Contacts of the helix formed by residues 378 - 390 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333C LEU* 3.4 22.4 - - - +
337C GLU* 3.6 23.1 + - - +
372C GLU* 3.3 31.8 + - - +
376C GLY 3.8 0.2 + - - -
377C THR* 1.3 73.1 - - - +
379C GLU* 1.3 67.4 + - - +
381C ARG* 3.3 8.1 + - - +
382C ARG* 3.0 36.8 + - - +
348D GLN* 3.9 6.9 + - - -
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Residues in contact with GLU 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C THR* 3.1 8.5 - - - -
378C SER* 1.3 81.4 - - - +
380C VAL* 1.3 65.5 + - - +
382C ARG* 3.0 20.9 + - - +
383C LEU* 3.1 18.5 + - - +
399C FAD 3.0 41.8 + - + +
292D LEU* 3.9 23.6 - - + +
293D MET* 3.4 30.7 - - + -
296D LYS* 3.5 24.4 + - - -
348D GLN* 3.7 15.4 + - - +
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Residues in contact with VAL 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C SER* 3.6 27.8 - - - -
255C ARG* 4.5 5.6 - - - +
376C GLY* 4.8 2.2 - - - -
377C THR* 3.1 24.4 + - - +
379C GLU* 1.3 77.7 - - - +
381C ARG* 1.3 57.4 + - - +
383C LEU* 3.5 12.5 + - + +
384C VAL* 3.0 34.0 + - + +
399C FAD 4.6 14.1 - - + +
400C COS 3.5 52.9 - - + +
283D PHE* 5.2 0.4 - - + -
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Residues in contact with ARG 381 (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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255C ARG* 4.5 13.4 - - - +
329C ALA* 4.2 7.7 - - + +
332C ILE* 3.5 46.4 + - - +
333C LEU* 3.9 22.8 - - + +
336C ALA* 3.7 15.8 - - - +
371C TYR 2.9 23.4 + - - -
372C GLU* 4.1 5.3 - - - +
374C GLY 2.7 29.5 + - - -
375C ALA* 3.6 7.7 + - - +
376C GLY* 2.8 19.4 + - - +
377C THR 3.0 12.6 + - - +
378C SER* 3.5 14.1 + - - +
379C GLU 3.1 0.2 - - - -
380C VAL* 1.3 77.2 - - - +
382C ARG* 1.3 64.5 + - - +
384C VAL* 3.4 9.0 + - - +
385C ILE* 3.3 30.0 + - - +
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Residues in contact with ARG 382 (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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294B GLN 3.6 11.4 - - - +
295B GLY* 4.3 16.5 + - - +
298B ALA* 4.1 16.6 - - + -
299B ASP* 2.7 39.3 + - - -
333C LEU* 3.9 20.5 - - + +
337C GLU* 2.7 42.6 + - - -
378C SER* 3.0 26.0 + - - +
379C GLU* 3.0 15.3 + - - +
381C ARG* 1.3 74.7 - - - +
383C LEU* 1.3 62.5 + - + +
385C ILE* 3.5 1.4 + - - +
386C GLY* 3.0 23.0 + - - -
292D LEU* 4.7 14.6 - - + -
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Residues in contact with LEU 383 (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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291B GLN* 3.5 38.1 - - + +
294B GLN* 3.6 25.1 + - + +
379C GLU 3.3 12.6 - - - +
380C VAL* 3.6 16.8 - - + +
382C ARG* 1.3 77.1 - - - +
384C VAL* 1.3 59.5 + - + +
387C ARG* 2.8 65.0 + - - +
399C FAD 3.6 25.1 - - + +
400C COS 5.9 2.7 - - + -
292D LEU* 4.1 9.9 - - + -
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Residues in contact with VAL 384 (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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255C ARG* 4.5 16.2 - - - +
325C ALA* 3.8 38.5 - - + +
329C ALA* 4.0 7.6 - - + -
380C VAL* 3.0 20.5 + - + +
381C ARG* 3.6 10.8 - - - +
383C LEU* 1.3 77.4 - - - +
385C ILE* 1.3 59.3 + - - +
387C ARG* 4.0 7.2 - - - +
388C ALA* 3.2 21.7 + - - +
400C COS 4.0 22.7 - - + -
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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
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298B ALA* 3.8 24.0 - - + -
301B TYR* 3.9 20.9 - - + -
302B THR* 4.2 8.1 - - + -
326C LYS* 3.5 26.7 - - + +
329C ALA* 4.2 4.3 - - + -
330C GLY* 3.7 28.5 - - - +
333C LEU* 3.9 20.2 - - + -
381C ARG 3.3 18.6 + - - +
382C ARG 3.9 3.1 - - - +
384C VAL* 1.3 75.7 - - - +
386C GLY* 1.3 66.6 + - - +
388C ALA* 3.1 13.5 + - - +
389C PHE* 3.3 20.5 + - + -
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Residues in contact with GLY 386 (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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294B GLN* 3.9 28.4 + - - -
297B MET* 4.4 3.5 - - - +
382C ARG 3.0 18.0 + - - -
383C LEU 3.8 0.7 - - - -
385C ILE* 1.3 76.2 - - - +
387C ARG* 1.3 56.2 + - - +
389C PHE* 3.1 15.6 + - - +
390C ASN* 2.9 31.4 + - - +
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Residues in contact with ARG 387 (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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291B GLN* 5.9 0.4 - - - +
294B GLN* 3.8 15.9 + - - +
383C LEU* 2.8 55.5 + - - +
384C VAL* 4.0 6.7 - - - +
386C GLY* 1.3 69.8 - - - +
388C ALA* 1.3 66.9 + - - +
390C ASN* 2.9 12.4 + - + +
391C ALA* 2.8 24.3 + - - +
399C FAD 5.3 3.8 + - - -
400C COS 3.5 55.7 + - - +
283D PHE* 5.7 3.2 - - - -
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Residues in contact with ALA 388 (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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325C ALA* 6.3 0.9 - - + -
326C LYS* 3.7 33.2 - - + +
384C VAL 3.2 14.2 + - - +
385C ILE 3.1 11.3 + - - +
387C ARG* 1.3 75.1 - - - +
389C PHE* 1.3 63.0 + - - +
391C ALA* 3.3 16.4 + - - +
392C ASP* 3.3 17.2 + - - +
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Residues in contact with PHE 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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270B LEU* 5.9 0.9 - - + -
274B ILE* 4.3 30.1 - - + +
278B HIS* 3.3 14.3 + - - +
297B MET* 3.8 39.3 - - + -
301B TYR* 3.8 46.4 - + + -
326C LYS* 3.8 24.2 - - + -
385C ILE* 3.3 25.7 + - + -
386C GLY 3.1 7.5 + - - +
388C ALA* 1.3 78.8 - - - +
390C ASN* 1.3 64.1 + - - +
392C ASP* 2.8 30.1 + - - +
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Residues in contact with ASN 390 (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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278B HIS* 2.9 28.9 + - - -
288B GLY 3.1 18.3 + - - +
289B HIS* 3.7 30.5 + - + +
294B GLN* 2.8 30.9 - - - +
297B MET* 4.1 0.9 - - - +
386C GLY 2.9 14.4 + - - +
387C ARG* 2.9 18.2 + - + +
389C PHE* 1.3 78.0 - - - +
391C ALA* 1.3 59.3 + - - +
392C ASP 4.4 2.4 - - - -
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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