Contacts of the helix formed by residues 487 - 495 (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 LEU 487 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260N TYR* 3.3 52.0 - - + +
263N GLY* 4.2 15.5 - - - +
264N LYS 4.4 16.2 - - - +
265N LYS* 5.2 3.1 - - + -
486N ASP* 1.3 91.6 + - + +
488N THR* 1.3 64.6 + - - +
489N THR* 3.1 9.6 + - - +
490N THR* 3.1 11.6 + - - +
491N ASN* 2.9 24.5 + - - +
19Q ARG* 4.1 23.8 - - - +
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Residues in contact with THR 488 (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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485N VAL* 3.5 27.5 + - + +
486N ASP 3.3 0.4 - - - -
487N LEU* 1.3 75.8 - - - +
489N THR* 1.3 68.2 + - - +
490N THR 3.1 1.3 + - - -
491N ASN* 3.3 23.4 + - - -
492N LEU 3.9 1.6 + - - -
494N TRP* 4.1 26.0 - - + +
495N LEU* 3.7 33.6 - - + +
11Q TYR 6.0 1.3 - - - +
71S TRP* 4.0 5.3 + - - +
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Residues in contact with THR 489 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487N LEU* 3.1 7.0 + - - +
488N THR* 1.3 82.2 + - - +
490N THR* 1.3 67.3 + - - +
491N ASN 3.6 0.2 - - - -
69S VAL 3.2 9.0 - - - +
70S ILE* 3.5 17.0 - - + +
71S TRP* 2.9 44.2 + - - +
72S PHE* 4.8 2.9 - - + -
83S PRO* 4.4 24.2 - - + -
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Residues in contact with THR 490 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256N HIS* 6.1 1.0 - - - -
264N LYS 4.5 1.7 + - - -
265N LYS* 3.3 47.5 + - + +
487N LEU* 3.1 9.9 + - - +
488N THR 3.1 0.4 - - - -
489N THR* 1.3 89.3 + - - +
491N ASN* 1.3 80.2 + - - +
492N LEU 3.9 1.3 - - - -
68S THR* 3.8 18.8 - - + -
69S VAL 4.4 4.3 - - - +
70S ILE* 4.2 9.2 - - + -
71S TRP* 4.6 2.9 - - - -
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Residues in contact with ASN 491 (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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256N HIS* 4.8 12.6 + - - +
259N THR* 6.3 0.6 - - - +
260N TYR* 3.4 36.5 - - + +
264N LYS 5.6 0.8 + - - -
395N HIS* 5.2 1.7 + - - -
396N TRP* 5.9 0.2 - - - -
487N LEU* 2.9 28.9 + - - +
488N THR* 3.3 9.4 + - - +
490N THR* 1.3 99.4 + - - +
492N LEU* 1.3 66.3 + - - +
493N GLU* 3.0 20.3 + - - +
494N TRP* 3.0 34.5 + - + +
495N LEU 4.0 1.0 + - - -
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Residues in contact with LEU 492 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85N LEU 3.2 22.8 - - - +
86N MET* 4.0 11.4 - - + +
88N GLY* 3.9 19.5 - - - +
488N THR 3.9 4.2 + - - -
490N THR 3.9 0.4 - - - -
491N ASN* 1.3 74.0 - - - +
493N GLU* 1.3 62.8 + - - +
494N TRP 3.1 0.2 - - - -
495N LEU* 3.1 35.1 + - + +
496N ASN* 4.6 1.9 + - - -
505N PHE* 4.2 15.9 - - + -
57S ILE* 4.2 8.5 - - + -
71S TRP* 3.8 59.8 - - + +
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Residues in contact with GLU 493 (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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82N LEU* 4.2 5.8 - - + -
85N LEU* 4.0 37.0 + - + +
86N MET* 3.6 27.7 - - + +
256N HIS* 4.8 2.4 + - - -
395N HIS* 4.7 0.2 + - - -
396N TRP* 2.6 43.7 + - - +
399N LEU* 3.6 30.5 - - + +
491N ASN* 3.4 22.3 - - - +
492N LEU* 1.3 77.8 + - - +
494N TRP* 1.3 75.2 + - + +
495N LEU 3.4 0.2 - - - -
496N ASN* 4.6 6.7 + - - +
497N GLY 5.1 0.2 - - - +
500N PRO* 5.4 1.0 - - - +
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Residues in contact with TRP 494 (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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260N TYR* 4.7 3.5 - + - -
395N HIS* 3.4 45.7 + + - -
396N TRP* 3.6 17.3 - + - +
398N PRO* 4.1 9.9 - - + -
399N LEU* 3.4 42.0 - - + -
485N VAL* 3.8 34.4 - - + +
488N THR* 4.1 19.0 - - + +
491N ASN* 3.0 24.7 + - + +
493N GLU* 1.3 100.5 + - - +
495N LEU* 1.3 64.8 + - - +
496N ASN 3.1 4.4 + - - -
497N GLY* 3.2 16.8 + - - +
498N CYS* 3.6 25.1 - - - -
11Q TYR* 5.4 1.0 - - - +
1Z ILE* 5.3 1.3 - - + -
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Residues in contact with LEU 495 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488N THR* 3.7 32.3 - - + +
491N ASN 4.0 1.2 + - - -
492N LEU* 3.1 27.7 + - + +
494N TRP* 1.3 77.6 - - - +
496N ASN* 1.3 58.5 + - - +
497N GLY 3.3 1.1 - - - -
11Q TYR* 3.5 15.5 - - - +
57S ILE* 3.9 13.7 - - + -
71S TRP* 3.6 44.2 - - + +
72S PHE* 3.8 7.4 - - - +
73S TRP* 3.0 49.3 + - + +
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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