Contacts of the helix formed by residues 390 - 396 (chain A) in PDB entry 5A5J
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 390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A SER* 3.3 23.9 + - - -
54A LEU* 5.1 10.1 - - - +
55A THR* 5.0 0.3 + - - -
76A VAL* 5.5 4.0 - - - +
77A LEU 3.0 15.1 + - - +
78A HIS* 3.7 15.3 + - - -
83A VAL* 5.0 0.2 - - - +
363A PRO 3.6 3.6 - - - -
364A THR* 4.5 4.4 - - - +
388A LEU 4.2 0.4 + - - -
389A ILE* 1.3 72.2 - - - +
391A LEU* 1.3 65.9 + - - +
392A THR* 3.7 0.3 - - - -
393A SER* 2.9 42.6 + - - -
394A VAL* 3.6 5.7 + - - +
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Residues in contact with LEU 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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83A VAL* 5.5 0.9 - - + -
87A LEU* 6.0 0.2 - - + -
360A ASP* 4.3 4.9 - - - +
362A LEU* 3.4 20.0 - - + +
363A PRO 2.9 9.3 + - - +
365A SER* 3.7 26.9 - - - +
389A ILE* 3.2 19.6 + - + -
390A SER* 1.3 72.0 - - - +
392A THR* 1.4 62.7 + - - +
394A VAL* 2.9 16.1 + - + +
395A LEU* 3.0 23.7 + - + +
426A MET* 3.5 40.4 - - + +
427A PRO* 4.1 3.8 - - + +
429A SER* 4.0 15.5 - - - +
430A ALA 5.3 0.2 - - - +
1493A HEM 3.9 15.5 - - + -
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Residues in contact with THR 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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48A LYS* 4.4 5.6 + - - +
51A SER* 2.5 38.4 + - - +
52A LYS* 6.3 0.9 - - - +
55A THR* 5.5 4.3 - - - +
360A ASP* 2.5 33.0 + - - +
363A PRO* 3.0 8.7 + - - +
390A SER* 3.7 0.7 - - - -
391A LEU* 1.4 73.5 - - - +
393A SER* 1.3 57.4 + - - +
394A VAL 2.9 0.2 + - - -
395A LEU* 5.0 0.9 - - - -
396A HIS* 2.7 54.4 + - + +
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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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55A THR* 5.1 1.7 + - - -
78A HIS* 3.0 43.8 + - - -
79A GLY* 2.7 28.4 + - - -
80A TYR 4.9 0.2 + - - -
83A VAL* 5.0 0.2 - - - +
390A SER* 2.9 16.3 + - - -
392A THR* 1.3 81.5 - - - +
394A VAL* 1.3 62.3 + - - +
396A HIS 4.2 1.7 - - - -
397A ASP* 3.8 19.5 + - - +
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Residues in contact with VAL 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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79A GLY 3.8 21.1 - - - +
80A TYR* 3.9 12.1 - - + +
83A VAL* 4.0 16.8 - - + -
390A SER 3.8 7.2 - - - +
391A LEU* 2.9 10.0 + - + +
393A SER* 1.3 91.2 + - - +
395A LEU* 1.3 63.5 + - + +
396A HIS 3.2 1.8 - - - -
397A ASP* 3.9 4.4 + - - +
401A PHE* 4.0 0.7 - - - -
424A TYR* 3.5 47.3 - - + +
426A MET* 3.8 27.1 - - + -
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Residues in contact with LEU 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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356A GLN 4.3 12.1 - - - +
357A ARG* 3.0 57.0 + - + +
360A ASP* 3.8 26.0 - - - +
391A LEU* 3.0 22.2 + - + +
392A THR* 4.2 0.9 - - - +
394A VAL* 1.3 74.9 - - - +
396A HIS* 1.3 63.8 + - + +
397A ASP 3.5 1.3 - - - -
401A PHE* 3.2 7.8 - - - -
424A TYR 3.8 7.6 - - - +
425A PHE* 4.2 2.2 - - - -
426A MET* 3.3 35.2 - - + +
427A PRO* 3.7 23.1 - - + -
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Residues in contact with HIS 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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48A LYS* 6.4 1.6 - - - -
357A ARG* 2.9 46.4 + - - +
358A TYR* 3.1 24.2 + + - -
360A ASP* 4.6 9.7 - - + +
392A THR* 2.7 33.9 + - + +
393A SER* 4.3 2.9 - - - -
395A LEU* 1.3 82.2 - - + +
397A ASP* 1.3 62.0 + - - +
398A ASN* 3.5 2.6 + - - +
404A PRO* 3.5 29.7 + - + +
405A GLU* 3.3 23.9 + - - -
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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