Contacts of the helix formed by residues 378 - 390 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348C GLN* 4.0 3.7 + - - -
333D LEU* 3.8 11.5 - - - +
337D GLU* 3.5 16.9 + - - +
372D GLU* 3.1 33.5 + - - +
377D THR* 1.3 71.7 - - - +
379D GLU* 1.3 68.0 + - - +
381D ARG* 3.0 12.1 + - - +
382D ARG* 2.9 54.3 + - - +
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Residues in contact with GLU 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C LEU* 3.7 30.9 - - + +
293C MET* 3.7 25.8 - - + -
296C LYS* 3.7 20.6 + - - -
348C GLN* 2.8 35.2 - - - +
377D THR* 3.5 1.2 - - - -
378D SER* 1.3 84.8 - - - +
380D VAL* 1.3 61.3 + - - +
382D ARG* 3.4 8.7 + - - +
383D LEU* 3.1 28.6 + - - +
399D FAD 3.2 32.2 + - + +
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Residues in contact with VAL 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C PHE* 5.7 0.4 - - + -
142D SER* 3.7 28.7 - - - +
255D ARG* 3.9 9.6 - - - +
376D GLY* 4.7 0.4 - - - -
377D THR* 3.0 29.1 + - - +
379D GLU* 1.3 76.9 - - + +
381D ARG* 1.3 57.0 + - - +
383D LEU* 3.3 13.9 + - + +
384D VAL* 3.0 31.0 + - - +
399D FAD 4.8 7.6 - - + +
400D COS 3.5 52.9 - - + +
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Residues in contact with ARG 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D ARG* 4.7 12.1 - - - +
329D ALA* 4.2 8.6 - - + +
332D ILE* 3.6 50.9 + - - +
333D LEU* 4.0 28.0 - - + +
336D ALA* 3.6 5.7 - - - +
371D TYR 2.8 22.8 + - - -
372D GLU* 4.1 5.9 - - - +
374D GLY 2.7 29.3 + - - -
375D ALA* 3.7 9.1 + - - +
376D GLY* 2.8 19.4 + - - +
377D THR 3.2 9.2 - - - +
378D SER* 3.0 14.0 + - - +
380D VAL* 1.3 76.7 - - - +
382D ARG* 1.3 63.3 + - - +
384D VAL* 3.5 9.7 + - - +
385D ILE* 3.3 29.8 + - - +
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Residues in contact with ARG 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLN* 3.9 7.9 - - - +
295A GLY* 4.0 22.0 - - - +
298A ALA* 4.0 13.9 - - + -
299A ASP* 3.3 32.3 + - - -
292C LEU* 4.8 15.5 - - + -
333D LEU* 3.4 20.2 - - + +
337D GLU* 2.9 29.7 + - - -
378D SER* 2.9 42.5 + - - +
379D GLU* 3.8 11.2 + - - +
380D VAL 3.3 0.2 - - - -
381D ARG* 1.3 76.3 - - - +
383D LEU* 1.3 53.2 + - - +
385D ILE* 3.3 2.6 + - - +
386D GLY* 2.8 32.9 + - - -
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Residues in contact with LEU 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A GLN* 3.4 38.6 - - + +
294A GLN* 3.0 34.7 - - + +
292C LEU* 4.5 4.9 - - + -
379D GLU 3.1 20.6 + - - +
380D VAL* 3.5 13.9 - - + +
381D ARG 3.2 0.2 - - - -
382D ARG* 1.3 76.2 - - + +
384D VAL* 1.3 59.2 + - - +
387D ARG* 2.8 66.4 + - - +
399D FAD 3.8 22.2 - - + +
400D COS 5.5 3.1 - - + -
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Residues in contact with VAL 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D ARG* 3.9 21.5 - - - +
325D ALA* 4.1 28.3 - - + +
326D LYS 4.3 0.2 - - - +
329D ALA* 3.9 17.9 - - + -
380D VAL 3.0 19.9 + - - +
381D ARG* 3.5 10.3 - - - +
382D ARG 3.3 0.2 - - - -
383D LEU* 1.3 76.6 - - - +
385D ILE* 1.3 57.2 + - - +
387D ARG* 3.8 6.9 - - - +
388D ALA* 3.0 26.7 + - - +
400D COS 3.7 22.9 - - + -
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Residues in contact with ILE 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A ALA* 3.8 20.2 - - + -
301A TYR* 4.0 13.2 - - + -
302A THR* 4.4 6.1 - - + -
326D LYS* 3.5 28.5 - - + +
329D ALA* 4.2 2.9 - - + -
330D GLY* 3.7 30.1 - - - +
333D LEU* 3.9 18.6 - - + -
381D ARG 3.3 17.6 + - - +
382D ARG 3.8 4.9 - - - +
384D VAL* 1.3 74.1 - - - +
386D GLY* 1.3 66.6 + - - +
388D ALA* 3.0 13.2 + - - +
389D PHE* 3.2 38.9 + - + -
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Residues in contact with GLY 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A GLN* 3.8 28.0 + - - -
297A MET* 3.7 7.4 - - - +
382D ARG 2.8 20.3 + - - -
385D ILE* 1.3 73.8 - - - +
387D ARG* 1.3 57.2 + - - +
389D PHE* 3.2 10.3 + - - +
390D ASN* 2.9 32.6 + - - +
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Residues in contact with ARG 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A GLN* 5.6 0.6 - - - +
294A GLN* 3.8 15.5 + - - +
283C PHE* 5.6 2.0 - - - -
383D LEU* 2.8 61.2 + - - +
384D VAL* 3.8 5.2 - - - +
386D GLY* 1.3 73.0 - - - +
388D ALA* 1.3 66.8 + - - +
390D ASN* 2.9 12.5 + - + +
391D ALA* 2.9 25.6 + - - +
399D FAD 5.3 3.6 + - - -
400D COS 3.1 61.9 + - - +
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Residues in contact with ALA 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D ALA* 6.2 1.1 - - + -
326D LYS* 3.7 34.1 - - + +
384D VAL 3.0 15.3 + - - +
385D ILE 3.0 10.7 + - - +
387D ARG* 1.3 77.0 - - - +
389D PHE* 1.3 63.6 + - - +
391D ALA* 3.3 7.0 + - - +
392D ASP* 3.2 23.8 + - - +
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Residues in contact with PHE 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 6.5 0.7 - - + -
274A ILE* 3.8 32.8 - - + +
278A HIS* 3.6 14.8 + - - +
297A MET* 3.7 36.3 - - + -
301A TYR* 3.5 44.6 - + + -
326D LYS* 3.8 19.3 - - + -
385D ILE* 3.2 40.2 + - + -
386D GLY 3.5 5.6 - - - +
388D ALA* 1.3 75.9 - - + +
390D ASN* 1.3 66.9 + - - +
392D ASP* 3.0 32.9 + - + +
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Residues in contact with ASN 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A HIS* 2.8 30.6 + - - -
286A LYS* 5.4 4.2 + - - -
288A GLY 2.9 13.4 + - - +
289A HIS* 3.3 29.9 + - + +
294A GLN* 2.7 29.1 + - - -
297A MET* 3.8 0.2 - - - +
386D GLY 2.9 13.8 + - - +
387D ARG* 2.9 20.3 + - + +
389D PHE* 1.3 78.4 - - - +
391D ALA* 1.3 58.6 + - - +
392D ASP 3.4 6.4 + - - +
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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