Contacts of the helix formed by residues 378 - 393 (chain C) in PDB entry 1UDY
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 378 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C SER* 4.1 14.9 + - - +
333C LYS* 4.6 0.2 - - - -
373C GLN 3.3 11.4 - - - -
374C ILE* 3.3 31.8 + - + +
377C GLY* 1.3 75.3 - - - +
379C ALA* 1.3 64.8 + - - +
380C GLN* 3.9 3.1 - - - -
381C ILE* 3.2 19.3 + - - +
382C GLN* 3.0 22.7 + - - +
2399C FAD 2.8 46.2 + - - +
349D GLN* 4.6 0.9 - - - +
352D GLY* 5.5 0.9 - - - -
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Residues in contact with ALA 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C LYS* 5.7 0.4 - - - +
334C ALA* 5.7 2.5 - - - +
337C ALA* 6.3 0.7 - - + -
338C ASP* 4.4 14.4 - - - +
373C GLN* 3.0 22.5 + - + +
378C THR* 1.3 74.5 - - - +
380C GLN* 1.3 76.9 + - - +
382C GLN* 3.5 5.3 + - - +
383C ARG* 2.9 47.0 + - - +
349D GLN* 4.5 5.2 - - - +
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Residues in contact with GLN 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PHE* 4.0 22.7 - - + -
378C THR* 3.1 2.6 + - - -
379C ALA* 1.3 80.3 - - - +
381C ILE* 1.3 66.6 + - - +
383C ARG* 2.9 16.9 + - - +
384C ILE* 3.1 14.8 + - - +
2399C FAD 2.5 61.3 + - + +
293D GLY 5.8 1.6 - - - +
294D ILE* 4.5 10.5 - - + -
297D LEU* 5.1 11.3 - - + +
349D GLN* 3.1 31.4 + - - +
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Residues in contact with ILE 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C SER* 3.8 33.2 - - - +
377C GLY* 4.0 12.1 - - - -
378C THR* 3.2 16.3 + - - +
380C GLN* 1.3 78.1 - - - +
382C GLN* 1.3 64.3 + - - +
384C ILE* 3.0 26.5 + - + +
385C ILE* 3.0 29.6 + - + +
2399C FAD 3.9 28.7 - - + +
2400C CS8 3.9 40.1 - - + +
284D PHE* 4.3 4.0 - - + -
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Residues in contact with GLN 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ARG* 3.6 18.2 + - - +
330C SER* 3.1 33.8 + - - +
333C LYS* 4.0 20.7 - - + +
334C ALA* 4.1 23.1 - - + +
376C GLU 3.1 17.4 + - - -
377C GLY* 3.1 29.1 + - - +
378C THR 3.0 18.8 + - - +
379C ALA* 3.6 7.9 - - - +
380C GLN 3.2 0.2 - - - -
381C ILE* 1.3 77.5 - - - +
383C ARG* 1.3 58.2 + - - +
385C ILE* 3.4 4.3 + - - +
386C ILE* 3.0 35.5 + - - +
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Residues in contact with ARG 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B SER 4.7 0.5 - - - +
296B PHE* 4.2 30.6 - - + -
299B ALA* 3.4 17.9 - - + +
300B ASP* 2.9 32.7 + - - +
303B MET* 3.8 22.7 - - - +
334C ALA* 3.5 21.2 + - - +
338C ASP* 3.1 27.7 + - - -
379C ALA* 2.9 48.2 + - - +
380C GLN* 2.9 10.6 + - - +
382C GLN* 1.3 74.4 - - - +
384C ILE* 1.3 65.2 + - - +
386C ILE* 4.6 0.9 - - - -
387C ALA* 3.1 26.3 + - - +
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Residues in contact with ILE 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLN* 4.0 6.7 - - - +
295B SER* 6.1 1.3 - - - -
296B PHE* 3.9 17.0 - - + -
380C GLN 3.1 12.0 + - - +
381C ILE* 3.0 24.7 + - + +
383C ARG* 1.3 78.5 - - - +
385C ILE* 1.3 59.7 + - + +
387C ALA* 3.6 4.6 + - - +
388C ARG* 3.1 31.8 + - + +
2399C FAD 3.8 37.0 - - + +
2400C CS8 5.7 9.6 - - + -
284D PHE* 5.5 2.0 - - + -
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Residues in contact with ILE 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ARG* 3.1 35.4 - - - +
326C THR* 3.6 27.4 - - + +
330C SER* 3.1 26.7 - - - +
381C ILE* 3.0 22.2 + - + +
382C GLN* 3.6 6.7 - - - +
384C ILE* 1.3 76.5 - - + +
386C ILE* 1.3 65.5 + - - +
388C ARG* 3.1 17.0 + - - +
389C GLU* 3.0 28.6 + - + +
2400C CS8 3.7 32.3 - - + -
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Residues in contact with ILE 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ALA* 4.0 25.8 - - + +
302B ALA* 4.3 5.2 - - + -
303B MET* 3.6 29.8 - - + -
327C TYR* 4.1 22.6 - - + +
330C SER* 3.6 18.8 - - - +
331C ILE* 3.7 31.0 - - + +
334C ALA* 4.4 1.6 - - + -
382C GLN 3.0 21.3 + - - +
383C ARG* 4.6 2.2 - - - -
385C ILE* 1.3 75.7 - - - +
387C ALA* 1.3 57.6 + - - +
389C GLU* 3.3 5.8 + - - +
390C HIS* 2.9 29.5 + - - +
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Residues in contact with ALA 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B SER* 3.6 37.5 - - - +
298B LEU* 5.4 1.1 - - + -
299B ALA* 4.0 6.5 - - + +
383C ARG 3.1 20.1 + - - +
384C ILE* 3.8 5.8 - - - +
386C ILE* 1.3 76.9 - - - +
388C ARG* 1.3 61.4 - - - +
390C HIS* 4.5 4.9 - - - -
391C ILE* 3.2 37.0 + - + +
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Residues in contact with ARG 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C ARG* 4.2 2.9 - - - +
326C THR* 4.0 12.9 - - - +
384C ILE* 3.1 21.8 + - + +
385C ILE* 3.1 17.0 + - - +
387C ALA* 1.3 79.2 - - - +
389C GLU* 1.3 89.0 + - - +
391C ILE* 4.6 3.0 - - - +
392C GLY* 3.4 16.5 + - - -
2400C CS8 3.4 65.1 + - - +
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Residues in contact with GLU 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C ARG* 3.1 32.0 + - - -
326C THR* 3.9 16.1 - - + -
327C TYR* 3.8 31.6 + - + +
385C ILE 3.0 18.2 + - - +
386C ILE 3.8 3.1 - - - +
388C ARG* 1.3 106.5 + - - +
390C HIS* 1.3 66.4 + - - +
392C GLY* 3.4 9.2 + - - -
393C ARG* 3.4 16.2 + - - +
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Residues in contact with HIS 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 3.6 27.6 - - + +
275B THR* 2.8 36.7 + - + +
298B LEU* 4.5 15.3 - - + +
299B ALA* 5.9 0.7 - - - -
302B ALA* 4.0 17.6 - - + +
327C TYR* 4.3 11.8 + - + -
386C ILE 2.9 18.9 + - - +
387C ALA* 4.0 3.6 - - - +
389C GLU* 1.3 78.2 - - - +
391C ILE* 1.3 70.7 + - + +
393C ARG* 3.2 26.6 + - - +
394C TYR* 3.1 50.7 - + - -
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Residues in contact with ILE 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B THR* 4.6 5.6 - - + -
279B LEU* 3.8 17.5 - - + -
289B ALA* 3.7 35.2 - - + +
295B SER* 5.4 2.2 - - - +
298B LEU* 4.1 14.6 - - + -
387C ALA* 3.2 24.6 + - + +
388C ARG* 4.6 3.6 - - - +
390C HIS* 1.3 89.6 - - + +
392C GLY* 1.3 61.4 + - - +
393C ARG 3.0 6.5 + - - -
394C TYR* 3.2 18.8 + - - +
395C LYS* 3.4 27.1 + - - +
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Residues in contact with GLY 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388C ARG 3.4 12.1 + - - -
389C GLU* 3.4 8.6 + - - -
390C HIS 3.3 0.8 - - - -
391C ILE* 1.3 79.1 - - - +
393C ARG* 1.3 60.1 + - - +
394C TYR 3.3 0.6 + - - -
395C LYS* 3.6 24.6 - - - +
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Residues in contact with ARG 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B GLN* 6.0 1.8 - - - +
271B LEU* 6.1 1.6 - - - +
306B GLU* 3.6 8.7 + - - -
327C TYR* 3.4 47.9 + - - -
328C TYR* 4.1 11.3 + - - -
389C GLU 3.4 15.0 + - - +
390C HIS* 3.3 24.6 + - - +
391C ILE 3.0 0.6 - - - -
392C GLY* 1.3 79.5 - - - +
394C TYR* 1.3 69.4 + - + +
395C LYS 3.2 7.5 + - - -
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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
------------------------------------------------------------
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