Contacts of the strand formed by residues 319 - 327 (chain B) 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 319 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A LYS 5.4 3.6 - - - -
218A THR 2.9 16.6 + - - +
219A PHE* 3.8 30.5 - + + -
220A TYR* 2.9 25.6 + - - +
311B TYR* 4.7 0.7 + - - -
317B LYS* 3.5 12.8 + - + -
318B THR* 1.3 76.6 - - - +
320B TYR* 1.4 60.1 + - - +
419C PHE* 3.4 44.4 - + + -
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Residues in contact with TYR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A THR* 4.8 3.7 - - + +
219A PHE* 5.9 0.7 - - - -
220A TYR* 3.4 17.5 - + - -
222A ASN* 5.8 5.1 + - + -
307B GLU* 4.0 18.0 + - - -
309B THR* 4.6 14.0 + - + +
311B TYR* 3.4 52.9 - + + -
318B THR* 5.3 1.3 - - + -
319B PHE* 1.4 75.1 - - - +
321B TYR* 1.3 64.9 + - - +
322B ASN* 3.5 33.3 + - + +
407C GLU* 6.0 0.2 - - - -
409C THR* 5.2 3.1 + - - +
411C TYR* 5.3 1.1 - - - +
419C PHE* 2.9 13.3 + - - +
420C TYR* 3.1 50.1 + + + -
421C TYR* 2.9 27.4 + - - +
422C ASN* 5.1 0.3 + - - -
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Residues in contact with TYR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A PHE* 5.2 5.2 - - + -
220A TYR 2.8 11.0 + - - +
221A TYR* 3.7 40.4 - + + -
222A ASN* 2.8 27.8 + - - +
320B TYR* 1.3 77.4 - - - +
322B ASN* 1.3 59.8 + - - +
323B ASN* 4.3 14.4 + - + -
421C TYR* 3.2 68.6 + + + -
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Residues in contact with ASN 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ASN* 3.4 16.4 + - + +
307B GLU* 3.6 24.0 + - - +
320B TYR* 3.5 26.2 + - + +
321B TYR* 1.3 72.6 - - - +
323B ASN* 1.3 69.1 + - - +
324B ARG* 3.7 25.5 + - - +
407C GLU* 3.6 3.4 + - - -
421C TYR* 2.8 17.4 + - - +
422C ASN* 3.2 34.2 + - - +
423C ASN 3.2 20.1 + - - -
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Residues in contact with ASN 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A TYR* 5.4 0.7 - - + -
222A ASN 3.2 5.1 + - - +
223A ASN* 2.7 53.8 + - + +
224A ARG 3.2 16.6 + - - +
321B TYR* 4.3 16.4 + - + -
322B ASN* 1.3 79.2 + - - +
324B ARG* 1.3 59.5 + - - +
325B THR* 4.2 11.0 + - - -
421C TYR* 4.5 4.2 + - - -
423C ASN* 2.8 35.9 + - - +
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Residues in contact with ARG 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A VAL* 4.0 8.1 - - - +
207A GLU* 2.9 37.4 + - - +
222A ASN* 4.6 6.0 + - - +
224A ARG* 3.8 21.4 - - - +
305B VAL* 3.4 37.7 - - + +
306B SER 2.8 27.9 + - - -
307B GLU* 3.1 26.1 - - + +
322B ASN* 3.7 20.7 + - - +
323B ASN* 1.3 72.3 - - - +
325B THR* 1.4 64.5 + - - +
326B LEU* 4.8 2.0 - - + -
407C GLU* 5.7 0.7 - - - +
423C ASN 2.9 8.5 + - - +
424C ARG* 3.8 27.6 - - + -
425C THR* 2.9 27.9 + - - -
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Residues in contact with THR 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ASN* 5.0 0.3 + - - -
224A ARG 3.4 7.3 + - - +
225A THR* 3.4 23.8 - - + +
226A LEU* 2.8 31.0 + - - +
323B ASN* 4.3 14.2 + - - -
324B ARG* 1.4 77.5 + - - +
326B LEU* 1.3 66.9 + - - +
327B GLU* 4.0 5.4 - - + +
425C THR* 3.2 24.8 + - + -
427C GLU* 4.5 11.0 - - - +
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU* 3.9 8.1 - - + -
303B THR* 3.5 30.1 - - + +
304B ALA* 3.6 1.6 - - - -
305B VAL* 3.4 44.9 - - + +
324B ARG* 4.8 2.0 - - + -
325B THR* 1.3 84.3 - - - +
327B GLU* 1.3 62.2 + - - +
403C THR* 4.3 2.4 - - + +
404C ALA 3.3 32.5 - - - +
405C VAL* 3.5 10.3 - - + -
425C THR 2.9 20.0 + - - +
426C LEU* 3.7 6.4 - - + -
427C GLU* 3.3 25.6 + - - +
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Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU 3.0 22.2 + - - +
227A GLU* 3.5 18.4 - - + -
228A SER* 3.5 2.5 + - - -
229A THR* 2.5 43.3 + - - -
230A TRP 3.0 14.7 + - - -
303B THR* 2.5 29.4 + - - +
325B THR* 4.0 6.5 - - + +
326B LEU* 1.3 73.3 - - - +
328B SER* 1.3 55.6 + - - +
329B THR* 2.4 36.3 + - + +
427C GLU* 3.9 13.2 - - - +
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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