Contacts of the helix formed by residues 386 - 395 (chain A) in PDB entry 5YGP
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 386 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A VAL* 4.0 6.1 - - + -
383A PRO* 3.3 30.3 + - + +
384A ALA 3.1 16.0 - - - +
385A ARG* 1.3 94.4 - - - +
387A TRP* 1.3 58.8 + - - +
388A LYS 3.4 2.0 - - - -
389A GLU* 2.4 48.3 + - - +
390A PHE* 2.7 30.3 + - - +
442B LEU* 3.4 35.9 - - + +
443B GLU* 6.0 0.4 + - - -
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Residues in contact with TRP 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 4.5 13.5 - - + -
378A VAL* 4.6 7.0 - - + -
379A MET* 4.7 1.6 - - - -
382A VAL* 4.0 21.8 - - + +
383A PRO 4.4 0.8 + - - -
385A ARG* 3.7 1.4 - - - +
386A ARG* 1.3 78.9 - - - +
388A LYS* 1.3 63.0 + - + +
390A PHE* 3.2 36.7 + + - +
391A VAL* 2.8 44.4 + - + +
405A GLU* 3.0 37.3 + - + -
408A ILE* 3.4 40.2 - - + -
409A GLY* 3.7 16.8 - - - +
412A ARG* 3.7 29.3 - - - +
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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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385A ARG 5.5 0.8 + - - -
387A TRP* 1.3 80.2 - - + +
389A GLU* 1.3 60.7 + - - +
391A VAL* 3.8 25.1 - - + +
392A ARG* 2.9 78.2 + - - +
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Residues in contact with GLU 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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385A ARG 5.0 2.7 + - - +
386A ARG* 2.4 59.7 + - - +
387A TRP 3.3 0.2 - - - -
388A LYS* 1.3 75.6 - - - +
390A PHE* 1.3 64.1 + - - +
392A ARG* 3.3 7.3 + - + +
393A THR* 3.0 35.1 + - - +
442B LEU* 3.9 9.7 - - + +
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Residues in contact with PHE 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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375A LEU* 4.3 8.1 - - + -
378A VAL* 4.1 16.4 - - + -
382A VAL* 4.0 15.9 - - + -
386A ARG 2.7 21.2 + - - +
387A TRP* 3.4 38.6 - + - +
389A GLU* 1.3 72.5 - - - +
391A VAL* 1.3 64.0 + - + +
393A THR* 3.3 5.1 + - - -
394A LEU* 3.2 50.8 + - + +
442B LEU* 3.6 20.1 - - + +
445B CYS* 3.5 36.1 - - + -
446B VAL* 3.5 22.2 - - + -
449B LEU* 4.2 8.7 - - + -
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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
----------------------------------------------------------
387A TRP* 2.8 48.0 + - + +
388A LYS* 3.8 27.6 - - + +
389A GLU 3.3 0.2 - - - -
390A PHE* 1.3 74.3 - - + +
392A ARG* 1.3 63.6 + - - +
393A THR 3.4 0.3 + - - -
394A LEU* 3.4 15.4 + - + +
395A GLY* 3.4 9.7 + - - -
396A LEU 4.7 1.7 + - - +
405A GLU* 3.2 51.4 - - + +
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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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388A LYS* 2.9 62.4 + - - +
389A GLU* 3.7 8.0 - - + +
390A PHE 3.3 0.2 - - - -
391A VAL* 1.3 77.8 - - - +
393A THR* 1.3 63.8 + - - +
395A GLY* 3.5 12.2 + - - +
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Residues in contact with THR 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 GLU* 3.0 21.1 + - - +
390A PHE 3.8 4.5 - - - -
391A VAL 3.3 0.2 - - - -
392A ARG* 1.3 75.4 - - - +
394A LEU* 1.3 66.2 + - - +
395A GLY* 3.3 0.9 + - - -
442B LEU* 4.5 10.9 - - + +
446B VAL* 3.9 25.4 - - + -
450B ARG* 3.2 26.9 + - - +
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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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375A LEU* 4.3 7.4 - - + -
390A PHE* 3.2 50.8 + - + +
391A VAL* 3.8 9.0 - - + +
392A ARG 3.4 0.2 - - - -
393A THR* 1.3 76.7 - - - +
395A GLY* 1.3 63.1 + - - +
396A LEU* 3.2 26.9 + - + +
405A GLU* 4.6 3.8 - - - +
446B VAL* 4.2 28.3 - - + +
449B LEU* 3.6 30.3 - - + -
450B ARG* 4.5 17.2 + - + +
453B LEU* 5.9 0.9 - - + -
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Residues in contact with GLY 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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391A VAL 3.4 8.9 + - - -
392A ARG 3.5 8.7 + - - -
393A THR 3.2 3.2 - - - -
394A LEU* 1.3 77.6 - - - +
396A LEU* 1.3 53.3 + - - +
397A ARG* 2.7 32.7 + - - +
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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