Contacts of the strand formed by residues 402 - 415 (chain C) 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 402 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301B GLY 3.6 3.0 + - - +
302B ALA* 3.2 18.8 - - - +
303B THR 3.3 8.8 + - - +
400C MET* 3.6 29.3 - - + +
401C GLY* 1.3 79.2 - - - +
403C THR* 1.3 65.3 + - - +
428C SER* 3.8 3.8 - - - -
502D ALA* 3.2 27.4 - - + +
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Residues in contact with THR 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B THR* 3.3 28.5 - - - +
326B LEU* 4.3 4.3 - - + +
328B SER* 3.5 11.2 - - - +
402C ALA* 1.3 81.9 - - - +
404C ALA* 1.3 60.4 + - - +
426C LEU* 3.2 15.6 - - - +
427C GLU 3.2 43.7 + - - +
428C SER* 2.6 22.5 + - - +
502D ALA 3.1 0.2 + - - -
503D THR* 3.4 4.7 - - - -
504D ALA 3.1 19.9 + - - -
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Residues in contact with ALA 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B THR 3.6 5.3 + - - -
304B ALA* 4.1 3.7 - - + +
305B VAL 3.5 12.8 + - - +
326B LEU* 3.3 15.9 - - - +
402C ALA* 6.4 0.2 - - + -
403C THR* 1.3 77.1 - - - +
405C VAL* 1.3 64.4 + - - +
406C SER* 4.1 4.6 + - - +
426C LEU* 4.4 1.3 - - - -
504D ALA* 3.2 25.6 - - + +
506D SER* 5.1 2.2 - - - +
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Residues in contact with VAL 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B VAL* 3.7 9.9 - - + -
326B LEU* 3.5 31.4 - - + -
404C ALA* 1.3 71.2 - - - +
406C SER* 1.4 50.9 + - - +
407C GLU* 3.4 4.8 + - + +
424C ARG* 4.0 27.5 - - + -
425C THR 4.5 2.2 - - - +
426C LEU* 3.5 31.0 - - + -
504D ALA 3.0 16.0 + - - +
505D VAL* 3.6 19.5 - - + -
506D SER* 2.5 38.4 + - - +
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Residues in contact with SER 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B VAL* 3.3 20.3 + - - +
306B SER* 3.3 13.6 - - - -
307B GLU 3.1 22.8 + - - +
308B TRP* 5.4 0.9 + - - -
404C ALA* 5.0 5.2 + - - +
405C VAL* 1.4 71.3 + - - +
407C GLU* 1.3 63.0 + - - +
408C TRP* 4.5 8.6 - - - -
506D SER* 3.9 10.0 + - - -
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Residues in contact with GLU 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B VAL* 6.4 1.1 - - + -
306B SER 5.0 0.2 - - - -
307B GLU* 3.9 27.1 - - + +
320B TYR* 6.0 0.2 - - - -
322B ASN* 3.6 10.7 + - - -
324B ARG* 5.7 0.7 - - - +
405C VAL 3.4 4.8 + - - +
406C SER* 1.3 77.1 - - - +
408C TRP* 1.3 65.8 + - - +
409C THR* 3.9 16.1 + - - +
420C TYR* 4.9 0.7 + - - -
422C ASN* 2.7 26.9 + - - -
424C ARG* 2.6 49.8 + - - +
506D SER 3.4 8.8 + - - +
507D GLU* 4.3 0.8 - - - +
508D TRP 3.2 19.8 + - - -
509D THR* 3.9 13.9 - - - +
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Residues in contact with TRP 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B GLU 3.1 18.5 + - - +
308B TRP* 4.6 15.5 - + + -
309B THR* 3.0 23.1 + - - +
406C SER* 4.5 10.8 - - - -
407C GLU* 1.3 82.1 - - - +
409C THR* 1.3 66.8 + - - +
506D SER 5.5 0.2 - - - -
508D TRP* 3.4 60.1 - + + -
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Residues in contact with THR 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLU* 5.4 0.7 + - - -
309B THR* 3.4 29.3 + - + -
320B TYR* 5.2 3.4 + - - +
407C GLU* 3.9 21.8 + - - +
408C TRP* 1.3 81.2 + - - +
410C GLU* 1.4 58.4 + - - +
411C TYR* 4.2 25.8 - - + +
420C TYR* 5.0 15.1 + - + +
508D TRP 2.9 25.0 + - - +
509D THR* 3.9 7.3 - - + -
510D GLU* 3.2 18.9 + - - +
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Residues in contact with GLU 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B THR 2.9 12.4 + - - +
310B GLU* 3.4 8.0 - - + +
311B TYR 3.1 23.4 + - - -
312B LYS* 3.5 28.1 + - - +
409C THR* 1.4 69.5 - - - +
411C TYR* 1.3 60.2 - - - +
510D GLU* 3.8 24.8 - - + +
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Residues in contact with TYR 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B TYR* 3.5 39.0 - + + -
312B LYS* 5.0 0.2 - - - -
318B THR* 5.0 3.1 - - - +
320B TYR* 5.3 1.8 - + + +
409C THR* 3.7 14.3 + - + -
410C GLU* 1.3 72.7 - - - +
412C LYS* 1.4 60.6 + - - +
413C THR* 3.0 26.0 - - - -
418C THR* 2.9 28.5 - - + +
419C PHE 4.2 2.6 + - - -
420C TYR* 3.6 47.7 - + + +
510D GLU* 3.0 20.7 + - - +
511D TYR* 3.9 22.7 - - + -
512D LYS* 3.3 18.2 + - - +
513D THR* 6.2 1.3 - - + -
518D THR* 6.4 2.0 - - + -
520D TYR* 5.8 3.8 - + - -
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Residues in contact with LYS 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B TYR 2.9 16.0 + - - +
312B LYS* 3.7 25.5 - - + +
313B THR 3.3 18.0 + - - +
314B ALA* 5.2 0.7 - - - -
411C TYR* 1.4 75.3 - - - +
413C THR* 1.3 73.2 + - - +
512D LYS* 3.7 31.6 - - + +
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Residues in contact with THR 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B THR 3.3 11.0 + - - +
314B ALA* 3.6 9.4 - - - +
411C TYR* 3.0 34.2 + - - -
412C LYS* 1.3 80.6 + - - +
414C ALA* 1.3 60.0 + - - +
415C ASP 3.5 24.5 - - - +
418C THR* 3.5 25.0 - - + +
512D LYS* 3.0 18.6 + - - +
513D THR* 3.1 25.0 - - + -
514D ALA* 3.1 3.3 + - - +
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Residues in contact with ALA 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ALA* 2.7 35.6 + - + +
413C THR* 1.3 71.6 - - - +
415C ASP* 1.4 70.1 + - - +
513D THR* 3.8 1.5 - - - +
514D ALA* 3.0 21.0 + - + -
515D ASP* 2.7 32.6 + - - +
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Residues in contact with ASP 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B ALA 3.3 3.1 + - - +
315B ASP* 5.2 2.3 - - - -
316B GLY* 3.1 33.4 + - - +
413C THR* 3.5 8.6 - - - +
414C ALA* 1.4 89.2 - - - +
416C GLY* 1.4 63.3 + - - +
417C LYS* 3.0 5.5 + - + +
418C THR 3.4 2.4 + - - -
515D ASP* 3.9 19.3 - - - +
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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