Contacts of the helix formed by residues 378 - 390 (chain B) in PDB entry 1IVH
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 SER 378 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A GLN* 3.9 6.0 + - - -
333B LEU* 3.7 16.0 - - - +
337B GLU* 3.7 15.6 + - - +
372B GLU* 3.2 31.8 + - - +
377B THR* 1.3 72.7 - - - +
379B GLU* 1.3 69.5 + - - +
381B ARG* 3.3 9.2 + - - +
382B ARG* 3.0 47.0 + - - +
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Residues in contact with GLU 379 (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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292A LEU* 4.1 20.3 - - + +
293A MET* 3.5 28.0 - - + -
296A LYS* 4.0 15.8 + - - -
348A GLN* 3.2 26.6 - - - +
377B THR* 3.8 0.2 - - - -
378B SER* 1.3 86.0 - - - +
380B VAL* 1.3 66.1 + - - +
382B ARG* 3.0 17.2 + - - +
383B LEU* 3.0 27.5 + - - +
399B FAD 3.1 45.9 + - + +
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Residues in contact with VAL 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PHE* 5.5 0.7 - - + -
142B SER* 3.6 29.2 - - - -
255B ARG* 4.8 3.4 - - - +
376B GLY* 4.8 4.7 - - - -
377B THR* 3.3 26.7 + - - +
379B GLU* 1.3 78.3 - - - +
381B ARG* 1.3 57.4 + - - +
383B LEU* 3.5 15.0 + - + +
384B VAL* 3.1 27.8 + - + +
399B FAD 4.8 8.3 - - + +
400B COS 3.6 51.3 - - + +
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Residues in contact with ARG 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ARG* 4.4 14.6 - - - +
329B ALA* 4.2 9.0 - - + +
332B ILE* 3.3 56.1 + - - +
333B LEU* 3.8 23.6 - - + +
336B ALA* 3.6 5.5 - - - +
371B TYR 2.8 29.5 + - - -
372B GLU* 4.1 5.6 - - - +
374B GLY 2.9 23.2 + - - -
375B ALA* 3.8 7.7 + - - +
376B GLY* 2.9 16.9 + - - +
377B THR 3.1 13.0 + - - +
378B SER* 3.5 12.4 + - - +
379B GLU 3.1 1.0 - - - -
380B VAL* 1.3 76.3 - - - +
382B ARG* 1.3 64.8 + - - +
384B VAL* 3.2 9.0 + - - +
385B ILE* 3.1 29.3 + - - +
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Residues in contact with ARG 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 5.0 13.4 - - + +
296A LYS* 6.0 1.4 - - - +
333B LEU* 4.0 19.2 - - + +
337B GLU* 3.1 30.9 + - - -
378B SER* 3.0 38.0 + - - +
379B GLU* 3.5 18.8 + - - +
381B ARG* 1.3 75.6 - - - +
383B LEU* 1.3 57.9 + - + +
385B ILE* 3.2 2.4 + - - +
386B GLY* 2.9 28.2 + - - -
294C GLN* 4.1 7.5 - - - +
295C GLY* 3.8 27.6 - - - -
298C ALA* 4.0 9.9 - - + -
299C ASP* 3.1 31.4 + - - -
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PHE* 5.9 0.2 - - + -
292A LEU* 4.3 6.5 - - + -
379B GLU 3.0 18.4 + - - +
380B VAL* 3.6 18.6 - - + +
382B ARG* 1.3 76.7 - - - +
384B VAL* 1.3 54.6 + - + +
387B ARG* 2.8 68.8 + - - +
399B FAD 3.8 33.4 - - + +
400B COS 5.6 6.3 - - + -
291C GLN* 3.5 25.8 - - + +
294C GLN* 3.4 28.3 - - + +
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ARG* 3.8 23.1 - - - +
325B ALA* 3.9 39.5 - - + +
326B LYS* 4.3 0.2 - - - -
329B ALA* 4.1 7.4 - - + -
380B VAL* 3.1 17.4 + - + +
381B ARG* 3.2 9.8 + - - +
383B LEU* 1.3 77.4 - - - +
385B ILE* 1.3 61.1 + - - +
387B ARG* 3.8 7.7 - - - +
388B ALA* 3.1 21.8 + - - +
400B COS 4.0 19.1 - - + -
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Residues in contact with ILE 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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326B LYS* 3.7 26.7 - - + +
329B ALA* 4.5 3.6 - - + -
330B GLY* 3.8 26.9 - - - +
333B LEU* 3.9 12.8 - - + -
381B ARG 3.1 15.1 + - - +
382B ARG 3.7 4.0 - - - +
384B VAL* 1.3 74.0 - - - +
386B GLY* 1.3 66.4 + - - +
388B ALA* 2.9 15.4 + - - +
389B PHE* 3.3 20.5 + - + -
298C ALA* 3.7 31.0 - - + +
301C TYR* 3.7 25.6 - - + -
302C THR* 4.0 8.1 - - + -
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Residues in contact with GLY 386 (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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382B ARG 2.9 17.8 + - - -
385B ILE* 1.3 74.2 - - - +
387B ARG* 1.3 57.4 + - - +
389B PHE* 3.2 6.7 + - - +
390B ASN* 2.9 33.7 + - - +
294C GLN* 3.8 29.7 + - - -
297C MET* 4.4 11.0 - - - +
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Residues in contact with ARG 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PHE* 5.6 4.4 - - - -
383B LEU* 2.8 57.7 + - - +
384B VAL* 3.8 7.9 - - - +
386B GLY* 1.3 69.3 - - - +
388B ALA* 1.3 67.0 + - - +
390B ASN* 3.0 13.1 + - + +
391B ALA* 3.0 23.9 + - - +
399B FAD 5.8 1.2 + - - -
400B COS 3.6 50.6 + - - +
294C GLN* 3.4 16.7 - - - +
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Residues in contact with ALA 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ALA* 6.3 0.7 - - + -
326B LYS* 3.7 32.3 - - + +
384B VAL* 3.1 12.9 + - + +
385B ILE 2.9 11.0 + - - +
387B ARG* 1.3 76.7 - - - +
389B PHE* 1.3 58.3 + - - +
391B ALA* 3.3 7.3 + - - +
392B ASP* 3.1 31.2 + - - +
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Residues in contact with PHE 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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326B LYS* 2.9 29.8 - - - -
385B ILE* 3.3 19.2 + - + -
386B GLY 3.2 7.5 + - - +
388B ALA* 1.3 77.2 - - - +
390B ASN* 1.3 65.0 + - - +
392B ASP* 3.1 27.1 + - + +
270C LEU* 5.4 2.9 - - + -
274C ILE* 4.1 30.4 - - + +
278C HIS* 3.6 13.6 + - - +
297C MET* 3.6 39.5 - - + -
301C TYR* 3.7 47.3 - + + -
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Residues in contact with ASN 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 GLY 2.9 12.2 + - - +
387B ARG* 3.0 16.0 + - - +
389B PHE* 1.3 78.8 - - - +
391B ALA* 1.3 59.5 + - - +
392B ASP 3.6 1.7 + - - -
278C HIS* 2.8 24.4 + - - -
288C GLY 2.8 23.3 + - - +
289C HIS* 3.8 27.6 + - + +
294C GLN* 2.8 33.1 - - - +
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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