Contacts of the strand formed by residues 85 - 90 (chain O) in PDB entry 2BDI
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 ALA 85 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62O SER* 3.4 3.8 - - - -
63O TYR* 2.9 32.0 + - + +
65O ILE* 4.3 8.7 - - + -
84O GLU* 1.3 79.9 - - - +
86O SER* 1.3 64.8 + - - +
106O ILE* 3.8 19.3 - - + -
107O LYS 3.2 21.5 - - - +
108O LEU* 3.6 9.0 - - - -
109O ASP* 3.6 10.5 + - - -
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Residues in contact with SER 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61O ASN* 3.3 26.9 - - - +
62O SER* 4.2 7.6 - - - +
63O TYR* 4.8 3.6 - - - -
85O ALA* 1.3 78.3 - - - +
87O LEU* 1.3 67.0 + - - +
88O SER* 3.3 10.5 + - - -
107O LYS 4.2 0.4 + - - -
109O ASP* 3.9 11.1 + - - -
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Residues in contact with LEU 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O TRP* 5.2 4.0 - - + -
86O SER* 1.3 80.8 + - - +
88O SER* 1.3 63.3 + - - +
89O VAL* 3.7 24.5 - - + -
106O ILE* 3.7 2.5 - - - +
107O LYS* 2.9 63.8 + - + +
109O ASP* 5.4 0.2 + - - -
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Residues in contact with SER 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59O PHE* 3.6 20.0 - - - -
60O GLN 3.5 9.5 + - - -
63O TYR* 2.8 42.4 + - - -
86O SER 3.3 5.7 + - - -
87O LEU* 1.3 76.5 - - - +
89O VAL* 1.3 68.8 + - - +
90O ARG 4.0 1.2 + - - -
104O MET* 4.1 6.5 - - - -
105O LEU 3.4 7.2 - - - -
106O ILE* 4.3 1.3 - - - +
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Residues in contact with VAL 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O TRP* 5.0 5.2 - - + -
87O LEU* 3.7 18.8 - - + -
88O SER* 1.3 77.3 - - - +
90O ARG* 1.3 63.3 + - - +
92O PRO* 6.1 0.2 - - + -
104O MET* 3.4 4.0 - - - -
105O LEU 2.7 36.8 + - - +
237O TRP* 3.4 24.9 - - + +
241O THR* 4.4 21.5 - - + +
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Residues in contact with ARG 90 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O ALA* 3.4 22.4 - - + -
59O PHE* 3.0 67.0 - - + +
88O SER 4.0 0.6 + - - -
89O VAL* 1.3 80.4 - - - +
91O HIS* 1.3 70.2 + - - +
92O PRO* 3.3 5.0 - - - +
94O TYR* 4.1 18.8 - - + -
104O MET* 4.0 15.9 - - + -
237O TRP* 3.8 3.5 - - - -
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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