Contacts of the strand formed by residues 468 - 474 (chain D) in PDB entry 2NT0
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 VAL 468 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D LEU* 4.2 12.8 - - + -
442D ASN* 5.7 2.2 - - + -
443D ASP* 5.5 8.3 - - + +
444D LEU* 4.0 35.9 - - + -
462D ASN* 3.9 7.6 - - - +
464D SER* 4.7 5.4 - - - +
466D LYS* 3.6 15.5 - - + +
467D ASP* 1.3 79.0 - - - +
469D PRO* 1.3 76.6 - - + +
470D LEU* 3.2 4.3 - - - +
483D ILE* 4.1 1.6 - - - -
484D SER 2.8 35.5 + - - +
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Residues in contact with PRO 469 (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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64D GLY* 5.1 6.1 - - - -
65D LEU* 4.0 13.1 + - - +
467D ASP* 3.8 7.9 - - + +
468D VAL* 1.3 94.3 - - + +
470D LEU* 1.3 62.8 + - - +
482D THR 3.8 8.5 - - - +
483D ILE* 4.2 15.2 - - + -
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Residues in contact with LEU 470 (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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64D GLY 5.6 0.2 - - - -
65D LEU* 3.4 25.4 - - + +
67D LEU* 3.6 31.0 - - + -
444D LEU* 4.1 11.9 - - + -
460D VAL* 4.6 9.0 - - + -
468D VAL 3.2 25.1 - - - +
469D PRO* 1.3 74.0 - - - +
471D THR* 1.3 65.1 + - - +
472D ILE* 4.3 15.3 - - + -
481D GLU* 3.9 0.2 - - - -
482D THR* 2.8 53.1 + - + +
484D SER* 3.5 25.6 - - - +
492D TYR* 5.7 0.7 - - + -
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Residues in contact with THR 471 (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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60D HIS* 3.0 32.6 + - + -
64D GLY 6.0 0.2 - - - -
65D LEU 3.0 7.3 + - - -
66D LEU* 3.3 13.9 - - + +
67D LEU* 2.8 26.7 + - - +
470D LEU* 1.3 79.5 + - - +
472D ILE* 1.3 65.6 + - - +
473D LYS 4.0 0.2 - - - -
479D PHE* 3.7 39.5 - - + -
480D LEU 3.1 10.3 - - - +
481D GLU* 3.9 9.5 - - + +
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Residues in contact with ILE 472 (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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67D LEU* 3.2 18.4 - - + +
69D LEU* 5.1 1.6 - - + +
436D LEU* 4.8 7.4 - - + -
458D VAL* 4.3 21.1 - - + -
460D VAL* 4.6 1.3 - - + -
470D LEU* 4.3 17.9 - - + -
471D THR* 1.3 78.0 - - - +
473D LYS* 1.3 68.2 + - - +
474D ASP 3.9 0.2 + - - -
478D GLY 3.7 0.7 - - - +
479D PHE* 3.3 3.8 - - - -
480D LEU* 2.8 51.4 + - + +
482D THR* 4.9 4.0 - - + -
492D TYR* 4.0 37.0 - - + -
494D TRP* 3.9 25.6 - - + -
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Residues in contact with LYS 473 (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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66D LEU* 3.8 23.1 - - + +
67D LEU 2.8 8.7 + - - -
68D THR* 3.5 27.7 - - + +
69D LEU* 2.8 32.7 + - - +
471D THR 4.0 1.0 - - - -
472D ILE* 1.3 73.5 - - - +
474D ASP* 1.3 66.2 + - - +
475D PRO* 4.0 19.8 - - - +
478D GLY 3.6 4.5 - - - +
479D PHE* 3.8 33.0 - - + -
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Residues in contact with ASP 474 (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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69D LEU* 3.5 11.3 - - + +
472D ILE 3.9 1.0 + - - -
473D LYS* 1.3 75.7 - - - +
475D PRO* 1.3 63.5 - - - +
476D ALA* 3.0 4.0 + - - +
477D VAL* 2.8 24.6 + - + +
478D GLY* 2.8 38.9 + - - +
480D LEU* 5.5 1.3 - - + -
494D TRP* 2.8 37.5 + - + +
496D ARG* 2.8 45.0 + - - +
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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