Contacts of the helix formed by residues 2287 - 2296 (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 SER2287 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2259L GLU* 2.6 27.1 + - - -
2283L TYR* 3.0 25.8 + - - +
2285L HIS 3.9 0.4 - - - -
2286L THR* 1.3 74.1 + - - +
2288L VAL* 1.3 62.4 + - - +
2289L ALA 3.5 0.2 + - - -
2290L ILE* 2.9 42.6 + - - +
2291L LEU 3.4 11.8 + - - -
2321L TYR* 3.9 14.6 - - - +
2322L VAL* 5.3 1.4 - - - +
2408L TRS 3.6 2.2 - - - -
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Residues in contact with VAL2288 (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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2082K ALA* 3.6 22.0 - - + +
2085K HIS* 4.3 9.6 - - + -
2086K THR* 3.6 25.3 - - + +
2116K PHE* 3.9 25.6 - - + -
2117K ARG* 4.2 13.2 - - - +
2286L THR 3.5 2.2 + - - -
2287L SER* 1.3 70.7 - - - +
2289L ALA* 1.3 59.9 + - - +
2291L LEU* 3.2 7.2 + - + +
2292L ASP* 2.8 29.0 + - - +
2321L TYR* 3.7 34.1 - - + +
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Residues in contact with ALA2289 (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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2015K PRO* 3.9 18.2 - - + -
2016K ASN* 3.1 12.0 + - - +
2082K ALA* 3.3 22.4 - - + +
2083K TYR* 4.0 12.1 - - + +
2086K THR* 5.6 0.4 - - - +
2259L GLU* 4.0 8.7 + - - +
2263L VAL* 4.0 15.2 - - + +
2287L SER* 3.2 7.3 + - - +
2288L VAL* 1.3 76.3 - - - +
2290L ILE* 1.3 58.7 + - - +
2292L ASP 3.3 0.2 + - - -
2293L ALA* 2.9 25.3 + - - +
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Residues in contact with ILE2290 (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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2259L GLU* 4.3 6.5 - - + +
2262L LEU* 3.9 30.5 - - + -
2263L VAL* 4.0 16.6 - - + +
2266L ILE* 3.9 15.7 - - + -
2278L ILE* 4.1 12.3 - - + -
2280L PRO* 5.2 4.3 - - + -
2283L TYR* 3.8 27.6 - - + -
2287L SER* 2.9 25.9 + - - +
2289L ALA* 1.3 74.7 - - - +
2291L LEU* 1.3 65.0 + - - +
2293L ALA* 3.2 6.7 + - - +
2294L LEU* 3.0 25.5 + - + +
2322L VAL* 4.0 21.3 - - + -
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Residues in contact with LEU2291 (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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2116K PHE* 3.9 29.6 - - + -
2117K ARG* 4.4 5.6 - - - +
2287L SER 3.4 10.9 + - - +
2288L VAL* 3.2 9.6 + - + +
2290L ILE* 1.3 80.0 - - - +
2292L ASP* 1.3 65.1 + - - +
2294L LEU* 3.3 7.0 + - - +
2295L ASN* 3.0 32.7 + - - +
2321L TYR* 3.4 38.6 - - + +
2322L VAL* 4.7 4.1 - - - +
2324L GLN* 4.1 13.0 - - + +
2325L ARG* 3.7 28.7 - - + +
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Residues in contact with ASP2292 (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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2016K ASN* 3.2 22.2 + - + +
2082K ALA* 3.4 13.9 + - - +
2117K ARG* 2.9 31.6 + - - -
2160K CA2 2.7 39.8 + - + +
2288L VAL* 2.8 19.5 + - - +
2289L ALA 3.6 1.8 - - - +
2291L LEU* 1.3 73.3 - - - +
2293L ALA* 1.3 62.0 + - - +
2295L ASN* 3.2 19.2 + - - +
2296L THR* 3.2 18.2 + - - +
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Residues in contact with ALA2293 (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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2016K ASN* 3.2 20.6 + - - +
2263L VAL* 4.0 14.6 - - + -
2266L ILE* 3.6 32.4 - - + +
2267L HIS* 4.2 2.9 - - - +
2289L ALA 2.9 15.4 + - - +
2290L ILE* 3.6 7.0 - - - +
2291L LEU 3.2 0.2 - - - -
2292L ASP* 1.3 76.3 - - - +
2294L LEU* 1.3 59.4 + - - +
2296L THR* 2.6 26.3 + - - -
2297L CYS* 3.8 1.4 - - - -
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Residues in contact with LEU2294 (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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2266L ILE* 4.0 16.4 - - + -
2276L ILE* 3.9 31.0 - - + -
2278L ILE* 4.6 8.5 - - + -
2290L ILE* 3.0 25.8 + - + +
2291L LEU* 3.7 6.3 - - - +
2293L ALA* 1.3 73.7 - - - +
2295L ASN* 1.3 66.2 + - - +
2297L CYS* 3.0 22.5 + - - +
2302L VAL* 4.2 23.1 - - + -
2322L VAL* 3.9 36.3 - - + +
2325L ARG* 3.3 29.6 + - + -
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Residues in contact with ASN2295 (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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2023K ARG* 3.1 34.8 + - - +
2117K ARG* 4.1 15.4 - - - +
2291L LEU* 3.0 32.5 + - - +
2292L ASP* 3.2 16.5 + - - +
2294L LEU* 1.3 76.2 - - - +
2296L THR* 1.4 57.3 + - - +
2297L CYS 3.2 1.5 + - - -
2298L ASP* 4.1 4.3 + - - +
2324L GLN 5.3 0.3 - - - +
2325L ARG* 3.5 30.8 + - - +
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Residues in contact with THR2296 (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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2016K ASN* 4.5 6.3 - - + +
2019K LEU* 3.7 26.8 - - + +
2023K ARG* 3.5 21.5 - - - +
2160K CA2 4.4 18.2 - - + -
2267L HIS* 4.2 3.8 - - - -
2270L ARG* 2.8 35.1 + - - -
2292L ASP 3.3 16.6 - - - +
2293L ALA* 2.6 20.8 + - - +
2295L ASN* 1.4 75.1 - - + +
2297L CYS* 1.3 52.8 + - - +
2298L ASP* 3.0 18.9 + - - +
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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