Contacts of the helix formed by residues 490 - 498 (chain D) in PDB entry 5NTI
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 HIS 490 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313D MET* 4.2 26.5 - - + -
314D TRP* 4.4 22.0 - + + +
486D PHE* 2.8 37.2 + + + +
487D GLN 3.4 3.4 - - - -
489D LEU* 1.3 94.6 + - + +
491D PRO* 1.4 64.8 - - - +
492D ILE* 3.2 4.4 + - - -
493D VAL* 3.4 19.9 + - + -
494D VAL* 3.4 22.5 + - - +
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Residues in contact with PRO 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487D GLN* 3.1 22.3 + - + +
488D HIS* 3.6 9.2 - - - +
489D LEU 3.6 8.5 - - - +
490D HIS* 1.4 88.4 - - - +
492D ILE* 1.3 75.9 + - + +
494D VAL* 4.0 1.8 + - - +
495D GLN* 3.3 25.3 + - - +
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Residues in contact with ILE 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490D HIS 3.2 0.4 - - - -
491D PRO* 1.3 90.6 - - + +
493D VAL* 1.3 61.1 + - + +
495D GLN* 3.2 7.4 + - - +
496D ALA* 2.9 31.5 + - + +
503R LEU* 3.9 57.4 - - + +
504R LEU* 3.9 27.4 - - + +
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Residues in contact with VAL 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C GLN* 4.5 8.5 - - - +
314D TRP* 3.9 41.5 - - + +
318D GLU* 4.2 15.3 - - - +
486D PHE* 4.2 4.7 - - + -
490D HIS* 3.4 19.1 + - + +
492D ILE* 1.3 80.9 - - + +
494D VAL* 1.3 57.1 + - - +
496D ALA* 5.0 2.2 - - - -
497D ALA* 2.8 32.7 + - + +
498D PHE* 3.6 21.5 + - + -
504R LEU* 5.5 6.1 - - + -
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Residues in contact with VAL 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483D LEU* 5.2 2.9 - - + -
486D PHE* 3.6 28.5 - - + -
487D GLN* 3.7 37.2 - - + +
490D HIS 3.4 16.5 + - - +
491D PRO 4.2 2.2 - - - +
492D ILE 3.3 0.2 - - - -
493D VAL* 1.3 72.7 - - - +
495D GLN* 1.3 65.0 + - - +
496D ALA 3.3 0.7 + - - -
498D PHE* 3.2 50.7 + - + +
503D LYS* 4.0 26.4 - - + +
507D SER* 5.0 0.9 - - - +
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Residues in contact with GLN 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500C PRO* 3.4 22.2 - - - +
491D PRO 3.3 17.2 + - - +
492D ILE* 3.2 8.3 + - - +
494D VAL* 1.3 79.5 - - - +
496D ALA* 1.3 58.2 + - - +
503D LYS* 4.0 24.8 + - - +
500R LEU* 3.6 22.6 - - + +
503R LEU* 3.6 26.1 - - + +
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Residues in contact with ALA 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C GLN* 6.0 1.3 - - - +
499C PRO 4.1 0.3 - - - -
500C PRO* 3.3 4.7 - - - +
501C LEU* 2.8 36.4 + - + +
492D ILE* 2.9 18.1 + - + +
493D VAL* 4.4 1.6 - - - +
495D GLN* 1.3 79.2 - - - +
497D ALA* 1.3 60.1 + - + +
500R LEU* 3.9 29.2 - - + +
504R LEU* 4.4 24.5 - - + -
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Residues in contact with ALA 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C HIS* 5.0 2.9 + - - -
325C THR* 4.6 3.8 - - + -
329C GLN* 3.7 16.6 - - - +
499C PRO* 3.5 23.6 - - - +
500C PRO* 3.9 2.2 - - - -
318D GLU* 3.4 41.0 - - + +
493D VAL 2.8 18.2 + - - +
496D ALA* 1.3 75.5 - - + +
498D PHE* 1.3 65.5 + - + +
499D PRO* 3.6 3.5 - - - +
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Residues in contact with PHE 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500C PRO* 3.3 20.0 - - - +
317D TRP* 3.6 23.1 - + + -
318D GLU* 3.5 23.8 - - + -
321D ALA* 3.8 15.5 - - + -
483D LEU* 4.1 13.0 - - + -
486D PHE* 3.4 31.0 - + - -
493D VAL* 3.8 14.1 - - + -
494D VAL* 3.2 41.7 + - + +
497D ALA* 1.3 77.9 - - - +
499D PRO* 1.4 73.7 - - + +
500D PRO* 3.4 1.4 - - - +
502D TYR* 3.7 30.3 - + + -
503D LYS* 5.5 4.5 - - + +
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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