Contacts of the strand formed by residues 502 - 515 (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 ALA 502 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C GLY 3.3 6.4 + - - +
402C ALA* 3.2 13.9 - - + -
403C THR 3.1 13.5 + - - -
428C SER* 2.4 22.7 + - - -
501D GLY* 1.4 70.5 - - - -
503D THR* 1.3 57.6 + - - +
528D SER* 3.7 5.2 - - - -
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Residues in contact with THR 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C THR 3.4 2.9 - - - -
426C LEU* 3.0 23.6 - - - +
428C SER* 3.4 6.0 + - - -
502D ALA* 1.3 78.8 - - - +
504D ALA* 1.4 60.8 + - - +
526D LEU* 3.7 23.6 - - + +
527D GLU 2.9 21.6 + - - -
528D SER* 3.5 27.5 + - - +
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Residues in contact with ALA 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C THR 3.1 8.3 + - - +
404C ALA* 3.2 17.1 - - + +
405C VAL* 3.0 27.5 + - - +
426C LEU* 4.1 0.3 - - - +
503D THR* 1.4 75.8 - - - +
505D VAL* 1.4 64.6 + - - +
506D SER* 4.1 5.3 + - - +
526D LEU* 3.5 8.2 - - - +
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Residues in contact with VAL 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C VAL* 3.6 15.9 - - + -
424C ARG* 4.0 6.7 - - - +
426C LEU* 5.2 0.2 - - + -
504D ALA* 1.4 76.3 - - - +
506D SER* 1.3 69.2 + - - +
507D GLU* 3.8 21.1 - - + +
524D ARG* 3.8 27.4 - - + -
526D LEU* 3.4 27.2 - - + +
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Residues in contact with SER 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C ALA* 5.1 1.6 - - - +
405C VAL 2.5 45.9 + - - +
406C SER* 3.9 8.6 + - - -
407C GLU* 3.4 14.0 + - - +
408C TRP* 5.5 0.3 - - - -
424C ARG* 6.0 0.2 - - - -
504D ALA* 4.1 9.1 + - - +
505D VAL* 1.3 87.6 - - - +
507D GLU* 1.4 57.2 + - - +
508D TRP* 4.1 20.1 - - - -
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Residues in contact with GLU 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C GLU* 3.6 4.9 - - - +
424C ARG* 2.9 40.5 + - - +
505D VAL* 3.8 9.3 - - + +
506D SER* 1.4 73.0 - - - +
508D TRP* 1.4 68.8 + - - +
509D THR* 3.5 23.7 + - + +
522D ASN* 2.9 28.6 + - - +
524D ARG* 2.8 33.0 + - - -
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Residues in contact with TRP 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C GLU 3.2 7.3 + - - -
408C TRP* 3.4 72.6 - + + -
409C THR 2.9 35.2 + - - +
506D SER* 4.1 16.4 - - - -
507D GLU* 1.4 85.3 - - - +
509D THR* 1.4 59.4 + - - +
510D GLU 3.7 1.1 + - - -
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Residues in contact with THR 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C GLU* 3.9 19.5 - - - +
409C THR* 4.0 9.2 - - + -
422C ASN* 6.0 0.2 - - - +
424C ARG* 4.1 1.3 - - - +
507D GLU* 3.5 37.8 + - + +
508D TRP* 1.4 74.6 - - - +
510D GLU* 1.3 59.9 + - - +
511D TYR* 3.4 31.3 + - - -
520D TYR* 4.4 8.5 - - - +
522D ASN* 4.8 0.7 - - - +
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Residues in contact with GLU 510 (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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409C THR 3.2 9.0 + - - +
410C GLU* 3.8 25.9 - - + +
411C TYR* 3.0 28.4 + - - +
508D TRP 3.7 2.5 + - - +
509D THR* 1.3 68.2 - - - +
511D TYR* 1.3 60.3 + - - +
512D LYS* 5.5 6.3 - - + +
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Residues in contact with TYR 511 (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* 3.5 28.9 - - + -
509D THR* 3.4 28.8 + - - -
510D GLU* 1.3 72.7 + - - +
512D LYS* 1.3 60.7 + - - +
513D THR* 4.1 7.3 + - - +
518D THR* 6.0 4.7 - - + -
520D TYR* 3.3 59.4 + + + -
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Residues in contact with LYS 512 (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* 3.3 12.6 + - - +
412C LYS* 3.7 25.5 - - + +
413C THR* 3.0 25.7 + - - +
510D GLU* 5.5 7.2 - - + +
511D TYR* 1.3 72.5 - - - +
513D THR* 1.3 88.1 + - - +
514D ALA* 4.0 13.0 + - + +
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Residues in contact with THR 513 (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* 6.2 1.3 - - + -
413C THR* 3.1 22.0 - - + -
414C ALA 3.8 10.3 - - - +
416C GLY* 3.8 29.4 - - - +
418C THR* 6.1 0.2 - - - -
511D TYR* 4.1 8.2 + - - -
512D LYS* 1.3 97.7 + - - +
514D ALA* 1.3 59.6 + - - +
515D ASP 3.4 3.1 + - - +
516D GLY* 3.9 13.5 + - - -
518D THR* 3.4 24.4 + - + +
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Residues in contact with ALA 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C THR 3.1 4.8 + - - +
414C ALA* 3.0 27.8 + - + +
512D LYS* 4.0 16.5 + - + +
513D THR* 1.3 73.3 - - - +
515D ASP* 1.3 59.4 + - + +
516D GLY 4.2 0.5 + - - -
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Residues in contact with ASP 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C ALA 2.7 13.0 + - - +
415C ASP* 4.2 18.4 - - - +
416C GLY* 2.8 21.1 + - - -
513D THR* 4.3 1.3 - - - -
514D ALA* 1.3 71.0 - - + +
516D GLY* 1.3 53.3 + - - +
517D LYS* 2.7 37.3 + - - +
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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