Contacts of the strand formed by residues 285 - 291 (chain B) in PDB entry 1NSC
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 THR 285 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B PHE* 3.8 1.7 - - - -
281B ALA* 2.9 31.4 + - + -
282B SER* 3.2 19.4 + - - +
284B LYS* 1.3 88.7 + - - +
286B ILE* 1.3 77.1 - - - +
287B GLU* 3.9 17.3 - - + +
303B LYS* 4.6 10.8 - - + -
304B LEU 3.3 13.2 + - - +
305B ASN* 5.0 3.0 + - - -
306B VAL* 5.3 0.4 - - - -
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Residues in contact with ILE 286 (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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229B ASN* 4.0 13.2 - - + +
236B TYR* 3.7 42.8 - - + -
252B PHE* 5.5 1.1 - - + -
278B CYS* 3.9 24.0 - - + -
279B GLY* 3.3 11.9 - - - +
280B PHE* 3.5 31.2 - - + -
285B THR* 1.3 76.6 - - - +
287B GLU* 1.3 62.1 + - - +
288B CYS* 4.1 7.2 - - - -
302B VAL* 3.9 0.7 - - - +
303B LYS* 3.7 0.2 - - - -
304B LEU* 2.8 49.1 + - + +
306B VAL* 4.1 8.9 - - + +
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Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B CYS* 3.3 1.6 - - - -
279B GLY 2.9 30.4 + - - +
281B ALA* 3.7 20.6 - - + +
285B THR* 3.9 10.6 + - + +
286B ILE* 1.3 77.4 - - - +
288B CYS* 1.3 62.9 + - - +
301B PHE* 3.5 24.3 - - + -
302B VAL 3.2 9.6 - - - +
303B LYS* 4.6 10.4 - - + +
351B PHE* 3.6 6.0 - - + -
353B HIS* 2.8 28.5 + - + +
362B ARG* 2.8 42.8 + - - -
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Residues in contact with CYS 288 (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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252B PHE* 3.9 20.6 - - - -
276B CYS* 3.7 0.2 - - + -
277B THR 3.1 6.1 - - - +
278B CYS* 2.0 48.9 - - - -
286B ILE* 4.1 6.5 - - - -
287B GLU* 1.3 75.5 - - - +
289B ALA* 1.3 59.2 + - - +
290B CYS* 3.7 16.8 - - - -
300B PRO 3.7 1.0 - - - +
301B PHE* 3.2 10.3 - - - -
302B VAL* 3.0 39.0 + - + -
351B PHE* 4.0 4.0 - - - -
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Residues in contact with ALA 289 (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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275B GLU 4.2 0.9 - - - +
277B THR* 2.9 31.5 + - - +
288B CYS* 1.3 71.7 - - - +
290B CYS* 1.3 60.4 + - - +
299B ARG* 4.1 20.1 - - + -
300B PRO 3.7 4.0 - - - -
301B PHE* 4.4 8.1 - - + -
316B MET* 4.8 0.9 - - - -
349B GLY 4.4 5.8 + - - +
350B GLY 5.3 0.7 - - - +
351B PHE* 3.6 29.4 - - + -
364B TYR* 4.4 13.9 - - + -
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Residues in contact with CYS 290 (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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273B THR* 3.6 17.9 - - + -
274B GLU 3.6 7.2 - - - +
275B GLU 4.3 1.8 - - - -
276B CYS* 2.0 53.2 - - - +
288B CYS* 3.7 11.9 - - - -
289B ALA* 1.3 74.6 - - - +
291B ARG* 1.3 61.4 + - - +
299B ARG* 2.9 35.0 + - - +
300B PRO* 2.9 21.3 + - + +
302B VAL* 3.8 8.7 - - - -
348B LYS* 6.3 0.2 - - - -
349B GLY 5.9 0.4 - - - -
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Residues in contact with ARG 291 (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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273B THR* 3.8 3.6 - - - -
274B GLU* 2.9 57.9 + - + +
275B GLU* 2.9 31.7 + - + +
290B CYS* 1.3 73.3 - - - +
292B ASP* 1.3 65.6 + - - +
293B ASN* 2.8 27.5 + - - +
299B ARG* 3.7 5.2 - - - +
300B PRO* 4.0 3.1 - - - -
323B ASP* 4.5 1.6 - - - +
345B GLY* 5.3 0.2 - - - -
346B GLY* 3.2 21.8 + - - +
347B ILE* 3.6 25.9 - - - +
348B LYS* 4.8 0.9 - - - -
373B ARG* 3.9 0.6 - - - +
408B TYR* 2.9 24.5 + - - -
467B SIA 3.0 40.4 + - - -
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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