Contacts of the helix formed by residues 381 - 397 (chain A) in PDB entry 7A62
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 GLY 381 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A LEU* 3.8 21.3 - - - +
379A THR* 2.8 10.4 + - - +
380A GLY* 1.3 72.2 - - - +
382A THR* 1.3 61.4 + - - -
383A ASP 3.4 0.7 - - - -
384A LEU* 3.6 6.3 + - - +
385A MET* 3.2 28.8 + - - +
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Residues in contact with THR 382 (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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380A GLY 3.0 8.6 + - - +
381A GLY* 1.3 71.2 - - - -
383A ASP* 1.3 61.1 - - + +
385A MET* 3.4 5.1 + - - +
386A ASN* 2.2 51.2 + - - +
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Residues in contact with ASP 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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380A GLY* 4.1 10.8 + - - +
381A GLY 3.4 0.2 - - - -
382A THR* 1.3 85.1 - - + +
384A LEU* 1.3 62.6 + - - +
386A ASN* 3.8 5.8 + - - +
387A PHE* 3.3 20.8 + - - +
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Residues in contact with LEU 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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350A VAL* 4.1 21.8 - - + -
354A ILE* 4.4 16.4 - - + -
355A LEU* 4.7 7.9 - - + -
379A THR* 4.7 12.8 - - + -
380A GLY* 4.5 7.6 - - - +
381A GLY 3.6 17.9 + - - +
382A THR 3.3 0.6 - - - -
383A ASP* 1.3 78.0 + - - +
385A MET* 1.3 66.8 + - + +
387A PHE* 3.5 6.8 + - + +
388A LEU* 3.2 25.1 + - + +
502A HEM 3.4 48.0 - - + +
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Residues in contact with MET 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 3.5 31.2 - - + -
350A VAL* 4.4 14.4 - - - -
351A THR* 3.8 9.6 - - - +
355A LEU* 3.4 36.6 - - + -
381A GLY 3.2 18.6 + - - +
382A THR* 3.4 6.3 + - - +
384A LEU* 1.3 76.4 - - + +
386A ASN* 1.3 55.8 + - - +
388A LEU* 3.1 5.0 + - - +
389A LYS* 2.7 59.7 + - + +
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Residues in contact with ASN 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 THR* 2.2 51.2 + - - +
383A ASP* 4.1 5.8 - - - +
385A MET* 1.3 77.8 - - - +
387A PHE* 1.3 51.0 + - - +
389A LYS* 3.6 12.5 - - - +
390A THR* 2.5 44.9 + - - +
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Residues in contact with PHE 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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287A HIS* 4.7 3.6 - - + -
288A ALA* 3.8 33.4 - - + -
291A PHE* 3.4 41.1 - + + -
292A LEU* 4.1 11.0 - - + -
383A ASP 3.3 13.3 + - - +
384A LEU* 3.6 10.3 - - + +
385A MET 3.2 0.4 - - - -
386A ASN* 1.3 77.3 - - - +
388A LEU* 1.3 89.2 + - + +
390A THR* 3.2 5.4 + - - -
391A VAL* 3.1 44.8 + - + +
502A HEM 4.0 19.1 - - + -
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Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ARG* 5.3 2.1 - - - +
346A HIS* 4.0 12.3 - - + +
347A LEU* 3.9 27.5 - - + +
350A VAL* 3.9 35.2 - - + -
384A LEU* 3.2 19.9 + - + +
385A MET* 3.1 7.9 + - - +
387A PHE* 1.3 102.4 - - + +
389A LYS* 1.3 63.0 + - - +
391A VAL* 3.3 5.3 + - - +
392A ARG* 3.0 22.5 + - - +
502A HEM 3.8 31.8 - - + +
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Residues in contact with LYS 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 3.9 19.3 - - + -
385A MET* 2.7 46.3 + - + +
386A ASN* 3.8 12.8 - - - +
388A LEU* 1.3 73.4 - - - +
390A THR* 1.3 52.5 + - - +
392A ARG* 3.3 27.4 + - - +
393A SER* 2.7 37.4 + - - -
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Residues in contact with THR 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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288A ALA* 4.2 20.2 - - + -
386A ASN* 2.5 32.0 + - - +
387A PHE* 3.2 7.6 + - - -
389A LYS* 1.3 73.6 - - - +
391A VAL* 1.3 53.6 + - - +
393A SER* 3.2 5.9 + - - -
394A THR* 2.7 47.1 + - - +
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Residues in contact with VAL 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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281A GLN* 3.2 23.3 + - - +
288A ALA* 4.5 5.6 - - + -
292A LEU* 4.0 15.3 - - + -
343A ARG* 3.2 35.0 - - - +
387A PHE* 3.1 45.2 + - + +
388A LEU* 3.8 6.3 - - - +
390A THR* 1.3 74.6 - - - +
392A ARG* 1.3 55.5 + - - +
394A THR 3.5 0.2 + - - -
395A THR* 2.6 34.0 + - - -
502A HEM 3.4 10.5 - - - +
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Residues in contact with ARG 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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340A VAL* 4.4 16.6 - - + -
343A ARG* 4.1 20.3 - - + +
344A SER* 3.3 36.4 + - - +
347A LEU* 3.9 21.4 - - + +
388A LEU 3.0 14.2 + - - +
389A LYS* 3.6 36.8 + - - +
391A VAL* 1.3 74.3 - - - +
393A SER* 1.3 60.1 + - - +
395A THR* 2.9 8.3 + - - -
396A GLU* 2.8 41.8 + - - +
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Residues in contact with SER 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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389A LYS 2.7 21.8 + - - -
390A THR* 3.6 7.0 - - - -
392A ARG* 1.3 73.7 - - - +
394A THR* 1.3 63.1 - - - +
395A THR 3.1 0.2 + - - -
396A GLU* 3.1 21.0 + - - +
397A LYS* 3.0 51.9 + - - +
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Residues in contact with THR 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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279A ILE* 4.3 5.6 - - + -
280A GLN* 4.1 16.8 - - + +
281A GLN* 3.3 31.8 + - - +
390A THR* 2.7 33.1 + - - +
391A VAL 3.6 0.9 - - - -
393A SER* 1.3 72.9 + - - +
395A THR* 1.3 62.2 + - - +
397A LYS* 3.6 18.4 + - + +
398A SER* 3.4 15.6 + - - +
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Residues in contact with THR 395 (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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279A ILE* 3.9 25.6 - - + -
281A GLN* 3.1 5.2 + - - -
336A VAL* 3.7 8.8 - - - +
339A LEU* 4.1 14.4 - - + -
340A VAL* 3.7 20.2 - - + +
343A ARG* 2.9 29.5 + - - +
391A VAL 2.6 20.1 + - - -
392A ARG* 2.9 13.0 + - - -
394A THR* 1.3 75.2 - - - +
396A GLU* 1.3 64.2 + - - +
398A SER* 3.0 19.8 + - - -
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Residues in contact with GLU 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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340A VAL* 3.8 26.6 - - + +
392A ARG* 2.8 36.7 + - - +
393A SER* 3.2 30.3 + - - +
395A THR* 1.3 73.8 - - - +
397A LYS* 1.3 63.0 + - + +
398A SER 3.0 1.4 + - - -
399A LEU* 3.1 33.0 + - + +
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Residues in contact with LYS 397 (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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317A ARG* 5.0 2.4 + - - -
393A SER* 3.0 40.7 + - - +
394A THR* 3.8 12.1 - - - +
395A THR 3.2 0.4 - - - -
396A GLU* 1.3 78.6 - - + +
398A SER* 1.3 59.6 + - - +
399A LEU* 3.3 6.7 + - - +
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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