Contacts of the strand formed by residues 307 - 313 (chain B) 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 GLY 307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278B LEU 3.5 2.6 + - - -
279B LEU* 3.2 17.1 - - - +
280B MET* 2.9 23.6 + - - +
305B VAL* 3.4 9.6 - - - +
306B HIS* 1.3 80.7 - - - +
308B ILE* 1.3 65.0 + - - -
334B THR* 3.8 4.0 - - - -
335B MET* 3.2 17.7 - - - -
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Residues in contact with ILE 308 (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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279B LEU* 4.9 0.7 - - - -
280B MET* 3.7 20.4 - - + -
281B LEU* 4.0 20.2 - - + -
288B LEU* 3.9 19.5 - - + -
292B ALA* 3.9 4.3 - - + -
296B LEU* 3.8 20.0 - - + -
307B GLY* 1.3 76.2 - - - -
309B ALA* 1.3 60.2 + - - +
310B VAL* 4.0 3.1 + - + -
327B THR* 3.6 28.9 - - + -
331B PHE* 5.2 1.6 - - + -
334B THR* 3.8 19.5 - - + +
335B MET* 2.8 8.4 + - - +
336B LEU* 3.5 23.8 - - + +
337B PHE* 2.9 28.1 + - - +
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Residues in contact with ALA 309 (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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231B THR* 4.2 3.8 - - + -
279B LEU* 4.1 20.6 - - + +
280B MET 2.8 13.3 + - - +
281B LEU* 3.4 12.1 - - - +
282B ASP* 2.8 41.5 + - + +
307B GLY 4.1 1.2 - - - -
308B ILE* 1.3 71.3 - - - +
310B VAL* 1.3 60.7 + - - +
337B PHE* 3.2 7.6 - - + +
339B SER* 3.5 22.2 - - - +
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Residues in contact with VAL 310 (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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281B LEU* 4.2 1.8 - - + -
283B ASP 3.5 6.7 - - - +
285B ARG* 4.5 15.7 - - + +
288B LEU* 3.7 29.6 - - + -
308B ILE* 4.1 10.5 - - + +
309B ALA* 1.3 79.0 - - - +
311B HIS* 1.3 67.5 + - - +
312B TRP* 6.2 0.2 - - + -
324B LEU* 4.2 20.2 - - + -
336B LEU* 4.2 6.3 - - + -
337B PHE 2.8 20.2 + - - +
338B ALA* 3.4 16.4 - - + +
339B SER* 2.9 23.8 + - - -
340B GLU 3.8 0.7 + - - +
370B ASN* 4.5 6.3 - - - +
375B VAL* 5.3 1.3 - - + -
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Residues in contact with HIS 311 (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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120B ARG* 3.7 3.0 + - - -
234B ASN* 3.1 26.7 - - - -
235B GLU* 2.9 27.5 + - + +
282B ASP* 2.6 40.5 + - - -
283B ASP* 2.9 16.6 + - - +
284B GLN* 3.6 1.6 - - - +
285B ARG* 3.5 22.0 + - - +
310B VAL* 1.3 77.1 - - - +
312B TRP* 1.3 69.2 + - - +
313B TYR* 4.4 7.9 - - + -
338B ALA* 6.4 0.2 - - - -
339B SER* 3.1 20.3 + - - -
340B GLU* 3.2 35.7 + - + +
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Residues in contact with TRP 312 (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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284B GLN* 3.8 27.8 - - + -
285B ARG* 3.8 45.1 - - + +
286B LEU* 4.3 9.4 - - + -
310B VAL* 4.3 0.6 + - + -
311B HIS* 1.3 81.7 - - - +
313B TYR* 1.3 92.3 + + + +
314B LEU* 3.7 26.4 + - + -
316B PHE* 2.8 42.7 + + + -
317B LEU 3.2 29.2 - - - -
318B ALA* 3.4 16.0 - - + +
338B ALA* 6.3 0.4 - - - +
340B GLU 3.0 8.3 + - - +
341B ALA* 3.1 27.7 - - + +
342B CYS 3.2 4.3 + - - -
366B SER* 5.4 1.6 - - - +
370B ASN* 6.0 0.9 - - - +
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Residues in contact with TYR 313 (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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235B GLU* 2.4 36.4 + - - -
244B TYR* 5.6 0.2 + - - -
284B GLN* 5.1 8.3 - - + -
311B HIS* 4.4 11.7 - - + -
312B TRP* 1.3 106.5 + + + +
314B LEU* 1.3 58.0 + - - +
315B ASP 3.0 4.3 - - - -
316B PHE* 2.9 40.8 + + + +
340B GLU* 3.7 6.9 + - - -
342B CYS* 3.7 25.8 - - - -
345B SER* 3.7 22.7 - - - +
506B GOL 3.2 26.0 - - - -
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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