Contacts of the helix formed by residues 383 - 390 (chain A) in PDB entry 6ZGI
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 383 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A VAL* 1.3 88.3 - - - +
384A PRO* 1.3 71.9 - - - +
385A THR* 4.1 4.0 - - - -
386A LYS* 3.1 31.7 + - - +
387A LEU* 3.8 2.6 + - - +
983B ARG 3.3 5.8 + - - -
984B LEU* 3.8 1.7 - - - -
985B ASP* 3.2 36.0 + - - -
988B GLU* 3.2 20.6 + - - -
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Residues in contact with PRO 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TYR* 4.1 9.9 + - - -
377A PHE* 4.6 9.6 - - + -
379A CYS* 4.9 11.4 - - + +
382A VAL 4.0 4.9 - - - +
383A SER* 1.3 85.5 - - - +
385A THR* 1.3 59.6 + - - +
386A LYS 3.3 0.7 + - - -
387A LEU* 3.6 31.3 + - + +
388A ASN 5.3 0.2 + - - -
985B ASP* 5.5 1.1 - - - +
413C GLY 3.7 24.7 - - - +
414C GLN* 4.9 7.9 - - - +
415C THR* 4.0 26.4 + - + -
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Residues in contact with THR 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A SER* 4.1 3.5 - - - -
384A PRO* 1.3 76.8 - - - +
386A LYS* 1.3 65.3 + - - +
387A LEU 3.5 0.4 - - - -
388A ASN* 4.8 5.1 + - - +
389A ASP* 4.4 7.1 - - - +
985B ASP* 4.0 25.1 + - - +
413C GLY* 4.3 18.7 + - - +
414C GLN 4.0 21.8 - - - +
415C THR* 5.0 2.7 - - - +
420C ASP* 6.2 0.2 - - - +
424C LYS* 4.5 10.3 - - - +
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Residues in contact with LYS 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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383A SER* 3.1 27.4 + - - +
385A THR* 1.3 84.2 - - - +
387A LEU* 1.3 65.8 + - - +
388A ASN 3.1 3.6 - - - -
389A ASP* 3.0 29.2 + - - +
390A LEU* 3.6 18.0 - - + +
981B LEU 3.6 14.5 + - - -
982B SER* 4.4 4.0 - - - +
983B ARG* 3.8 37.2 - - - +
984B LEU 3.9 14.5 + - - +
985B ASP* 4.2 5.5 - - + +
986B PRO* 6.2 0.6 - - - +
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Residues in contact with LEU 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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365A TYR* 4.3 24.7 - - + +
377A PHE* 4.4 21.3 - - + -
379A CYS* 4.5 4.3 - - - -
382A VAL* 4.3 26.2 - - + -
383A SER 3.8 5.3 + - - +
384A PRO* 3.6 25.8 - - + +
385A THR 3.5 1.6 - - - -
386A LYS* 1.3 77.6 - - - +
388A ASN* 1.3 61.7 + - - +
389A ASP 3.3 0.7 + - - -
390A LEU* 3.6 6.8 + - - +
392A PHE* 3.6 45.3 - - + -
432A CYS* 4.9 5.2 - - - -
515A PHE* 4.7 7.2 - - + -
526A GLY* 5.0 2.9 - - - -
415C THR* 5.5 0.7 - - + -
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Residues in contact with ASN 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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329A PHE* 5.3 0.2 - - - -
363A ALA 4.8 0.5 - - - +
364A ASP* 5.9 0.2 - - - -
365A TYR* 3.4 32.3 + - - -
384A PRO 5.3 0.2 + - - -
385A THR 4.8 4.6 + - - +
386A LYS 3.1 1.4 + - - -
387A LEU* 1.3 77.8 - - - +
389A ASP* 1.3 69.1 + - - +
390A LEU 3.5 1.3 + - - -
526A GLY 4.4 8.1 - - - +
527A PRO* 3.7 41.4 + - - +
528A LYS* 4.3 6.4 - - - +
460C ASN* 5.8 4.0 - - - +
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Residues in contact with ASP 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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329A PHE* 3.9 10.1 - - - -
385A THR 4.4 10.6 - - - +
386A LYS* 3.0 24.2 + - - +
388A ASN* 1.3 84.3 - - - +
390A LEU* 1.3 62.3 + - + +
528A LYS* 3.6 34.1 + - + +
542A ASN* 4.2 7.6 + - - +
545A GLY* 3.4 20.6 - - - +
547A THR* 6.0 1.3 - - + +
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A PHE* 4.5 6.0 - - - -
382A VAL* 3.9 28.3 - - + -
386A LYS* 3.6 20.9 - - + +
387A LEU* 3.6 1.5 + - - -
388A ASN 3.5 1.4 - - - -
389A ASP* 1.3 81.0 - - + +
391A CYS* 1.3 61.5 - - - +
392A PHE* 3.7 25.7 - - + -
517A LEU* 3.9 18.4 - - + -
518A LEU* 4.5 19.5 - - + -
525A CYS* 3.8 1.0 - - - -
526A GLY* 3.2 23.9 + - - -
545A GLY* 4.0 23.1 - - - +
982B SER* 5.0 1.1 - - - -
983B ARG* 4.3 20.9 - - + +
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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