEU* 3.6 7.3 - - + +
379B SER* 1.3 73.4 - - - +
381B ILE* 1.3 55.4 + - - +
382B LYS 3.2 1.9 + - - -
383B PRO* 3.6 22.1 - - + +
384B LEU* 2.8 36.4 + - - +
504C A 3.5 25.9 + - - +
505C A 3.3 28.0 + - - +
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU 5.8 3.6 - - - +
340B SER* 6.0 0.4 - - - -
341B LEU* 4.1 31.2 - - + +
379B SER 2.8 10.8 + - - +
380B GLU* 1.3 71.4 - - - +
382B LYS* 1.3 75.0 + - + +
384B LEU* 4.3 2.9 - - - -
385B HIS* 3.3 22.3 + - - +
409B ILE* 3.6 24.9 - - + +
412B LEU* 3.7 27.6 - - + -
503C T 4.9 11.9 - - + +
504C A 2.8 22.5 + - - +
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Residues in contact with LYS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ASN* 5.7 8.3 - - - +
381B ILE* 1.3 83.6 - - + +
383B PRO* 1.3 76.6 - - + +
384B LEU 3.0 1.3 - - - -
385B HIS* 3.1 37.8 + - - +
386B ASN* 3.0 22.3 + - - +
409B ILE* 4.3 11.1 - - - +
410B GLU* 5.9 1.6 - - - +
504C A 5.3 0.6 + - - -
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Residues in contact with PRO 383 (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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305B TYR* 5.2 0.5 + - - -
364B VAL* 4.0 31.8 - - + +
378B LEU* 4.5 4.2 - - + +
380B GLU* 3.3 34.5 - - + +
382B LYS* 1.3 96.4 - - + +
384B LEU* 1.3 54.5 + - - +
386B ASN* 3.5 11.9 + - + +
387B PHE* 2.9 30.9 + - - +
504C A 5.6 0.2 - - - +
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Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 3.7 36.6 - - + +
342B THR 4.3 1.8 - - - +
343B PHE* 3.7 28.7 - - + +
378B LEU* 3.8 32.0 - - + +
379B SER 4.1 7.4 - - - +
380B GLU 2.8 20.5 + - - +
381B ILE* 3.9 3.8 - - - +
383B PRO* 1.3 76.3 - - - +
385B HIS* 1.3 60.0 + - - +
387B PHE* 3.5 1.4 + - + +
388B LEU* 2.9 43.1 + - + +
405B VAL* 4.6 3.8 - - + -
409B ILE* 4.3 12.3 - - + -
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Residues in contact with HIS 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ILE 3.3 15.5 + - - +
382B LYS* 3.1 30.1 + - - +
384B LEU* 1.3 76.0 - - - +
386B ASN* 1.3 68.8 + - - +
389B THR* 2.9 49.5 + - + -
406B LEU* 3.6 22.9 - - + +
409B ILE* 4.1 14.6 - - + -
410B GLU* 3.2 39.5 + - + +
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Residues in contact with ASN 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ASN* 2.7 40.5 + - - +
303B THR* 3.1 33.9 + - - +
305B TYR* 3.8 18.4 + - - -
382B LYS* 3.0 12.1 + - - +
383B PRO* 3.5 13.6 + - + +
385B HIS* 1.3 83.0 + - - +
387B PHE* 1.3 60.9 + - - +
389B THR* 3.9 3.5 - - - -
390B GLN* 3.4 27.5 + - - +
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Residues in contact with PHE 387 (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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305B TYR* 3.8 29.2 - + + +
309B PHE* 4.7 1.3 - + - -
310B LEU* 4.5 12.6 - - + -
313B LEU* 3.6 23.1 - - + -
343B PHE* 3.4 43.3 - + + -
362B ILE* 3.4 34.8 - - + -
378B LEU* 4.3 13.7 - - + -
383B PRO 2.9 18.8 + - - +
384B LEU 3.8 2.7 - - - +
385B HIS 3.2 0.2 - - - -
386B ASN* 1.3 75.3 - - - +
388B LEU* 1.3 76.7 + - + +
390B GLN* 3.1 5.5 + - - +
391B LEU* 2.9 34.3 + - + +
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Residues in contact with LEU 388 (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* 4.6 9.9 - - + -
343B PHE* 4.4 14.4 - - + -
384B LEU* 2.9 34.9 + - + +
387B PHE* 1.3 88.7 - - + +
389B THR* 1.3 62.4 + - - +
391B LEU* 2.9 11.6 + - + +
392B GLN* 2.6 36.9 + - - +
395B LEU* 5.3 0.4 - - + -
402B ALA* 3.8 27.4 - - + +
405B VAL* 3.5 38.4 - - + -
406B LEU* 3.7 15.3 - - + -
409B ILE* 6.0 0.2 - - + -
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Residues in contact with THR 389 (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* 2.9 39.7 + - + -
386B ASN* 3.9 5.4 - - - +
388B LEU* 1.3 76.0 - - - +
390B GLN* 1.3 67.4 + - + +
392B GLN* 4.0 4.5 - - - +
393B PRO* 3.4 15.6 - - - +
406B LEU* 3.3 24.3 - - - +
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Residues in contact with GLN 390 (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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303B THR 2.8 28.5 + - - -
304B LYS* 3.3 12.8 - - - +
305B TYR* 2.9 40.1 + - + +
310B LEU* 3.5 26.7 - - + +
386B ASN* 3.4 20.5 + - - +
387B PHE 3.1 7.9 + - - +
388B LEU 3.0 0.8 - - - -
389B THR* 1.3 84.5 - - + +
391B LEU* 1.3 60.6 + - - +
393B PRO* 3.6 10.0 - - - +
394B PHE* 3.7 8.0 - - - -
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LEU* 3.7 40.8 - - + +
313B LEU* 4.3 5.6 - - + -
314B ALA* 3.8 12.8 - - + +
317B VAL* 4.3 6.7 - - + -
323B ILE* 6.0 0.2 - - + -
343B PHE* 4.2 13.0 - - + -
387B PHE* 2.9 42.4 + - + +
388B LEU* 2.9 11.3 + - + +
390B GLN* 1.3 75.2 - - - +
392B GLN* 1.3 56.1 + - - +
393B PRO 3.2 2.5 - - - -
394B PHE* 2.7 32.4 + - - +
395B LEU* 3.5 33.8 + - + -
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Residues in contact with GLN 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B LEU* 2.6 23.3 + - - +
389B THR* 4.0 6.4 - - - +
391B LEU* 1.3 73.4 - - - +
393B PRO* 1.3 70.6 - - + +
394B PHE 3.2 1.2 + - - -
395B LEU* 3.5 17.2 + - - +
399B GLN* 2.6 56.8 + - + +
402B ALA* 4.5 6.1 - - + -
403B ASN* 2.9 40.7 - - - +
406B LEU* 4.4 6.6 - - + +
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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