Contacts of the strand formed by residues 281 - 288 (chain A) in PDB entry 3NGN
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 ASP 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A CYS* 4.2 18.7 - - + -
200A LYS* 4.5 10.0 + - - -
201A TYR* 4.7 7.2 + - - -
240A GLU* 3.6 40.3 - - - +
241A VAL 3.2 13.9 - - - +
242A GLU* 4.2 1.8 - - - +
263A PHE* 4.5 0.2 - - - -
265A PRO* 4.1 1.6 - - - -
266A LYS* 2.9 59.0 + - - +
279A HIS 3.7 1.7 + - - +
280A VAL* 1.3 77.5 - - - +
282A GLY* 1.3 58.5 + - - +
360A HIS* 4.9 2.3 + - - -
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Residues in contact with GLY 282 (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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239A GLN 3.8 0.9 - - - -
240A GLU 3.1 24.3 + - - -
241A VAL* 2.8 15.9 + - - +
263A PHE* 3.6 8.9 - - - -
264A SER 3.2 15.7 - - - -
265A PRO* 3.8 1.3 - - - -
266A LYS* 4.2 4.7 - - - -
281A ASP* 1.3 75.4 - - - +
283A CYS* 1.3 63.9 + - - -
326A ILE* 4.3 4.5 - - - -
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Residues in contact with CYS 283 (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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238A LEU 3.3 3.6 - - - -
239A GLN* 4.2 11.2 - - - -
240A GLU 5.4 0.2 - - - -
262A PHE 3.9 0.3 - - - +
263A PHE* 3.4 3.6 - - - -
264A SER 3.1 29.4 + - - +
282A GLY* 1.3 77.7 - - - -
284A ALA* 1.3 60.3 + - - +
326A ILE* 4.2 17.4 - - + +
328A VAL* 3.9 24.3 - - + +
358A ASN* 3.7 12.6 - - - +
359A ALA* 4.2 7.2 - - - -
360A HIS* 4.1 35.0 - - - -
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Residues in contact with ALA 284 (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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236A ILE 3.6 0.6 - - - +
237A SER* 3.3 0.9 - - - -
238A LEU* 2.8 35.4 + - + -
241A VAL* 4.5 12.7 - - + +
246A TYR* 4.1 15.3 - - + -
262A PHE 3.1 12.6 - - - +
263A PHE* 4.2 6.7 - - + -
282A GLY 4.3 0.4 + - - -
283A CYS* 1.3 74.6 - - - +
285A ILE* 1.3 61.8 + - - +
286A PHE* 3.8 25.6 - - + -
358A ASN* 2.9 8.7 + - - -
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Residues in contact with ILE 285 (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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235A ILE* 4.2 4.9 - - + -
236A ILE 3.1 6.5 - - - +
237A SER* 4.1 3.8 - - - +
261A GLY* 3.2 2.8 - - - -
262A PHE* 2.8 33.8 + - + +
284A ALA* 1.3 79.5 - - - +
286A PHE* 1.3 72.8 + - - +
287A PHE* 4.9 5.1 - - + -
328A VAL* 3.7 24.9 - - + +
329A ALA* 4.2 4.9 - - - +
330A VAL* 4.1 26.8 - - + +
332A LEU* 5.8 0.2 - - + -
356A VAL* 3.4 45.1 - - + +
358A ASN* 3.6 23.1 - - + +
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Residues in contact with PHE 286 (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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235A ILE* 3.3 7.8 - - - +
236A ILE* 2.7 52.9 + - + +
238A LEU* 3.9 16.4 - - + -
246A TYR* 3.7 24.2 - + - -
250A PHE* 3.9 13.5 - - + -
251A LEU* 3.9 27.6 - - + -
254A LEU* 3.7 37.2 - - + -
259A TYR* 4.0 14.6 - - + -
260A ASP 3.3 10.3 - - - +
261A GLY* 3.7 13.9 - - - -
284A ALA* 3.8 16.8 - - + -
285A ILE* 1.3 76.1 - - - +
287A PHE* 1.3 64.8 + - - +
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Residues in contact with PHE 287 (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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234A ASP 3.2 10.1 - - - +
235A ILE* 4.2 15.7 - - + -
259A TYR* 3.2 6.6 - - - -
260A ASP* 2.9 64.0 + - + -
261A GLY* 4.4 6.7 - - - -
262A PHE* 6.2 0.7 - - + -
285A ILE* 4.9 3.8 - - + -
286A PHE* 1.3 78.9 - - - +
288A LYS* 1.3 60.2 + - - +
289A THR* 4.2 11.7 - - + -
292A PHE* 3.5 42.0 - - + -
293A THR* 4.6 0.2 - - - -
294A LEU* 3.6 36.3 - - + -
330A VAL* 5.3 6.7 - - + -
332A LEU* 3.9 21.1 - - + -
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Residues in contact with LYS 288 (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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232A ASP* 3.8 31.5 + - - -
233A ALA 4.0 0.8 + - - -
234A ASP* 3.0 43.1 + - - +
257A ARG 4.1 11.7 - - - +
258A GLY* 3.4 13.5 - - - +
259A TYR* 3.6 31.0 - - + -
287A PHE* 1.3 70.1 - - - +
289A THR* 1.3 60.9 + - - +
290A GLU* 4.5 10.8 - - + +
291A LYS* 2.9 25.7 + - + +
292A PHE* 2.9 29.0 + - + +
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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