Contacts of the strand formed by residues 288 - 293 (chain A) in PDB entry 4BDG
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 ILE 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A ILE* 3.7 44.2 - - + -
277A LEU* 3.8 28.7 + - + +
278A LYS* 3.7 31.9 - - + +
286A ILE 4.1 1.6 + - - -
287A LYS* 1.3 76.8 - - - +
289A LYS* 1.3 63.6 + - - +
290A ASN* 3.7 20.6 - - - +
291A PHE* 4.2 6.7 - - + -
299A ILE* 3.8 13.2 - - + -
300A VAL 3.7 5.6 - - - +
301A LEU* 4.2 2.9 - - - +
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Residues in contact with LYS 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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220A TYR* 4.7 3.0 + - - +
239A GLU* 3.6 19.7 + - - -
246A VAL* 4.0 26.2 - - + -
287A LYS* 4.3 3.4 - - + +
288A ILE* 1.3 76.8 - - - +
290A ASN* 1.3 62.7 + - + +
300A VAL* 2.7 24.6 + - + +
301A LEU 4.2 1.1 - - - -
302A GLU* 4.2 31.6 - - + +
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Residues in contact with ASN 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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219A GLU* 3.1 33.9 + - - -
220A TYR* 3.3 20.2 + - - +
288A ILE* 3.7 9.8 - - - +
289A LYS* 1.3 81.4 + - - +
291A PHE* 1.3 78.6 + - - +
292A PHE* 3.8 8.8 - - - -
299A ILE* 3.7 0.7 - - - -
300A VAL* 2.8 36.7 + - + +
1515A EDO 3.2 31.1 + - - -
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Residues in contact with PHE 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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270A VAL* 3.8 22.0 - - + -
271A GLU* 5.8 1.3 - - - -
274A ILE* 3.6 24.0 - - + -
288A ILE* 4.2 11.4 - - + -
290A ASN* 1.3 89.2 + - - +
292A PHE* 1.3 70.2 + - - +
293A ASP* 3.6 23.6 - - + -
297A TYR* 3.3 37.5 - + + -
298A TYR 3.3 20.2 - - - -
299A ILE* 3.6 17.3 - - + -
1515A EDO 3.9 7.4 + - - -
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Residues in contact with PHE 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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213A PRO* 5.0 5.2 - - + -
215A ALA* 3.6 31.0 - - + -
216A LEU* 3.6 48.2 - - + -
219A GLU* 3.9 15.5 - - - -
220A TYR* 3.7 17.5 - + - -
290A ASN* 3.8 19.5 - - - -
291A PHE* 1.3 79.9 - - - +
293A ASP* 1.3 61.0 + - - +
294A ALA* 3.6 3.3 + - + +
296A ASP 3.6 1.0 - - - +
297A TYR* 3.5 4.0 - - - -
298A TYR* 2.7 57.7 + - + +
300A VAL* 4.0 7.4 - - + -
1515A EDO 4.3 16.4 - - - -
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Residues in contact with ASP 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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253A LYS* 2.7 32.3 + - - -
291A PHE* 3.6 22.3 + - + -
292A PHE* 1.3 68.3 - - - +
294A ALA* 1.4 56.8 + - - +
297A TYR* 3.3 21.6 + - - -
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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