Contacts of the strand formed by residues 2257 - 2262 (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 ALA2257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2246B PRO* 6.4 0.2 - - - -
2247B GLY* 3.9 9.4 - - - +
2250B ARG 4.9 0.4 - - - +
2251B ALA* 3.8 22.7 - - + -
2255B VAL 3.2 2.4 + - - +
2256B PRO* 1.3 73.2 - - - +
2258B GLU* 1.3 61.1 + - - +
2295B VAL 3.9 0.2 - - - +
2296B ALA* 3.3 2.8 - - - -
2297B TYR* 2.7 70.3 + - + +
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Residues in contact with GLU2258 (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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2246B PRO* 3.5 17.4 - - + +
2247B GLY* 2.9 24.3 + - - +
2256B PRO* 4.2 20.2 - - - +
2257B ALA* 1.3 79.6 - - - +
2259B PHE* 1.3 62.8 + - - +
2286B GLU* 5.7 1.5 - - - +
2288B ARG* 3.8 21.1 + - - +
2295B VAL 3.3 6.7 - - - +
2296B ALA* 4.2 16.5 - - + +
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Residues in contact with PHE2259 (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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2243B ALA* 4.2 2.0 - - + -
2244B GLY 3.4 19.3 - - - +
2245B GLY* 3.9 3.8 - - - -
2247B GLY 4.4 1.3 - - - -
2248B LEU* 3.7 29.6 - - + +
2258B GLU* 1.3 77.6 - - - +
2260B SER* 1.3 71.7 + - - +
2261B ILE* 4.1 14.6 - - + -
2273B ILE* 4.0 9.6 - - + -
2288B ARG* 3.7 3.2 + - - -
2294B GLY* 3.6 2.8 - - - -
2295B VAL* 2.9 63.1 + - + +
2297B TYR* 4.0 19.7 - + - -
2307B VAL* 3.7 32.5 - - + -
2309B VAL* 3.9 20.4 - - + -
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Residues in contact with SER2260 (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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2242B ARG 4.1 0.3 - - - +
2243B ALA* 3.2 6.8 - - - +
2244B GLY 3.0 34.0 + - - -
2259B PHE* 1.3 73.9 - - - +
2261B ILE* 1.3 62.7 + - - +
2262B TRP* 4.2 10.3 - - - -
2288B ARG* 3.2 25.8 + - - -
2290B ASP* 5.0 2.1 + - - -
2292B SER* 3.4 20.8 + - - -
2293B CYS 3.4 4.7 - - - -
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Residues in contact with ILE2261 (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* 3.5 32.8 - - + -
2242B ARG 3.4 5.4 - - - +
2243B ALA* 4.3 3.4 - - + -
2259B PHE* 4.1 13.9 - - + -
2260B SER* 1.3 77.2 - - - +
2262B TRP* 1.3 62.8 + - - +
2263B THR* 3.6 18.1 + - + -
2271B LEU* 4.0 12.3 - - + -
2273B ILE* 3.7 27.8 - - + -
2292B SER* 3.4 2.1 - - - -
2293B CYS* 2.8 47.9 + - + +
2295B VAL* 3.8 11.0 - - + -
2309B VAL* 3.7 23.6 - - + -
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Residues in contact with TRP2262 (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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2240B LYS 4.3 3.3 - - - +
2241B VAL* 3.7 10.2 - - - +
2242B ARG* 2.8 47.8 + - + +
2243B ALA* 5.6 0.4 - - - -
2244B GLY 6.0 0.7 - - - -
2260B SER* 4.6 9.8 - - - -
2261B ILE* 1.3 76.7 - - - +
2263B THR* 1.3 61.1 + - - +
2264B ARG* 3.5 41.9 - - + +
2292B SER* 4.2 18.5 - - - +
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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