Contacts of the helix formed by residues 909 - 913 (chain E) 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 ASN 909 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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908E SER* 1.3 69.5 - - - +
910E ILE* 1.3 58.9 + - - +
911E HIS* 2.9 28.9 + - - +
912E GLN* 2.9 39.6 + - + +
913E ARG* 3.6 7.6 - - - +
931E ALA* 4.4 2.0 - - - -
932E GLY* 3.5 10.5 - - - +
2323L SER 3.1 19.0 + - - -
2326L ALA 2.8 27.5 + - - -
2327L ASP 3.8 16.1 + - - +
2329L VAL* 3.9 12.9 - - - +
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Residues in contact with ILE 910 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885E HIS* 4.4 5.6 - - + -
906E HIS* 4.0 35.7 - - + +
908E SER* 3.2 8.2 + - - +
909E ASN* 1.3 71.5 + - - +
911E HIS* 1.3 79.9 + - + +
912E GLN 3.2 0.2 - - - -
913E ARG* 3.2 20.0 + - - +
917E ARG* 3.3 27.3 - - + +
918E HIS* 3.1 31.7 - - - +
920E SER* 5.0 8.1 - - - -
931E ALA* 4.6 5.6 - - + -
960E CA2 3.9 33.0 - - + +
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Residues in contact with HIS 911 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909E ASN* 2.9 21.3 + - - +
910E ILE* 1.3 94.4 - - + +
912E GLN* 1.3 57.7 + - - +
913E ARG 3.4 0.4 - - - -
918E HIS* 3.2 42.7 + - - -
929E VAL* 6.1 2.4 - - - +
931E ALA* 4.6 9.3 - - + +
2422E GOL 2.4 36.9 + - - +
2311L HIS* 4.1 26.7 + + - -
2318L HIS 5.5 0.2 - - - -
2323L SER* 3.8 30.3 - - - +
2324L GLN* 4.6 12.4 - - + +
2329L VAL* 4.6 14.0 - - + +
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Residues in contact with GLN 912 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909E ASN* 2.9 24.3 + - + +
911E HIS* 1.3 77.3 - - - +
913E ARG* 1.3 64.5 + - + +
918E HIS* 4.6 0.2 - - - -
2323L SER 3.5 9.6 + - - +
2324L GLN* 3.2 30.2 + - - +
2325L ARG* 3.5 8.5 + - - +
2326L ALA 2.9 28.5 + - - -
2327L ASP* 4.8 1.8 - - - +
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Residues in contact with ARG 913 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824E GLN* 5.0 10.3 + - - +
827E ILE* 4.7 12.5 - - - +
828E TYR* 2.7 34.1 + - - -
908E SER* 3.0 32.3 + - - -
909E ASN 3.6 15.3 - - - +
910E ILE* 3.2 13.9 + - - +
912E GLN* 1.3 86.4 - - + +
914E GLU* 1.3 80.6 + - - +
915E PRO* 3.6 2.1 - - - +
917E ARG* 3.9 33.3 - - - +
918E HIS* 2.9 18.6 + - - -
960E CA2 4.1 12.5 + - - +
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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