Contacts of the strand formed by residues 288 - 293 (chain A) in PDB entry 3EBL
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 SER 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A ASN* 3.4 14.7 + - - +
223A LEU* 5.7 1.3 - - - +
285A PHE* 3.9 6.2 - - - -
286A ALA 3.8 7.6 + - - -
287A LYS* 1.3 77.6 + - - +
289A LEU* 1.3 59.7 + - - +
290A ILE* 3.9 25.1 - - - -
305A TYR* 4.9 1.3 + - - -
309A LEU* 3.6 19.7 - - - +
315A HIS* 3.1 13.0 + - - -
316A VAL* 3.6 2.8 - - - -
317A LYS* 2.9 28.6 + - - +
347A PHE* 3.9 7.0 - - - -
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Residues in contact with LEU 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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221A ASN 2.8 12.4 + - - +
222A ILE* 4.3 7.1 - - + +
223A LEU* 3.0 25.5 + - - +
288A SER* 1.3 71.2 - - - +
290A ILE* 1.3 62.3 + - - +
291A ILE* 4.0 13.6 - - + +
317A LYS* 3.4 29.4 - - + +
319A VAL* 4.0 21.8 - - + -
343A GLU* 3.7 17.0 - - + +
344A ILE* 3.8 24.5 - - + -
347A PHE* 3.7 42.3 - - + -
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Residues in contact with ILE 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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223A LEU* 3.8 19.3 - - + +
226A ALA* 6.1 1.3 - - + -
288A SER* 3.9 17.9 - - - -
289A LEU* 1.3 76.7 - - - +
291A ILE* 1.3 64.0 + - - +
292A VAL* 3.8 19.0 + - + -
302A GLN* 4.5 14.1 - - + +
305A TYR* 3.7 32.1 - - + -
306A ALA* 3.9 12.3 - - + -
309A LEU* 4.1 2.7 - - + -
316A VAL* 3.7 24.0 - - + -
317A LYS 2.7 12.6 + - - +
318A VAL* 3.3 10.2 - - + +
319A VAL* 2.8 25.6 + - - +
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Residues in contact with ILE 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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222A ILE* 4.2 5.4 - - + -
223A LEU 2.8 14.9 + - - +
224A LEU* 4.1 23.1 - - + -
225A ASN* 2.9 28.7 + - - +
226A ALA 4.8 0.2 + - - -
289A LEU* 4.0 28.5 - - + +
290A ILE* 1.3 77.3 - - - +
292A VAL* 1.3 62.5 + - - +
302A GLN* 3.7 3.6 - - - +
319A VAL* 3.5 21.3 - - + +
321A CYS* 4.4 2.0 - - - -
328A PHE* 3.7 32.3 - - + -
340A VAL* 3.9 32.5 - - + +
343A GLU* 5.8 1.1 - - + -
344A ILE* 4.1 7.9 - - + -
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Residues in contact with VAL 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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225A ASN* 3.7 1.6 - - - -
290A ILE* 3.9 24.9 - - + +
291A ILE* 1.3 80.9 - - - +
293A SER* 1.3 58.6 + - - +
294A GLY* 3.7 1.0 + - - -
299A CYS* 3.7 32.8 - - + +
302A GLN* 3.6 29.4 - - + +
303A LEU* 4.1 25.4 - - + -
318A VAL* 4.4 2.9 - - + -
319A VAL 2.9 12.0 + - - +
320A GLN* 3.5 6.4 - - + +
321A CYS* 2.7 34.4 + - - +
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Residues in contact with SER 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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225A ASN* 2.8 38.7 + - - -
292A VAL* 1.3 72.2 - - - +
294A GLY* 1.3 64.7 + - - +
296A ASP* 3.1 24.0 + - - +
299A CYS* 3.6 10.9 - - - +
321A CYS* 3.7 6.3 - - - -
324A ALA* 3.3 16.3 - - - +
325A THR 3.0 16.7 + - - -
328A PHE* 3.2 14.4 - - - -
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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