Contacts of the helix formed by residues 385 - 396 (chain A) in PDB entry 1IVS
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 ARG 385 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383A PRO* 3.0 16.0 + - + +
384A GLU* 1.3 77.9 - - - +
386A TRP* 1.3 100.3 + - + +
387A LYS 3.3 0.7 - - - -
388A LYS* 3.5 12.5 + - - +
389A VAL* 3.2 19.8 + - + +
489A TYR* 5.6 1.2 - - - -
561A GLY 4.4 5.9 + - - -
562A GLY 3.9 20.0 + - - -
563A GLN* 4.0 17.0 - - - +
904C C 3.5 25.3 + - - +
905C G 3.5 40.9 + - - +
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Residues in contact with TRP 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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381A PHE* 4.0 17.9 - - + -
383A PRO* 3.1 49.3 - - + +
384A GLU 3.0 1.8 - - - -
385A ARG* 1.3 108.6 - - + +
387A LYS* 1.3 67.1 + - - +
388A LYS 3.2 1.8 - - - -
389A VAL* 3.6 31.8 - - + +
390A ASN* 2.9 25.3 + - - +
489A TYR* 3.2 48.9 - + + -
492A LEU* 4.1 10.2 - - + +
517A LEU* 3.5 25.9 + - + +
562A GLY 5.5 1.1 + - - -
904C C 5.8 1.1 - - - -
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Residues in contact with LYS 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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374A LEU* 4.1 22.2 + - + +
375A ARG* 5.5 2.2 + - - +
377A GLY* 5.0 8.1 - - - -
379A ILE 4.7 11.4 + - - +
381A PHE* 4.0 35.0 - - + -
384A GLU* 3.5 11.1 + - + +
386A TRP* 1.3 79.2 - - - +
388A LYS* 1.3 77.2 + - - +
390A ASN* 3.0 2.9 + - - +
391A MET* 2.9 54.9 + - + +
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Residues in contact with LYS 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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384A GLU* 2.9 27.9 + - - -
385A ARG* 3.5 13.1 + - - +
387A LYS* 1.3 91.2 - - + +
389A VAL* 1.3 59.4 + - + +
391A MET* 3.5 25.1 - - + -
392A ASP* 2.8 49.1 + - - +
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Residues in contact with VAL 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ARG* 3.2 21.3 - - + +
386A TRP* 3.3 38.7 + - + +
388A LYS* 1.3 76.5 - - + +
390A ASN* 1.3 60.2 + - - +
392A ASP* 4.5 5.1 - - - +
393A TRP 3.6 6.6 + - - -
492A LEU* 4.1 2.7 - - + -
493A PHE* 3.2 33.7 - - + -
903C G 5.6 5.6 - - - +
904C C 5.6 10.3 - - - +
970C C 5.7 2.0 - - - +
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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
----------------------------------------------------------
374A LEU* 4.4 5.0 - - - +
381A PHE* 3.2 21.9 - - + -
386A TRP 2.9 12.5 + - - +
387A LYS 3.2 9.2 - - - +
389A VAL* 1.3 73.6 - - - +
391A MET* 1.3 59.7 + - + +
393A TRP* 2.6 34.5 + - - +
394A LEU* 3.1 10.1 + - - +
492A LEU* 4.3 15.9 + - + +
496A VAL* 4.6 0.5 - - - +
497A SER* 2.8 29.7 + - - -
500A GLU* 2.8 32.9 + - - +
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Residues in contact with MET 391 (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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371A LEU* 3.9 17.5 - - + +
374A LEU* 3.9 34.1 - - + -
375A ARG* 4.8 10.1 - - - -
381A PHE* 6.4 0.2 - - + -
387A LYS* 2.9 36.6 + - + +
388A LYS* 3.5 35.7 - - + +
390A ASN* 1.3 76.1 - - - +
392A ASP* 1.3 55.2 + - - +
394A LEU* 2.9 6.4 + - - +
395A GLU* 2.7 41.9 + - + +
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Residues in contact with ASP 392 (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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388A LYS* 2.8 38.2 + - - +
389A VAL* 4.5 4.7 - - - +
391A MET* 1.3 78.1 - - - +
393A TRP* 1.3 62.7 + - - +
395A GLU* 3.4 25.9 - - + +
396A ASN* 3.7 15.9 + - - +
903C G 5.7 1.0 + - - -
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Residues in contact with TRP 393 (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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186A LEU* 3.9 30.7 - - + +
363A MET* 5.2 7.4 - - + -
389A VAL 3.6 2.5 + - - +
390A ASN* 2.6 21.6 + - - +
392A ASP* 1.3 71.0 - - - +
394A LEU* 1.3 99.8 - - + +
396A ASN* 3.2 16.3 + - - +
397A VAL* 3.6 31.8 - - + +
493A PHE* 3.3 60.1 - + + +
497A SER* 3.9 16.4 - - - -
498A ARG* 4.4 22.0 - - - -
971C C 5.5 7.6 + - - -
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Residues in contact with LEU 394 (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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363A MET* 5.6 0.7 - - + -
367A ALA* 3.9 23.6 - - + +
370A VAL* 3.8 20.6 - - + -
371A LEU* 3.3 35.7 - - + +
374A LEU* 3.8 21.5 - - + -
390A ASN* 3.9 16.6 - - - +
391A MET* 2.9 1.9 + - - +
393A TRP* 1.3 106.8 - - + +
395A GLU* 1.3 61.9 + - - +
397A VAL* 2.7 23.9 + - - +
497A SER* 4.1 14.4 - - - +
500A GLU* 4.4 2.0 - - - +
501A VAL* 5.3 6.3 - - + -
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Residues in contact with GLU 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LEU* 3.7 24.0 - - - +
375A ARG* 4.1 10.7 + - - -
391A MET* 2.7 26.7 + - + +
392A ASP* 3.4 22.7 - - - +
394A LEU* 1.3 73.3 - - - +
396A ASN* 1.3 71.9 + - - +
397A VAL 4.0 0.5 + - - -
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Residues in contact with ASN 396 (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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392A ASP* 3.7 14.2 + - - +
393A TRP 3.2 9.5 + - - +
394A LEU 3.2 0.6 - - - -
395A GLU* 1.3 94.4 - - - +
397A VAL* 1.3 61.5 + - - +
398A LYS* 4.2 4.3 + - - +
971C C 5.8 1.8 + - - -
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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