Contacts of the strand formed by residues 1051 - 1055 (chain F) 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 VAL1051 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1008F PRO* 4.0 5.7 - - - +
1009F ILE* 3.2 13.5 - - + +
1011F ILE* 3.7 23.6 - - + -
1037F GLU* 5.9 0.2 - - - +
1040F CYS* 3.6 26.5 - - + +
1041F VAL* 3.8 32.0 - - + +
1044F ALA* 3.7 9.2 - - + -
1050F THR* 1.3 83.4 - - - +
1052F ASP* 1.3 63.1 + - - +
1053F PHE* 4.2 15.6 + - + +
1142F VAL* 4.8 0.7 - - + -
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Residues in contact with ASP1052 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008F PRO* 4.2 7.1 - - + +
1009F ILE 2.8 7.6 + - - +
1010F MET* 3.6 6.1 - - - +
1011F ILE 2.9 23.9 + - - +
1051F VAL* 1.3 73.4 - - - +
1053F PHE* 1.3 61.5 + - - +
1054F ARG* 2.8 44.0 + - - +
1073F HIS* 2.9 35.5 + - + +
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Residues in contact with PHE1053 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011F ILE* 3.6 27.4 - - + -
1013F ASN* 3.1 27.1 - - - -
1033F LEU* 3.8 34.3 - - + -
1036F VAL* 4.0 13.2 - - + -
1037F GLU* 3.6 69.7 - - + +
1040F CYS* 4.1 10.3 - - + -
1051F VAL* 3.9 8.5 + - + +
1052F ASP* 1.3 72.1 + - - +
1054F ARG* 1.3 71.3 + - - +
1055F GLN* 5.3 0.2 - - + -
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Residues in contact with ARG1054 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010F MET* 3.6 19.3 - - - +
1011F ILE 2.9 7.4 + - - +
1012F LEU* 4.0 5.6 - - + -
1013F ASN* 2.8 32.3 + - - -
1052F ASP* 2.8 39.7 + - - +
1053F PHE* 1.3 84.5 - - - +
1055F GLN* 1.3 61.6 + - - +
1065F TRP* 3.2 57.8 - - + +
1068F GLU* 2.9 41.6 + - - -
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Residues in contact with GLN1055 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013F ASN* 3.2 15.9 - - + +
1014F GLY 2.9 23.0 + - - +
1016F ASN 3.7 1.2 - - - +
1017F LEU* 4.3 0.4 - - + -
1018F ASN* 3.5 32.1 + - - +
1033F LEU* 3.6 32.1 - - + -
1053F PHE* 5.3 0.2 - - + -
1054F ARG* 1.3 77.7 - - - +
1056F SER* 1.4 71.8 + - - +
1057F ASN* 3.2 24.0 + - - -
1065F TRP* 3.5 9.9 - - - -
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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