Contacts of the strand formed by residues 2269 - 2277 (chain B) 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 GLY2269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2268B ALA* 1.3 76.2 - - - +
2270B GLY* 1.3 59.5 + - - -
2311B PHE* 3.5 11.3 - - - -
2312B ASN* 3.3 13.2 - - - -
785D THR* 3.6 7.4 - - - +
786D ILE* 2.7 42.4 + - - +
787D ASN* 5.2 0.2 - - - +
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Residues in contact with GLY2270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2269B GLY* 1.3 70.3 - - - -
2271B LEU* 1.3 61.6 + - - -
2272B ALA* 3.8 2.0 + - - +
2310B LYS 3.7 1.0 - - - +
2311B PHE* 3.5 5.2 - - - -
2312B ASN* 2.9 40.2 + - - -
2313B GLU 4.7 0.3 + - - -
783D THR* 4.4 12.6 - - - -
784D THR 3.6 6.5 - - - -
785D THR* 4.5 5.4 - - - -
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Residues in contact with LEU2271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2241B VAL* 4.8 4.0 - - + -
2261B ILE* 4.0 26.0 - - + -
2263B THR* 4.0 11.4 - - + -
2269B GLY 3.8 1.6 + - - -
2270B GLY* 1.3 71.4 - - - -
2272B ALA* 1.3 58.3 + - - +
2273B ILE* 4.1 12.3 - - + -
2285B PHE* 4.4 1.9 - - - -
2293B CYS* 4.3 15.0 - - + -
2309B VAL* 4.0 21.8 - - + -
2310B LYS 3.6 13.9 - - - +
2311B PHE* 4.2 12.6 - - + -
3329B GSH 5.3 0.4 - - - +
782D ILE 3.8 1.7 - - - +
783D THR* 3.2 2.1 - - - -
784D THR* 2.9 49.7 + - + +
786D ILE* 3.4 29.8 - - + -
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Residues in contact with ALA2272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2270B GLY 3.8 2.1 + - - +
2271B LEU* 1.3 72.5 - - - +
2273B ILE* 1.3 64.2 + - - +
2274B ALA* 6.3 0.7 - - + -
2308B SER 3.7 0.9 - - - +
2309B VAL* 3.4 4.2 - - - +
2310B LYS* 2.8 53.7 + - + +
2313B GLU* 6.1 2.0 - - - +
781D ALA* 5.9 3.4 - - + -
782D ILE 3.4 4.7 - - - +
783D THR* 3.4 22.2 - - + +
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Residues in contact with ILE2273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2259B PHE* 4.0 21.5 - - + -
2261B ILE* 3.7 29.6 - - + -
2271B LEU* 4.1 8.1 - - + -
2272B ALA* 1.3 78.8 - - - +
2274B ALA* 1.3 69.1 + - - +
2275B VAL* 5.1 1.3 - - + -
2283B ILE* 4.1 11.5 - - + +
2285B PHE* 3.0 40.4 - - + -
2295B VAL* 4.2 15.5 - - + -
2297B TYR* 6.4 0.2 - - + -
2307B VAL* 4.5 3.4 - - + -
2308B SER 3.2 9.6 - - - +
2309B VAL* 4.5 4.0 - - + -
781D ALA* 3.2 3.6 - - - +
782D ILE* 2.9 38.8 + - + +
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Residues in contact with ALA2274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2272B ALA* 6.3 1.1 - - + -
2273B ILE* 1.3 73.8 - - - +
2275B VAL* 1.3 66.1 + - - +
2276B GLU 4.2 0.2 - - - -
2283B ILE* 4.3 0.4 - - - -
2306B GLU 3.6 1.2 - - - +
2307B VAL* 3.3 5.4 - - - +
2308B SER* 2.9 45.7 + - - +
779D LYS* 3.6 28.3 - - - +
780D SER 3.1 11.4 - - - +
781D ALA* 3.8 10.3 - - + -
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Residues in contact with VAL2275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2273B ILE* 5.1 2.9 - - + -
2274B ALA* 1.3 78.4 - - - +
2276B GLU* 1.3 63.4 + - - +
2279B SER 6.0 0.2 - - - +
2281B ALA* 3.6 25.9 - - + +
2283B ILE* 3.8 17.3 - - + -
2297B TYR* 4.1 26.9 - - + -
2299B VAL* 4.0 7.4 - - + -
2305B TYR* 3.8 29.6 - - + -
2306B GLU 3.4 3.6 - - - +
2307B VAL* 4.3 16.2 - - + -
778D TYR 3.8 0.7 - - - +
779D LYS* 3.3 4.4 - - - -
780D SER* 2.8 33.9 + - - -
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Residues in contact with GLU2276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2274B ALA 5.7 0.2 - - - -
2275B VAL* 1.3 76.4 - - - +
2277B GLY* 1.3 61.6 + - - +
2304B ASP 4.4 0.2 - - - +
2305B TYR* 3.1 8.3 - - - -
2306B GLU* 2.7 61.4 + - + +
777D LEU* 3.6 30.4 - - + +
778D TYR 3.3 11.4 - - - +
779D LYS* 4.1 33.6 + - + +
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Residues in contact with GLY2277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2276B GLU* 1.3 77.1 - - - +
2278B PRO* 1.3 67.9 - - - +
2279B SER 3.2 10.6 + - - -
2304B ASP 4.1 3.8 - - - -
2305B TYR* 3.5 8.5 - - - -
777D LEU* 3.7 15.4 - - - +
778D TYR* 2.9 33.9 + - - +
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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