Contacts of the helix formed by residues 426 - 434 (chain N) in PDB entry 2DYS
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 PHE 426 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379N TYR* 3.4 23.1 + + - +
422N ASN 2.9 19.4 + - - +
425N PHE* 1.3 73.9 - - - +
427N PRO* 1.3 69.2 - - + +
428N GLN 3.1 0.2 + - - -
429N HIS* 2.7 43.9 + + - +
430N PHE* 3.8 26.5 + + - -
303O TGL 3.5 124.3 - - + -
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Residues in contact with PRO 427 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422N ASN 3.8 0.7 - - - +
423N MET 3.2 25.6 - - - +
424N THR 3.8 3.8 - - - +
425N PHE 3.5 2.7 - - - -
426N PHE* 1.3 94.6 - - + +
428N GLN* 1.3 54.7 + - - +
429N HIS 3.1 0.9 - - - -
430N PHE* 3.0 39.6 + - + +
431N LEU* 3.3 7.7 + - - +
450N TRP* 4.1 35.7 - - + +
453N ILE* 4.0 11.7 - - + -
454N SER* 4.8 0.9 - - - +
303O TGL 3.9 22.2 - - + -
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Residues in contact with GLN 428 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N ARG* 3.1 17.2 - - - +
371N TYR* 3.3 35.7 - - + +
374N VAL* 3.7 19.2 - - - +
375N ALA* 4.1 8.0 + - + -
424N THR* 3.6 14.4 + - - +
425N PHE* 3.1 32.5 + - - +
426N PHE 3.1 1.8 - - - -
427N PRO* 1.3 74.3 - - - +
429N HIS* 1.3 63.2 + - - +
430N PHE 3.2 0.2 - - - -
431N LEU* 3.6 15.4 + - + -
432N GLY 3.0 16.6 + - - -
454N SER* 3.0 25.2 + - - +
604N HEA 3.5 10.9 + - - -
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Residues in contact with HIS 429 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350N VAL* 4.9 3.6 - - + +
354N THR* 4.0 19.6 + - + +
372N TYR* 3.7 21.5 - + + -
375N ALA* 3.8 18.3 - - + +
379N TYR* 3.5 35.9 - + - -
425N PHE 4.1 2.2 - - - -
426N PHE* 2.7 41.3 + + - +
427N PRO 3.1 0.4 - - - -
428N GLN* 1.3 77.7 - - - +
430N PHE* 1.3 54.4 + - + +
432N GLY* 3.1 2.4 + - - -
433N LEU* 2.9 40.8 + - - +
303O TGL 3.8 41.0 - - + +
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Residues in contact with PHE 430 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426N PHE* 3.8 22.9 - + - -
427N PRO* 3.1 28.3 - - + +
429N HIS* 1.3 73.2 - - + +
431N LEU* 1.3 64.2 + - - +
432N GLY 3.0 1.6 - - - -
433N LEU* 3.3 2.3 + - - +
434N SER* 2.9 30.6 + - - -
450N TRP* 3.7 32.1 - + + -
6O GLN 3.7 6.5 - - - +
7O LEU* 3.4 44.9 - - + +
303O TGL 3.4 69.1 - - + -
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Residues in contact with LEU 431 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N ARG* 5.5 0.7 - - - +
371N TYR* 4.1 8.1 - - + -
427N PRO 3.3 2.6 + - - +
428N GLN* 3.8 27.6 - - + +
430N PHE* 1.3 78.2 - - - +
432N GLY* 1.3 59.8 + - - +
434N SER* 3.2 10.1 + - - -
435N GLY 3.3 0.2 + - - -
436N MET* 2.8 42.4 + - + -
447N TYR* 3.6 27.1 - - + +
450N TRP* 3.6 35.0 - - + +
451N ASN* 3.4 44.0 - - - +
454N SER* 5.5 0.9 - - - -
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Residues in contact with GLY 432 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366N VAL* 5.0 1.4 - - - +
367N LEU* 4.4 3.7 - - - +
370N THR* 3.8 14.5 + - - +
371N TYR* 3.9 7.6 - - - +
372N TYR* 3.4 32.1 - - - -
428N GLN 3.0 9.5 + - - -
429N HIS 3.1 3.6 + - - -
430N PHE 3.0 1.0 - - - -
431N LEU* 1.3 75.7 - - - +
433N LEU* 1.3 64.6 + - - +
435N GLY* 3.0 13.7 + - - -
9O PHE* 5.1 0.2 - - - -
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Residues in contact with LEU 433 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366N VAL* 5.2 1.0 - - - +
367N LEU* 3.6 24.5 - - + -
372N TYR* 3.7 17.7 - - + -
429N HIS 2.9 22.4 + - - +
430N PHE 3.3 0.2 + - - -
432N GLY* 1.3 71.0 - - - +
434N SER* 1.3 58.6 + - - +
435N GLY* 3.2 4.5 + - - -
7O LEU 3.6 10.1 - - - +
8O GLY* 3.6 21.8 - - - -
9O PHE* 2.9 46.8 - - + +
10O GLN* 4.4 1.2 + - - +
24O HIS* 4.1 15.7 - - + +
166O PRO* 6.0 1.4 - - - +
303O TGL 3.3 40.6 - - + +
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Residues in contact with SER 434 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430N PHE 2.9 20.8 + - - -
431N LEU* 3.2 11.4 + - - +
433N LEU* 1.3 76.3 - - - +
435N GLY* 1.3 55.6 + - - +
447N TYR* 2.8 35.9 + - - -
450N TRP* 5.6 0.7 - - - -
2O ALA* 3.6 1.0 - - - +
6O GLN* 3.6 40.9 + - - +
8O GLY 3.5 7.2 - - - -
10O GLN* 3.2 17.8 - - - +
166O PRO* 5.8 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