Contacts of the strand formed by residues 2275 - 2279 (chain L) in PDB entry 2BT4
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 GLY2275 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2209L ILE* 3.7 6.9 - - - -
2210L MET* 3.0 25.2 + - - +
2273L HIS* 3.4 5.3 - - - +
2274L CYS* 1.3 81.8 - - - +
2276L ILE* 1.4 66.4 + - - +
2300L LEU* 3.5 8.4 - - - +
2301L PRO 3.3 13.5 - - - -
2345L ILE* 4.1 11.4 - - - -
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Residues in contact with ILE2276 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2210L MET* 3.3 8.5 - - + +
2212L LEU* 4.3 11.9 - - + -
2266L ILE* 4.2 9.2 - - + -
2269L ALA* 3.8 30.1 - - + -
2275L GLY* 1.4 78.8 - - - +
2277L VAL* 1.3 76.9 + - - +
2278L ILE* 4.0 18.2 - - + -
2294L LEU* 3.9 25.1 - - + -
2297L CYS* 4.1 9.6 - - - -
2300L LEU* 3.9 17.7 - - + -
2301L PRO 2.9 10.0 + - - +
2302L VAL* 3.3 8.1 - - + -
2303L VAL 3.0 24.6 + - - +
2345L ILE* 3.8 3.3 - - - +
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Residues in contact with VAL2277 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2209L ILE* 4.0 11.9 - - + -
2210L MET 2.8 9.5 + - - +
2211L ILE* 3.2 23.3 - - + +
2212L LEU 2.8 25.3 + - - +
2276L ILE* 1.3 75.8 - - - +
2278L ILE* 1.3 62.5 + - - +
2279L ASN 4.4 0.2 - - - -
2303L VAL* 3.4 5.2 - - + +
2305L VAL* 3.6 28.9 - - + -
2338L TYR* 4.5 11.9 - - + +
2341L GLY* 3.8 33.7 - - - +
2342L VAL* 4.0 3.1 - - + +
2345L ILE* 3.9 11.2 - - + -
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Residues in contact with ILE2278 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2212L LEU* 3.3 23.1 - - + +
2213L ASN 6.1 0.2 - - - -
2262L LEU* 5.8 6.3 - - + -
2266L ILE* 4.4 13.5 - - + -
2276L ILE* 4.0 14.4 - - + -
2277L VAL* 1.3 75.4 - - - +
2279L ASN* 1.3 62.3 + - - +
2280L PRO* 3.4 23.1 - - + +
2290L ILE* 4.1 28.0 - - + -
2294L LEU* 4.6 7.4 - - + -
2302L VAL* 4.5 9.6 - - + -
2303L VAL 2.9 17.7 + - - +
2304L GLU* 3.2 7.7 - - - -
2305L VAL* 2.9 26.0 + - - -
2322L VAL* 4.3 15.9 - - + -
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Residues in contact with ASN2279 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2212L LEU 2.9 7.7 + - - -
2213L ASN* 3.4 4.5 - - - +
2214L GLY 2.9 24.8 + - - -
2217L LEU* 3.6 14.3 - - + +
2278L ILE* 1.3 71.0 - - - +
2280L PRO* 1.3 62.1 - - - +
2281L ALA* 3.0 6.1 + - - -
2305L VAL* 3.1 18.6 + - + +
2306L HIS* 4.3 0.2 - - - +
2307L ILE* 4.0 10.9 - - - +
2338L TYR* 3.1 36.0 + - + +
2360L CA2 2.7 42.3 + - - -
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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