Contacts of the strand formed by residues 287 - 291 (chain A) in PDB entry 6ABP
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 VAL 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ARG* 5.1 3.6 - - - +
252A LEU 3.6 0.5 - - - -
253A LEU* 2.8 62.5 + - + +
286A VAL* 1.3 84.5 - - - +
288A LEU* 1.3 73.6 + - - +
289A ILE* 4.1 6.5 - - + -
293A ASN* 5.4 0.9 - - - +
297A GLU* 3.8 27.4 - - - +
301A LYS* 6.1 0.4 - - + -
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Residues in contact with LEU 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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116A ARG* 4.3 15.7 - - - +
120A GLU* 3.8 26.5 - - + +
229A ILE* 3.9 23.6 - - + -
249A TYR* 4.8 10.8 - - + +
250A GLY* 4.6 2.9 - - - -
251A SER 3.6 18.6 - - - +
252A LEU* 3.7 22.9 - - + +
287A VAL* 1.3 81.1 - - - +
289A ILE* 1.3 59.9 + - - +
290A THR* 3.9 21.8 - - + +
293A ASN* 3.3 20.1 + - - -
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Residues in contact with ILE 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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233A GLY* 3.7 34.5 - - - +
237A VAL* 5.3 2.5 - - + -
240A LEU* 3.9 17.6 - - + +
250A GLY* 2.9 5.9 - - - -
251A SER* 2.7 54.5 + - - +
253A LEU* 4.1 10.5 - - + -
287A VAL* 4.1 13.2 - - + -
288A LEU* 1.3 76.7 - - - +
290A THR* 1.3 64.9 + - - +
293A ASN* 3.3 5.6 - - - +
294A PHE* 4.0 15.3 - - + +
297A GLU* 3.6 32.1 - - + -
298A LEU* 4.8 11.2 - - + +
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Residues in contact with THR 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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240A LEU* 4.0 7.6 - - - -
249A TYR* 3.8 40.6 - - + +
250A GLY* 4.2 1.8 - - - -
288A LEU* 3.9 26.2 - - + +
289A ILE* 1.3 80.2 - - - +
291A ARG* 1.4 66.5 + - - +
292A ASP* 3.1 19.2 + - - +
293A ASN* 2.9 14.5 + - - +
294A PHE* 3.0 24.7 + - - +
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Residues in contact with ARG 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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239A GLU 4.9 1.4 + - - -
240A LEU* 3.8 34.0 + - + +
242A LYS* 2.8 26.7 + - - +
243A ALA 3.0 20.1 + - - -
244A GLN 3.5 13.9 + - - -
245A ALA* 3.9 30.9 - - - +
246A THR 5.3 0.9 - - - +
248A PHE 5.7 3.8 - - - +
249A TYR* 4.3 4.3 + - - +
290A THR* 1.4 74.9 - - - +
292A ASP* 1.3 68.4 - - - +
294A PHE* 3.4 22.6 - - - -
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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