Contacts of the strand formed by residues 519 - 527 (chain D) in PDB entry 2NNT
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 519 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416C GLY 3.4 8.4 + - - -
417C LYS* 4.0 24.5 - - + -
418C THR* 3.5 18.4 + - - +
419C PHE* 3.1 48.0 - + + -
420C TYR* 3.1 29.1 + - - +
517D LYS 4.4 6.5 - - - -
518D THR* 1.3 79.0 - - - +
520D TYR* 1.3 57.8 + - - +
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Residues in contact with TYR 520 (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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411C TYR* 5.8 3.1 - + - -
420C TYR* 3.0 48.1 + + + -
507D GLU* 5.1 0.2 + - - -
509D THR* 4.4 8.1 + - - +
511D TYR* 3.3 60.4 + + + -
518D THR* 3.6 21.2 + - + -
519D PHE* 1.3 71.3 - - - +
521D TYR* 1.3 57.6 + - - +
522D ASN* 3.6 39.7 + - + +
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Residues in contact with TYR 521 (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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420C TYR* 3.1 16.0 + - - +
421C TYR* 3.4 47.9 - + + -
422C ASN* 2.8 36.9 + - - +
423C ASN* 4.8 3.1 + - - -
520D TYR* 1.3 70.0 - - - +
522D ASN* 1.3 58.9 + - - +
523D ASN* 3.6 36.4 - - + +
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Residues in contact with ASN 522 (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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420C TYR* 5.7 0.2 - - - -
422C ASN* 3.3 13.6 - - + +
424C ARG* 3.7 14.6 - - - +
507D GLU* 2.9 22.0 + - - -
509D THR* 4.8 1.6 - - - +
520D TYR* 3.6 35.3 + - + +
521D TYR* 1.3 78.3 - - - +
523D ASN* 1.4 61.5 + - - +
524D ARG* 3.3 28.2 + - - -
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Residues in contact with ASN 523 (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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422C ASN* 2.9 7.8 + - - +
423C ASN* 2.8 25.2 + - - +
424C ARG* 3.0 35.3 + - - +
521D TYR* 3.6 28.5 - - + +
522D ASN* 1.4 76.0 - - - +
524D ARG* 1.3 74.7 + - - +
525D THR* 2.8 27.4 + - - +
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Residues in contact with ARG 524 (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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424C ARG* 3.6 11.0 - - + +
426C LEU* 5.6 1.6 - - + -
505D VAL* 3.8 35.2 - - + +
507D GLU* 2.8 33.3 + - - -
522D ASN* 3.3 18.8 + - - -
523D ASN* 1.3 83.8 + - - +
525D THR* 1.4 59.0 + - - +
526D LEU* 4.3 10.9 + - + +
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Residues in contact with THR 525 (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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423C ASN* 4.7 0.2 + - - -
424C ARG 2.9 11.4 + - - -
425C THR* 3.3 19.4 + - + -
426C LEU* 3.1 30.8 + - - +
523D ASN* 2.8 22.7 + - - -
524D ARG* 1.4 68.8 - - - +
526D LEU* 1.3 58.6 + - - +
527D GLU* 4.7 15.9 - - + +
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Residues in contact with LEU 526 (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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426C LEU* 3.6 21.1 - - + -
503D THR* 3.6 18.4 - - + +
504D ALA* 3.5 20.4 - - - +
505D VAL* 3.4 41.1 - - + +
524D ARG* 4.3 15.5 + - + +
525D THR* 1.3 78.1 - - - +
527D GLU* 1.4 68.0 + - - +
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Residues in contact with GLU 527 (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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426C LEU 3.2 10.8 + - - +
427C GLU* 3.6 11.4 - - + -
428C SER 3.2 19.4 + - - -
503D THR* 2.9 16.1 + - - -
525D THR* 4.7 13.1 - - + +
526D LEU* 1.4 85.1 + - - +
528D SER* 1.4 57.4 + - - +
529D THR* 3.2 10.0 + - - +
530D TRP* 3.4 33.6 + - + +
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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