Contacts of the strand formed by residues 850 - 854 (chain B) in PDB entry 1E42
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 LEU 850 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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847B GLU 5.6 2.0 - - - +
848B ASN 3.9 4.7 - - - +
849B GLU* 1.3 81.0 - - - +
851B GLN* 1.3 65.4 + - - +
852B PHE* 3.6 24.5 - - + -
915B SER* 3.4 1.7 - - - -
916B LEU 2.8 38.7 + - - +
921B PRO* 3.6 37.0 - - + +
924B SER* 3.8 12.1 - - - +
925B GLN 5.4 0.4 - - - +
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Residues in contact with GLN 851 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849B GLU* 2.9 44.6 + - - +
850B LEU* 1.3 77.2 - - - +
852B PHE* 1.3 71.6 + - - +
853B GLN* 6.0 0.7 - - - +
913B THR* 4.5 13.7 - - + -
914B LEU 3.4 2.9 - - - +
915B SER* 3.5 15.2 + - - +
961B MG 4.1 3.0 - - - -
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Residues in contact with PHE 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850B LEU* 3.6 40.2 - - + -
851B GLN* 1.3 79.2 - - - +
853B GLN* 1.3 66.4 + - - +
913B THR* 3.5 5.2 - - - +
914B LEU* 2.8 45.8 + - + +
916B LEU* 3.9 22.2 - - + -
924B SER* 3.9 2.5 - - - -
925B GLN* 3.8 38.6 - - + -
928B TYR* 3.4 44.2 - + + -
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Residues in contact with GLN 853 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851B GLN* 6.0 0.8 - - - +
852B PHE* 1.3 74.7 + - - +
854B ILE* 1.3 60.0 + - - +
855B LYS* 3.5 25.9 + - + +
909B ASN* 5.4 2.1 + - - -
911B ASN* 3.3 30.2 + - + +
912B TYR 3.6 2.9 - - - +
913B THR* 2.9 40.0 + - - +
928B TYR* 3.0 25.4 + - - -
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Residues in contact with ILE 854 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852B PHE 4.0 0.2 + - - -
853B GLN* 1.3 71.6 - - - +
855B LYS* 1.3 61.5 + - - +
856B GLU 3.7 0.2 + - - -
857B CYS* 4.0 18.5 - - + +
903B LEU* 3.6 20.0 - - + -
911B ASN* 3.3 4.7 - - - -
912B TYR* 2.9 35.2 + - + +
914B LEU* 4.1 10.1 - - + -
928B TYR* 4.1 16.2 - - + -
931B TYR* 3.3 40.8 - - + -
932B ASP* 3.5 23.1 - - + +
935B LEU* 4.0 15.5 - - + -
936B LYS* 3.8 7.6 - - - +
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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