Contacts of the helix formed by residues 383 - 400 (chain B) in PDB entry 1O9U
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 VAL 383 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384B GLU* 1.3 67.0 + - - +
385B PRO* 3.5 9.5 - - - +
386B GLN* 3.5 12.8 + - + +
387B LYS* 3.0 52.0 + - + +
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Residues in contact with GLU 384 (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 TYR* 4.4 6.0 + - - +
383B VAL* 1.3 80.6 - - - +
385B PRO* 1.3 72.6 - - + +
387B LYS* 3.7 8.7 - - - +
388B PHE* 2.9 39.8 + - - +
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Residues in contact with PRO 385 (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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287A ASN* 4.0 24.0 - - + +
288A TYR* 3.3 28.6 - - + +
291A PHE* 3.8 17.3 - - + -
383B VAL 3.8 7.0 - - - +
384B GLU* 1.3 96.2 - - + +
386B GLN* 1.3 55.7 + - - +
388B PHE* 3.7 0.5 - - - +
389B ALA* 2.8 37.4 + - - +
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Residues in contact with GLN 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PHE* 3.7 25.6 - - + -
383B VAL* 3.7 15.5 - - + +
384B GLU 3.3 0.4 - - - -
385B PRO* 1.3 80.1 - - - +
387B LYS* 1.3 61.9 + - + +
389B ALA* 3.7 1.4 - - - +
390B GLU* 3.1 58.1 + - - +
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Residues in contact with LYS 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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383B VAL* 3.0 41.3 + - + +
384B GLU* 3.8 9.2 - - - +
386B GLN* 1.3 76.4 - - + +
388B PHE* 1.3 67.0 + - - +
390B GLU* 3.3 14.8 + - - +
391B GLU* 3.1 22.7 + - - +
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Residues in contact with PHE 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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228A ILE* 3.5 38.1 - - + -
229A PHE* 4.2 10.8 - + - -
262A GLY* 4.8 2.0 - - - -
263A VAL* 3.6 31.8 - - + +
266A LEU* 3.9 21.8 - - + -
288A TYR* 3.6 31.2 - + - +
384B GLU* 2.9 30.8 + - - +
385B PRO 3.7 0.2 - - - +
387B LYS* 1.3 75.6 - - - +
389B ALA* 1.3 63.9 + - - +
391B GLU* 3.2 11.0 + - - +
392B LEU* 3.0 26.9 + - + +
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Residues in contact with ALA 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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288A TYR* 4.4 2.2 - - + -
291A PHE* 3.6 39.5 - - + -
293A PHE* 4.2 15.9 - - + -
385B PRO 2.8 21.9 + - - +
386B GLN* 3.7 4.3 - - - +
388B PHE* 1.3 77.4 - - - +
390B GLU* 1.3 55.8 + - - +
392B LEU* 3.3 2.8 + - - +
393B ILE* 2.8 39.4 + - + +
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Residues in contact with GLU 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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386B GLN* 3.1 42.6 + - - +
387B LYS* 3.5 18.8 - - - +
388B PHE 3.3 0.2 - - - -
389B ALA* 1.3 75.5 - - - +
391B GLU* 1.3 63.6 + - - +
393B ILE* 3.7 8.8 - - + +
394B HIS* 3.0 24.8 + - - +
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Residues in contact with GLU 391 (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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261A SER* 4.8 4.9 + - - -
263A VAL* 3.6 34.2 - - + +
387B LYS 3.1 12.7 + - - +
388B PHE* 3.5 11.2 - - - +
390B GLU* 1.3 77.2 - - - +
392B LEU* 1.3 63.8 + - - +
394B HIS* 3.1 10.7 + - + +
395B ARG* 3.0 32.2 + - + +
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Residues in contact with LEU 392 (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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229A PHE* 4.4 10.8 - - + -
263A VAL* 4.1 15.8 - - + +
266A LEU* 3.7 31.6 - - + -
267A VAL* 3.9 19.3 - - + -
270A ILE* 4.3 10.1 - - + -
293A PHE* 3.8 24.2 - - + -
388B PHE* 3.0 22.0 + - + +
389B ALA* 3.7 4.5 - - - +
391B GLU* 1.3 76.3 - - - +
393B ILE* 1.3 57.2 + - - +
395B ARG* 3.3 1.0 + - - +
396B LEU* 2.8 60.8 + - + +
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Residues in contact with ILE 393 (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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291A PHE* 3.5 26.0 - - + +
292A ALA 3.7 9.9 - - - +
293A PHE* 3.8 19.3 - - + -
294A PRO* 4.2 14.4 - - + -
389B ALA* 2.8 35.7 + - + +
390B GLU* 3.7 8.7 - - + +
392B LEU* 1.3 72.5 - - - +
394B HIS* 1.3 64.6 + - - +
396B LEU* 3.4 1.3 + - - +
397B GLU* 2.9 51.5 + - + +
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Residues in contact with HIS 394 (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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390B GLU 3.0 13.9 + - - +
391B GLU* 3.1 13.4 + - + +
393B ILE* 1.3 78.6 - - - +
395B ARG* 1.3 72.1 + - - +
397B GLU* 3.6 13.7 + - - +
398B ALA* 3.4 20.0 + - + +
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Residues in contact with ARG 395 (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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263A VAL* 3.8 16.7 - - + +
264A ASP* 2.7 41.7 + - - +
267A VAL* 3.9 31.6 - - + +
391B GLU* 3.0 23.9 + - + +
392B LEU 3.7 7.0 - - - +
394B HIS* 1.3 83.7 - - + +
396B LEU* 1.3 67.0 + - - +
398B ALA* 3.1 17.7 + - - +
399B VAL* 3.1 23.0 + - - +
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Residues in contact with LEU 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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267A VAL* 4.1 21.3 - - + -
270A ILE* 3.8 41.7 - - + -
271A LYS* 6.3 0.9 - - + -
275A THR* 5.1 0.7 - - + +
293A PHE* 4.3 11.9 - - + -
294A PRO* 4.0 32.1 - - + +
296A ILE* 4.1 12.4 - - + +
392B LEU* 2.8 44.3 + - + +
393B ILE 3.9 2.5 - - - +
395B ARG* 1.3 72.9 - - - +
397B GLU* 1.3 63.5 + - - +
398B ALA 3.2 0.2 + - - -
399B VAL* 3.2 6.4 + - + +
400B GLN* 3.0 27.9 + - - +
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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
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294A PRO* 3.5 21.7 - - + +
393B ILE* 2.9 36.8 + - - +
394B HIS* 3.9 13.6 + - - +
395B ARG 3.3 0.2 - - - -
396B LEU* 1.3 76.2 - - - +
398B ALA* 1.3 61.8 + - - +
400B GLN* 3.2 17.1 - - - +
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Residues in contact with ALA 398 (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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394B HIS* 3.4 11.9 + - + +
395B ARG* 3.1 14.5 + - - +
397B GLU* 1.3 79.5 - - - +
399B VAL* 1.3 69.6 + - + +
400B GLN* 3.9 2.4 - - - +
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Residues in contact with VAL 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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267A VAL* 4.0 24.0 - - + -
271A LYS* 3.3 46.4 + - + +
296A ILE* 5.7 2.7 - - + -
395B ARG* 3.1 21.0 + - - +
396B LEU* 3.7 9.2 - - + +
398B ALA* 1.3 78.6 - - + +
400B GLN* 1.3 69.2 + - - +
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Residues in contact with GLN 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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271A LYS* 5.9 1.1 - - - +
294A PRO* 3.7 9.4 - - - +
295A GLN 2.7 41.7 + - - +
296A ILE* 3.3 23.5 - - + +
396B LEU 3.0 17.7 + - - +
397B GLU* 3.2 18.5 - - - +
398B ALA 3.9 2.6 - - - +
399B VAL* 1.3 82.5 - - - +
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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
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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