Contacts of the strand formed by residues 2269 - 2277 (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 GLY2269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2268A ALA* 1.3 75.8 - - - +
2270A GLY* 1.3 60.5 + - - -
2271A LEU 3.8 0.5 + - - -
2311A PHE* 3.5 14.9 - - - -
2312A ASN* 3.3 13.0 - - - -
785C THR* 3.5 8.5 - - - +
786C ILE* 2.8 34.7 + - - +
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Residues in contact with GLY2270 (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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2269A GLY* 1.3 71.6 - - - -
2271A LEU* 1.3 59.7 + - - -
2272A ALA* 3.9 1.7 + - - +
2310A LYS 3.6 1.7 - - - +
2311A PHE* 3.3 5.9 - - - -
2312A ASN* 2.9 35.9 + - - -
2313A GLU 4.7 0.7 + - - -
783C THR* 4.3 11.7 - - - -
784C THR 3.5 8.3 - - - -
785C THR* 4.6 2.9 - - - -
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Residues in contact with LEU2271 (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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2241A VAL* 4.6 4.0 - - + -
2261A ILE* 4.2 18.4 - - + -
2263A THR* 4.0 18.6 - - + -
2269A GLY 3.8 1.0 + - - -
2270A GLY* 1.3 72.1 - - - -
2272A ALA* 1.3 57.8 + - - +
2273A ILE* 4.3 4.5 - - + -
2285A PHE* 3.9 12.9 - - + -
2293A CYS* 3.9 27.1 - - - -
2309A VAL* 4.0 22.7 - - + -
2310A LYS 3.5 13.5 - - - +
2311A PHE* 4.1 16.2 - - + -
782C ILE 3.9 1.2 - - - +
783C THR* 3.4 2.1 - - - -
784C THR* 2.7 37.8 + - + +
786C ILE* 3.9 22.2 - - + -
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Residues in contact with ALA2272 (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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2270A GLY 3.9 2.0 + - - +
2271A LEU* 1.3 73.0 - - - +
2273A ILE* 1.3 63.6 + - - +
2274A ALA* 5.7 0.4 - - - -
2308A SER 3.8 0.9 - - - +
2309A VAL* 3.4 4.3 - - - +
2310A LYS* 2.9 49.3 + - + +
2313A GLU* 6.3 0.7 - - - +
781C ALA* 5.9 3.1 - - + -
782C ILE 3.4 4.5 - - - -
783C THR* 3.3 24.5 - - + +
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Residues in contact with ILE2273 (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* 4.0 19.3 - - + -
2261A ILE* 3.8 28.9 - - + -
2271A LEU* 4.3 7.2 - - + -
2272A ALA* 1.3 78.4 - - - +
2274A ALA* 1.3 66.0 + - - +
2275A VAL* 4.9 2.0 - - + -
2283A ILE* 3.8 21.7 - - + +
2285A PHE* 3.1 37.9 - - + -
2295A VAL* 3.9 7.9 - - + -
2307A VAL* 4.3 7.9 - - + -
2308A SER 3.3 7.6 - - - +
2309A VAL* 4.3 7.0 - - + -
781C ALA* 3.1 3.7 - - - +
782C ILE* 2.8 38.9 + - + -
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Residues in contact with ALA2274 (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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2272A ALA* 4.4 1.1 + - + -
2273A ILE* 1.3 77.3 - - - +
2275A VAL* 1.3 64.8 + - - +
2283A ILE* 4.2 0.4 - - - -
2306A GLU 3.6 1.0 - - - +
2307A VAL* 3.2 5.9 - - - +
2308A SER* 2.8 48.5 + - - +
2310A LYS* 6.4 0.9 - - + -
779C LYS* 3.9 22.0 - - - +
780C SER 3.1 10.8 - - - +
781C ALA* 3.9 10.8 - - + -
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Residues in contact with VAL2275 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2273A ILE* 4.9 2.9 - - + -
2274A ALA* 1.3 78.2 - - - +
2276A GLU* 1.3 62.3 + - - +
2279A SER 5.8 0.2 - - - +
2281A ALA* 3.7 26.2 - - + +
2283A ILE* 3.8 17.0 - - + -
2297A TYR* 4.1 28.7 - - + -
2299A VAL* 3.9 16.2 - - + -
2305A TYR* 3.9 18.4 - - + -
2306A GLU 3.4 3.6 - - - +
2307A VAL* 4.2 16.6 - - + -
778C TYR 3.8 0.9 - - - +
779C LYS* 3.3 2.5 - - - -
780C SER* 2.7 36.0 + - - +
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Residues in contact with GLU2276 (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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2274A ALA 5.8 0.2 - - - -
2275A VAL* 1.3 77.1 - - - +
2277A GLY* 1.3 60.0 + - - +
2305A TYR* 3.1 9.5 - - - -
2306A GLU* 2.8 56.4 + - + +
777C LEU* 3.9 30.5 - - + +
778C TYR 3.1 11.0 - - - +
779C LYS* 4.1 33.9 + - + +
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Residues in contact with GLY2277 (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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2276A GLU* 1.3 76.9 - - - +
2278A PRO* 1.4 71.2 - - - +
2279A SER 3.1 8.8 + - - -
2304A ASP 4.1 3.4 - - - -
2305A TYR* 3.6 8.1 - - - -
777C LEU* 3.8 14.5 - - - +
778C TYR* 2.9 33.3 + - - +
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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