Contacts of the strand formed by residues 2293 - 2299 (chain A) in PDB entry 2BRQ
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 CYS2293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2260A SER* 3.5 1.0 - - - -
2261A ILE* 2.8 48.2 + - + +
2263A THR* 4.0 8.5 + - + -
2271A LEU* 3.9 9.9 - - - -
2285A PHE* 3.5 22.4 - - - -
2286A GLU 4.4 0.2 - - - -
2288A ARG* 4.2 0.9 - - - -
2292A SER* 1.3 71.4 - - - +
2294A GLY* 1.3 60.7 + - - +
2295A VAL* 3.9 3.7 + - - -
3330A GSH 2.0 69.3 + - - +
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Residues in contact with GLY2294 (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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2259A PHE 3.6 1.6 - - - -
2260A SER* 4.5 0.2 - - - -
2285A PHE* 3.3 5.9 - - - -
2286A GLU* 2.6 45.5 + - - -
2288A ARG* 3.5 35.7 - - - +
2293A CYS* 1.3 72.9 - - - +
2295A VAL* 1.3 60.0 + - - +
3330A GSH 3.7 2.6 - - - -
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Residues in contact with VAL2295 (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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2257A ALA 3.9 0.6 - - - +
2258A GLU* 3.3 4.3 - - - -
2259A PHE* 2.9 66.2 + - + +
2261A ILE* 3.7 31.9 - - + -
2273A ILE* 3.9 15.3 - - + -
2283A ILE* 3.7 28.3 - - + -
2284A SER 3.4 4.9 - - - +
2285A PHE* 4.2 8.1 - - + -
2286A GLU* 4.2 0.7 - - - -
2288A ARG* 3.4 5.1 + - - +
2293A CYS 4.5 0.9 - - - +
2294A GLY* 1.3 79.3 - - - +
2296A ALA* 1.3 64.8 + - - +
2297A TYR* 4.8 0.7 - - + +
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Residues in contact with ALA2296 (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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2256A PRO* 4.9 11.0 - - + -
2257A ALA 3.3 9.0 - - - +
2258A GLU* 4.2 10.3 - - + +
2282A GLU 3.9 0.3 - - - +
2283A ILE* 3.5 2.9 - - - +
2284A SER* 2.9 40.5 + - - +
2286A GLU* 3.4 27.5 - - - +
2295A VAL* 1.3 77.4 - - - +
2297A TYR* 1.3 59.3 + - - +
2298A VAL* 6.4 0.4 - - + -
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Residues in contact with TYR2297 (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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2247A GLY 2.6 30.3 + - - -
2251A ALA* 4.0 8.1 - - + +
2255A VAL 3.9 0.3 - - - +
2256A PRO* 3.4 1.6 - - - +
2257A ALA* 2.8 66.1 + - + +
2259A PHE* 3.9 25.8 - + - -
2273A ILE* 6.1 0.2 - - + -
2275A VAL* 4.1 19.7 - - + -
2281A ALA* 5.2 0.9 - - + -
2282A GLU 3.1 12.1 - - - +
2283A ILE* 4.2 17.3 - - + -
2295A VAL* 5.0 0.9 - - + -
2296A ALA* 1.3 74.6 - - - +
2298A VAL* 1.3 66.1 + - - +
2299A VAL* 4.2 21.8 - - + -
2305A TYR* 5.9 1.3 - - + -
2307A VAL* 3.9 15.4 - - + +
2323A VAL* 3.4 21.5 - - + +
2325A VAL* 5.2 3.4 - - + -
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Residues in contact with VAL2298 (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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2254A GLY* 3.6 35.2 - - - +
2255A VAL 4.1 2.9 - - - +
2256A PRO* 3.7 28.7 - - + -
2280A LYS 4.0 0.5 - - - +
2281A ALA* 3.3 4.0 - - - -
2282A GLU* 3.0 41.6 + - + +
2296A ALA* 6.4 0.2 - - + -
2297A TYR* 1.3 80.5 - - - +
2299A VAL* 1.3 67.2 - - - +
2300A GLN* 4.1 13.7 + - - +
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Residues in contact with VAL2299 (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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2251A ALA* 5.6 1.1 - - + -
2252A GLU 5.0 2.2 + - - +
2253A ALA* 4.6 1.1 - - - -
2254A GLY* 2.8 27.6 + - - +
2255A VAL 5.3 0.6 + - - -
2275A VAL* 3.9 7.6 - - + -
2279A SER* 3.9 1.1 - - - +
2280A LYS 3.5 4.7 - - - +
2281A ALA* 3.7 23.6 - - + -
2297A TYR* 4.2 12.3 - - + -
2298A VAL* 1.3 74.1 - - - +
2300A GLN* 1.3 63.6 + - - +
2301A GLU 3.8 2.9 - - - +
2305A TYR* 3.5 43.5 - - + -
2325A VAL* 3.5 34.8 - - + -
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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