Contacts of the strand formed by residues 286 - 293 (chain A) in PDB entry 2EC8
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 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A ASP 3.6 1.3 + - - -
285A SER* 1.3 74.1 - - - +
287A VAL* 1.3 65.0 + - - -
288A PHE* 3.8 9.6 + - - -
304A THR* 4.6 1.1 - - - -
305A LEU* 3.0 33.5 + - - +
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Residues in contact with VAL 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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247A LYS 3.6 0.7 - - - +
249A GLU* 3.2 56.3 + - + +
286A GLY* 1.3 75.1 - - - -
288A PHE* 1.3 61.3 + - - +
289A MET 3.8 0.3 + - - -
302A THR* 2.7 31.4 - - - +
303A THR 3.7 3.1 - - - +
304A THR* 3.7 25.6 - - + +
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Residues in contact with PHE 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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229A PHE* 3.4 42.2 - + + -
246A TRP* 3.5 15.9 - + + -
247A LYS 4.0 1.6 - - - -
248A ARG* 3.7 35.4 - - + -
275A LEU* 4.7 16.4 - - + -
277A ILE* 4.4 13.2 - - + -
284A ASP 5.0 11.0 - - - -
286A GLY 4.1 13.0 - - - -
287A VAL* 1.3 73.2 - - - +
289A MET* 1.3 60.2 + - - +
302A THR* 4.6 0.2 - - - -
303A THR* 2.9 50.7 + - + +
305A LEU* 4.2 20.2 - - + -
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Residues in contact with MET 289 (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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245A THR 3.6 0.2 - - - +
246A TRP* 3.2 7.6 - - - -
247A LYS* 3.0 45.4 + - + +
249A GLU* 3.8 29.2 - - + +
287A VAL 3.8 0.4 + - - -
288A PHE* 1.3 74.6 - - - +
290A CYS* 1.3 71.0 + - - +
291A TYR* 3.6 12.5 + - + +
300A ASN* 3.5 33.9 - - + +
301A VAL 3.7 5.8 - - - +
302A THR* 4.4 9.2 - - - +
800A NAG 4.9 15.3 - - + +
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Residues in contact with CYS 290 (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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214A VAL* 3.6 14.4 - - + +
216A VAL* 4.6 3.4 - - + -
233A CYS* 2.1 47.8 - - + -
235A ILE* 4.2 9.4 - - - -
244A SER* 5.4 0.4 - - - -
245A THR 3.7 9.4 - - - -
246A TRP* 3.6 16.5 - - + -
289A MET* 1.3 74.9 - - - +
291A TYR* 1.3 58.5 + - - +
299A ALA 3.8 0.5 - - - +
300A ASN* 3.0 5.2 - - - -
301A VAL* 2.8 40.2 + - + +
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Residues in contact with TYR 291 (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* 4.1 1.7 - - - +
243A TYR* 4.1 15.0 - + - -
244A SER* 3.1 6.9 - - - -
245A THR* 3.0 46.3 + - + -
247A LYS* 6.0 2.0 - - + -
289A MET* 3.6 13.9 + - + +
290A CYS* 1.3 72.8 - - - +
292A ALA* 1.3 64.2 + - - +
293A ASN* 3.6 16.4 - - + -
298A SER* 3.1 37.4 + - - -
299A ALA 3.6 5.8 - - - -
300A ASN* 4.2 11.9 - - + -
750A NAG 3.0 39.3 + - + +
800A NAG 3.5 24.1 + - + -
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Residues in contact with ALA 292 (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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212A PRO* 3.7 23.8 - - + -
214A VAL* 4.3 8.5 - - + -
235A ILE* 3.5 25.6 - - + -
242A VAL* 5.0 0.2 - - + -
243A TYR 3.1 6.7 - - - +
291A TYR* 1.3 77.1 - - - +
293A ASN* 1.3 62.1 + - - +
298A SER* 3.0 6.9 - - - -
299A ALA 2.6 39.4 + - - +
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Residues in contact with ASN 293 (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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212A PRO* 3.9 3.8 - - - +
241A SER 4.7 0.2 - - - +
242A VAL* 3.6 2.1 - - - +
243A TYR* 2.7 50.4 + - + +
291A TYR* 3.6 17.9 + - + -
292A ALA* 1.3 78.6 - - - +
294A ASN* 1.3 70.5 + - - +
297A GLY 3.6 7.8 - - - +
298A SER* 3.2 14.7 - - - -
750A NAG 1.5 64.0 + - - +
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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