Contacts of the strand formed by residues 274 - 280 (chain A) 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 GLU 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A ARG* 2.8 19.4 + - - +
238A MET* 4.0 4.5 - - - -
240A THR* 3.6 18.6 - - + -
272A HIS* 3.7 12.6 - - - +
273A THR* 1.3 76.3 - - - +
275A GLU* 1.3 70.2 + - + +
276A CYS 3.1 4.4 + - - -
290A CYS* 3.4 1.9 - - - +
291A ARG* 2.8 61.8 + - + +
293A ASN* 3.3 14.2 - - - +
467A SIA 2.6 43.8 + - - -
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ARG* 6.2 3.1 - - + +
223A THR 4.3 15.4 + - - +
224A GLN* 3.8 13.5 - - - +
225A GLU* 4.0 9.1 - - + +
238A MET* 3.8 8.1 - - - +
240A THR* 5.1 0.2 - - - +
274A GLU* 1.3 77.8 - - + +
276A CYS* 1.3 66.2 + - - +
277A THR* 3.4 1.7 + - - -
289A ALA 4.2 0.5 - - - +
290A CYS* 4.2 5.5 - - - -
291A ARG* 2.7 36.9 + - + -
348A LYS* 3.3 34.9 + - + +
349A GLY 5.1 0.2 + - - -
408A TYR* 2.8 31.1 + - - -
467A SIA 3.6 23.8 + - - +
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Residues in contact with CYS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLN* 3.4 19.8 - - - +
226A SER* 3.5 0.9 + - - -
238A MET* 3.3 38.8 - - + +
252A PHE* 4.7 0.4 - - - -
273A THR* 3.4 10.5 - - - -
274A GLU 3.1 2.2 + - - -
275A GLU* 1.3 75.6 - - - +
277A THR* 1.3 58.0 + - - +
278A CYS* 3.7 19.3 - - - -
288A CYS* 4.2 2.9 - - - -
290A CYS* 2.0 48.7 - - - -
302A VAL* 4.2 5.4 - - - -
348A LYS* 3.1 10.9 + - - -
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Residues in contact with THR 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A SER* 3.8 9.2 - - - +
275A GLU 3.4 0.7 + - - -
276A CYS* 1.3 71.9 - - - +
278A CYS* 1.3 62.2 + - - +
288A CYS* 3.1 2.9 - - - -
289A ALA 3.0 32.9 + - - -
348A LYS* 2.8 25.6 + - - +
349A GLY 2.8 27.5 + - - +
351A PHE* 3.4 22.3 - - - +
410A PHE* 3.9 4.0 - - + -
411A GLY* 3.4 31.6 - - - +
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Residues in contact with CYS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLN* 4.0 22.4 - - - +
226A SER* 4.7 1.0 + - - -
227A ALA* 4.5 4.6 + - - +
229A ASN* 2.9 27.7 + - - +
236A TYR 6.2 0.2 - - - +
252A PHE* 4.2 7.4 - - - -
276A CYS* 3.7 14.5 + - - -
277A THR* 1.3 77.6 - - - +
279A GLY* 1.3 58.8 + - - +
286A ILE* 4.0 8.3 - - + -
287A GLU 3.3 4.7 - - - +
288A CYS* 2.0 45.8 - - - -
351A PHE* 5.2 4.8 - - - +
411A GLY 5.5 3.3 - - - +
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Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ASN* 3.6 12.3 - - - -
278A CYS* 1.3 76.1 - - - +
280A PHE* 1.3 63.6 + - - -
286A ILE* 3.4 6.4 - - - -
287A GLU 2.9 31.8 + - - +
351A PHE* 4.8 0.8 - - - -
352A VAL* 6.3 1.3 - - - -
353A HIS* 3.4 15.6 - - - -
413A GLU* 5.2 4.7 - - - -
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Residues in contact with PHE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PRO* 3.6 36.6 - - + -
229A ASN* 3.7 31.8 - - + +
230A CYS 3.5 31.2 - - - -
231A ILE* 3.6 31.0 - - + -
279A GLY* 1.3 71.2 - - - -
281A ALA* 1.3 60.4 + - - +
282A SER 3.6 19.1 - - - +
283A ASN 5.4 0.7 - - - -
285A THR 3.6 2.9 - - - -
286A ILE* 3.4 26.9 - - + -
306A VAL* 4.7 2.7 - - + -
353A HIS* 3.4 10.0 + - - -
355A ARG* 2.9 31.0 + - - +
413A GLU* 4.7 2.9 + - - -
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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