Contacts of the helix formed by residues 378 - 390 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A LEU* 3.8 12.4 - - - +
337A GLU* 3.7 20.9 + - - +
372A GLU* 3.0 38.8 + - - +
376A GLY 3.8 0.4 + - - -
377A THR* 1.3 70.2 - - - +
379A GLU* 1.3 65.3 + - - +
381A ARG* 3.3 12.6 + - - +
382A ARG* 3.0 37.4 + - - +
348B GLN* 3.5 10.0 + - - +
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Residues in contact with GLU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A THR* 3.0 0.9 - - - -
378A SER* 1.3 82.7 - - - +
380A VAL* 1.3 62.7 + - - +
382A ARG* 3.2 15.5 + - - +
383A LEU* 3.1 26.2 + - - +
399A FAD 3.1 40.8 + - + +
292B LEU* 3.9 24.8 - - + +
293B MET* 3.6 26.5 - - + -
296B LYS* 3.7 21.7 + - - -
348B GLN* 3.0 30.5 + - - +
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Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A SER* 3.7 28.3 - - - +
255A ARG* 4.5 7.4 - - - +
376A GLY* 4.7 1.1 - - - -
377A THR* 2.8 31.7 + - - +
379A GLU* 1.3 72.3 - - - +
381A ARG* 1.3 56.3 + - - +
383A LEU* 3.3 15.0 + - + +
384A VAL* 3.0 24.9 + - - +
399A FAD 4.7 9.6 - - + +
400A COS 3.6 54.1 - - + +
283B PHE* 5.3 0.7 - - + -
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Residues in contact with ARG 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ARG* 4.6 9.2 - - - +
329A ALA* 4.3 15.4 - - + +
332A ILE* 3.3 38.9 + - + +
333A LEU* 3.8 29.6 + - + +
336A ALA* 3.5 18.4 - - - +
371A TYR 2.6 29.1 + - - -
372A GLU* 4.0 7.3 - - - +
374A GLY 3.1 19.0 + - - -
375A ALA* 4.2 4.9 + - - +
376A GLY* 3.0 18.4 + - - +
377A THR 3.1 12.4 + - - +
378A SER* 3.5 15.7 + - - +
380A VAL* 1.3 74.7 - - - +
382A ARG* 1.3 64.1 + - - +
383A LEU 3.1 0.2 - - - -
384A VAL* 3.2 10.1 + - - +
385A ILE* 3.1 28.9 + - - +
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Residues in contact with ARG 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU* 3.7 19.3 - - + +
337A GLU* 2.9 41.0 + - - -
378A SER* 3.0 28.2 + - - +
379A GLU* 3.6 16.3 + - - +
381A ARG* 1.3 75.6 - - - +
383A LEU* 1.3 56.8 + - - +
385A ILE* 3.4 2.1 + - - +
386A GLY* 2.9 27.2 + - - -
292B LEU* 4.7 15.0 - - + +
294D GLN 3.7 8.7 - - - +
295D GLY* 4.0 25.8 - - - -
298D ALA* 3.9 12.8 - - + -
299D ASP* 3.2 31.7 + - - -
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A GLU 3.1 15.4 + - - +
380A VAL* 3.3 19.7 - - + +
381A ARG 3.1 0.2 - - - -
382A ARG* 1.3 76.0 - - - +
384A VAL* 1.3 59.0 + - - +
387A ARG* 2.8 67.4 + - - +
399A FAD 3.6 32.1 - - + +
400A COS 5.3 2.9 - - + -
292B LEU* 4.2 8.7 - - + -
291D GLN* 3.3 29.4 - - + +
294D GLN* 3.4 24.2 - - + +
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ARG* 4.1 18.2 - - - +
325A ALA* 3.9 37.9 - - + +
326A LYS* 4.4 0.3 - - - +
329A ALA* 4.0 9.9 - - + -
380A VAL* 3.0 23.3 + - + +
381A ARG* 3.2 9.4 + - - +
383A LEU* 1.3 76.5 - - - +
385A ILE* 1.3 57.4 + - - +
387A ARG* 4.0 6.7 - - - +
388A ALA* 3.2 24.3 + - - +
400A COS 3.6 25.4 - - + -
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Residues in contact with ILE 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A LYS* 3.6 27.6 - - + +
329A ALA* 4.4 4.0 - - + -
330A GLY* 3.9 21.8 - - - +
333A LEU* 3.6 26.5 - - + -
381A ARG 3.1 16.0 + - - +
382A ARG 3.8 4.0 - - - +
384A VAL* 1.3 74.0 - - - +
386A GLY* 1.3 67.3 + - - +
388A ALA* 3.0 18.2 + - - +
389A PHE* 3.2 34.1 + - + -
298D ALA* 3.8 23.3 - - + -
301D TYR* 4.0 13.2 - - + -
302D THR* 4.1 6.1 - - + -
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Residues in contact with GLY 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A ARG 2.9 16.7 + - - -
383A LEU 3.9 0.4 - - - -
385A ILE* 1.3 77.2 - - - +
387A ARG* 1.3 56.9 + - - +
389A PHE* 3.3 12.2 + - - +
390A ASN* 2.9 34.0 + - - -
294D GLN* 3.9 25.9 + - - -
297D MET* 4.3 6.4 - - - +
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Residues in contact with ARG 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A LEU* 2.8 58.4 + - - +
384A VAL* 4.0 5.8 - - - +
386A GLY* 1.3 69.6 - - - +
388A ALA* 1.3 66.5 + - - +
390A ASN* 2.9 19.0 + - + +
391A ALA* 2.9 24.4 + - - +
399A FAD 5.3 2.8 + - - -
400A COS 3.3 57.9 + - - +
283B PHE* 5.7 3.6 - - - -
291D GLN* 5.6 1.2 - - - +
294D GLN* 4.3 11.2 + - - +
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Residues in contact with ALA 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ALA* 6.4 0.2 - - + -
326A LYS* 3.6 33.9 - - + +
384A VAL 3.2 14.4 + - - +
385A ILE 3.0 11.1 + - - +
387A ARG* 1.3 74.3 - - - +
389A PHE* 1.3 65.1 + - - +
391A ALA* 3.2 15.9 + - - +
392A ASP* 3.5 19.3 + - - +
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Residues in contact with PHE 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A LYS* 3.1 27.4 - - + -
385A ILE* 3.2 41.1 + - + -
386A GLY 3.6 6.7 - - - +
387A ARG 3.2 0.4 - - - -
388A ALA* 1.3 79.2 - - - +
390A ASN* 1.3 62.2 + - - +
392A ASP* 3.0 24.5 + - + +
270D LEU* 5.9 1.3 - - + -
274D ILE* 4.2 31.2 - - + +
278D HIS* 2.9 19.2 + - + +
297D MET* 3.8 33.7 - - + -
301D TYR* 3.4 39.9 - + + -
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Residues in contact with ASN 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A GLY 2.9 21.6 + - - -
387A ARG* 2.9 20.0 + - + +
389A PHE* 1.3 78.0 - - - +
391A ALA* 1.3 56.5 + - - +
392A ASP 3.2 2.5 + - - -
278D HIS* 3.4 19.7 + - - -
286D LYS* 5.9 1.0 + - - -
288D GLY 3.1 23.5 + - - +
289D HIS* 3.7 32.6 + - + -
294D GLN* 2.8 32.7 - - - +
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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