Contacts of the helix formed by residues 391 - 401 (chain A) in PDB entry 4YOZ
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 THR 391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A GLU 4.0 1.7 + - - +
390A PHE* 1.3 76.5 - - - +
392A GLN* 1.3 67.5 + - - +
393A SER* 3.8 3.9 + - - -
394A VAL* 3.4 27.1 + - + +
395A SER* 2.9 21.0 + - - -
512A ALA 4.0 5.5 + - - -
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Residues in contact with GLN 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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389A GLU* 4.2 17.4 + - - +
390A PHE 4.9 2.6 + - - +
391A THR* 1.3 75.4 - - - +
393A SER* 1.3 58.3 + - - +
395A SER* 3.0 9.6 + - - -
396A ARG* 2.9 32.2 + - - +
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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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391A THR* 3.2 4.1 + - - -
392A GLN* 1.3 79.7 - - - +
394A VAL* 1.3 57.7 + - - +
396A ARG* 4.4 0.2 - - - -
397A LEU* 3.0 25.6 + - - +
511A PHE* 4.7 8.7 - - - -
512A ALA* 3.7 30.1 - - - +
548A SER* 4.6 4.8 + - - -
550A ASP* 5.0 5.9 - - - +
551A MET* 3.2 30.4 - - - +
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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
----------------------------------------------------------
390A PHE* 3.7 28.7 - - + -
391A THR* 3.2 18.5 + - + +
393A SER* 1.3 73.4 - - - +
395A SER* 1.3 59.9 - - - +
397A LEU* 3.3 7.6 + - + +
398A GLN* 2.9 34.9 + - + +
512A ALA* 3.3 24.5 - - + +
513A TYR* 3.7 48.5 - - + +
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Residues in contact with SER 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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390A PHE* 4.1 14.1 - - - +
391A THR 2.9 14.5 + - - -
392A GLN* 3.0 19.8 + - - -
394A VAL* 1.3 73.8 - - - +
396A ARG* 1.3 62.4 + - - +
398A GLN* 3.2 16.2 + - - +
399A SER* 2.9 32.0 + - - -
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Residues in contact with ARG 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 GLN 2.9 20.3 + - - +
393A SER* 3.6 4.5 - - - +
395A SER* 1.3 74.8 + - - +
397A LEU* 1.3 64.9 + - - +
399A SER* 3.0 12.4 + - - -
400A ILE* 3.0 31.5 + - + +
545A GLU 5.4 0.4 + - - -
546A GLY* 3.0 33.6 + - - +
547A LEU 4.0 0.6 + - - -
548A SER* 3.7 12.6 - - - +
551A MET* 3.8 17.7 - - + -
1002A SO4 2.6 45.3 + - - -
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Residues in contact with LEU 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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393A SER 3.0 14.2 + - - +
394A VAL* 3.4 9.9 - - - +
396A ARG* 1.3 77.1 - - - +
398A GLN* 1.3 61.4 + - - +
400A ILE* 3.1 23.6 + - + +
401A VAL* 3.2 21.9 + - + +
463A LEU* 3.7 33.0 - - + -
467A LEU* 3.8 30.7 - - + -
508A ILE* 3.9 14.6 - - + -
509A VAL* 4.0 19.7 - - + -
512A ALA* 3.8 22.0 - - + -
513A TYR* 4.4 5.2 - - + -
551A MET* 4.2 5.6 - - + +
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Residues in contact with GLN 398 (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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390A PHE* 3.1 55.9 - - - -
394A VAL* 2.9 22.8 + - + +
395A SER* 3.2 13.8 + - - +
397A LEU* 1.3 76.7 - - + +
399A SER* 1.3 59.4 + - - +
401A VAL* 3.5 11.9 - - + +
402A ALA* 3.3 23.4 + - - +
463A LEU* 5.8 6.7 - - + -
513A TYR* 5.2 3.2 + - - +
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Residues in contact with SER 399 (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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395A SER 2.9 16.7 + - - -
396A ARG* 3.0 19.6 + - - -
398A GLN* 1.3 74.7 - - - +
400A ILE* 1.3 65.6 - - - +
401A VAL 3.4 0.3 + - - -
402A ALA* 3.4 17.4 + - - +
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Residues in contact with ILE 400 (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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396A ARG* 3.0 21.3 + - + +
397A LEU* 3.1 16.1 + - + +
399A SER* 1.3 79.5 - - - +
401A VAL* 1.3 59.8 + - + +
402A ALA 3.3 2.0 + - - +
404A LEU* 4.0 3.3 - - - +
467A LEU* 3.7 22.4 - - + -
470A LYS* 3.3 25.6 - - + +
544A GLU* 3.7 23.3 - - + +
546A GLY* 3.5 38.4 - - - +
547A LEU* 3.9 21.5 - - + +
551A MET* 4.9 1.3 - - - -
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Residues in contact with VAL 401 (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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397A LEU* 3.4 19.5 - - + +
398A GLN* 3.5 16.4 - - + +
400A ILE* 1.3 79.4 - - + +
402A ALA* 1.3 64.1 + - - +
403A GLY 3.3 0.5 + - - -
404A LEU* 3.2 24.6 + - - +
463A LEU* 4.2 28.7 - - + +
466A ILE* 3.7 33.4 - - + +
467A LEU* 4.3 23.3 - - + +
470A LYS* 5.4 0.4 - - + -
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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