Contacts of the helix formed by residues 404 - 412 (chain D) in PDB entry 2NYM
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 404 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366D LEU* 3.8 20.9 - - + -
369D PHE* 4.5 4.7 - - + -
370D LEU* 3.7 26.9 - - + -
373D LEU* 4.2 16.6 - - + +
388D LEU* 4.2 13.0 - - + -
391D VAL* 4.1 20.0 - - + -
395D ILE* 4.2 8.5 - - + -
399D GLN 4.6 0.9 - - - +
400D LEU* 3.1 37.6 + - + +
403D SER* 1.3 79.0 - - - +
405D LEU* 1.3 69.3 + - - +
406D PRO* 3.1 3.9 - - - +
407D ALA* 3.1 18.3 + - - +
408D ILE* 3.2 19.2 + - + +
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Residues in contact with LEU 405 (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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400D LEU* 2.9 6.7 + - + +
401D SER* 3.5 33.2 - - - +
404D LEU* 1.3 76.2 - - - +
406D PRO* 1.3 62.3 - - + +
408D ILE* 3.0 15.7 + - + +
409D VAL* 2.7 48.4 + - + -
430D LEU* 3.8 28.5 - - + -
434D LEU* 4.2 6.3 - - + -
438D PHE* 4.3 18.2 - - + -
443D LEU* 3.9 20.0 - - + -
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Residues in contact with PRO 406 (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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401D SER 4.4 1.6 - - - +
402D GLN 3.6 18.6 - - - +
403D SER 4.1 2.2 - - - -
404D LEU 3.1 14.6 - - - +
405D LEU* 1.3 104.3 - - + +
407D ALA* 1.3 63.8 + - - +
409D VAL* 2.8 17.4 + - + +
410D GLU* 2.9 12.9 + - - +
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Residues in contact with ALA 407 (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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370D LEU* 4.4 14.8 - - + -
373D LEU* 4.2 15.0 - - + -
374D LYS* 4.4 19.1 - - + +
404D LEU 3.1 10.3 + - - +
406D PRO* 1.3 77.8 - - - +
408D ILE* 1.3 52.0 + - - +
410D GLU* 2.7 13.7 + - - +
411D LEU* 2.6 50.2 + - + +
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Residues in contact with ILE 408 (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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373D LEU* 5.3 6.3 - - + -
388D LEU* 3.7 20.6 - - + -
400D LEU* 5.2 2.2 - - + -
404D LEU* 3.2 20.6 + - + +
405D LEU* 3.0 22.1 + - + +
407D ALA* 1.3 79.4 - - + +
409D VAL* 1.3 59.2 + - + +
411D LEU* 3.6 9.3 + - - +
412D ALA* 3.2 19.2 + - - +
423D ILE* 3.9 22.7 - - + +
426D TYR* 3.3 34.8 - - + +
427D MSE 5.2 2.7 - - + -
430D LEU* 3.8 25.6 - - + -
443D LEU* 6.3 0.2 - - + -
446D LEU* 5.4 0.2 - - - +
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Residues in contact with VAL 409 (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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405D LEU* 2.7 41.5 + - + +
406D PRO* 2.8 11.2 + - + +
408D ILE* 1.3 71.6 - - + +
410D GLU* 1.3 62.9 + - + +
412D ALA* 3.2 21.7 - - - +
413D GLU* 5.8 0.2 - - - +
442D LYS 4.8 6.7 - - - +
443D LEU* 4.2 14.4 - - + -
446D LEU* 4.1 21.1 - - + +
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Residues in contact with GLU 410 (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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374D LYS* 5.8 4.5 - - - -
406D PRO 2.9 9.0 + - - +
407D ALA* 2.7 13.3 + - - +
409D VAL* 1.3 78.0 - - + +
411D LEU* 1.3 68.1 + - + +
412D ALA 2.8 2.8 + - - -
413D GLU* 2.9 19.4 + - - +
414D ASP* 4.9 1.1 - - - +
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Residues in contact with LEU 411 (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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373D LEU* 3.5 38.4 - - + +
374D LYS* 5.9 1.3 - - + -
381D ARG* 4.0 19.1 - - - +
385D ILE* 3.5 20.4 - - + -
407D ALA* 2.6 44.9 + - + +
408D ILE* 3.8 3.1 - - - +
410D GLU* 1.3 73.1 - - + +
412D ALA* 1.3 53.1 + - - +
413D GLU 2.4 14.9 + - - -
414D ASP* 3.2 33.3 + - + +
419D VAL* 4.3 2.9 - - + -
420D ARG* 4.3 4.7 - - - -
423D ILE* 3.6 24.6 - - + +
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Residues in contact with ALA 412 (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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408D ILE 3.2 10.5 + - - +
409D VAL 3.2 19.3 - - - +
410D GLU 2.8 0.6 + - - -
411D LEU* 1.3 76.6 - - - +
413D GLU* 1.3 62.7 + - + +
420D ARG* 3.7 7.1 - - - +
423D ILE* 4.2 7.4 - - + +
446D LEU* 3.7 20.0 - - + -
450D TRP* 2.5 53.5 + - + +
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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