Contacts of the helix formed by residues 419 - 426 (chain S) in PDB entry 5GJQ
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 LEU 419 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417S ILE 3.4 1.0 + - - -
418S SER* 1.3 71.2 - - - +
420S ALA* 1.3 65.0 + - - +
421S ASP 3.1 0.3 + - - -
422S ILE* 3.2 23.7 + - + +
423S ALA* 3.0 23.6 + - - +
431S PRO* 4.1 24.2 - - + +
434S ALA* 4.4 15.8 - - + +
435S GLU* 4.2 27.6 - - + +
438S VAL* 5.5 1.8 - - + -
451S ILE* 4.9 9.4 - - + -
453S HIS* 5.2 7.9 - - + +
456S GLY* 2.6 40.2 + - - +
458S VAL* 4.3 16.4 - - + +
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Residues in contact with ALA 420 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418S SER* 3.0 9.5 - - - +
419S LEU* 1.3 77.7 - - - +
421S ASP* 1.3 66.2 + - - +
423S ALA* 3.2 4.0 + - - +
424S GLN* 3.0 33.9 + - + +
431S PRO* 4.1 14.7 - - + +
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Residues in contact with ASP 421 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349R LYS* 3.4 32.0 - - + +
350R VAL* 5.1 0.2 - - - -
417S ILE* 3.6 10.8 - - + +
418S SER* 2.9 26.0 + - - +
420S ALA* 1.3 77.8 - - - +
422S ILE* 1.3 69.0 + - - +
424S GLN* 2.9 10.4 + - - +
425S LYS* 2.8 39.1 + - - +
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Residues in contact with ILE 422 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407S VAL* 5.9 1.3 - - + -
410S ILE* 4.0 28.0 - - + -
417S ILE* 3.6 28.5 - - + +
418S SER 3.6 0.2 + - - -
419S LEU* 3.2 34.2 + - + +
421S ASP* 1.3 75.6 - - - +
423S ALA* 1.3 65.4 + - - +
425S LYS* 3.0 4.1 + - - +
426S LEU* 2.9 48.0 + - + +
428S LEU* 6.3 0.4 - - + -
434S ALA* 5.1 11.4 - - + -
438S VAL* 5.0 13.9 - - + -
458S VAL* 4.2 15.3 - - + -
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Residues in contact with ALA 423 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419S LEU 3.0 12.9 + - - +
420S ALA* 3.4 9.9 - - - +
422S ILE* 1.3 77.9 - - - +
424S GLN* 1.3 56.9 + - + +
426S LEU* 4.7 1.3 - - - +
427S GLN 3.1 4.9 + - - -
428S LEU* 3.1 44.8 + - + +
429S ASP 5.2 1.6 - - - +
430S SER* 4.2 26.0 - - - +
431S PRO* 4.4 9.0 - - + -
434S ALA* 5.2 4.7 - - + +
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Residues in contact with GLN 424 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420S ALA* 3.0 18.8 + - + +
421S ASP* 2.9 12.6 + - - +
423S ALA* 1.3 78.3 - - + +
425S LYS* 1.3 64.6 + - + +
426S LEU 3.2 0.2 - - - -
427S GLN* 3.2 15.6 + - - +
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Residues in contact with LYS 425 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331R ASP* 3.5 19.6 + - - -
349R LYS* 5.7 3.2 - - - +
370S GLY 5.5 0.7 - - - +
371S ASN* 6.0 1.7 - - - -
410S ILE* 4.2 29.6 - - + -
414S TYR* 3.6 27.2 + - + -
417S ILE* 5.6 2.7 - - - -
421S ASP* 2.8 36.5 + - - +
422S ILE* 3.7 4.5 - - - +
424S GLN* 1.3 74.2 - - + +
426S LEU* 1.3 65.7 + - + +
427S GLN* 3.3 6.7 + - - +
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Residues in contact with LEU 426 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370S GLY 4.2 18.6 - - - +
372S LEU* 5.2 9.2 + - - +
403S ILE* 4.8 13.2 - - + -
406S GLY* 4.2 11.7 - - - -
407S VAL* 4.4 19.5 - - + -
410S ILE* 3.7 29.8 - - + -
422S ILE* 2.9 28.0 + - + +
425S LYS* 1.3 82.1 - - + +
427S GLN* 1.3 65.5 + - - +
428S LEU* 3.0 43.0 + - + +
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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