Contacts of the strand formed by residues 66 - 71 (chain C) in PDB entry 1BRR
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 66 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C THR* 3.6 14.1 - - + +
6C GLY* 3.5 32.3 - - - -
63C GLY* 3.0 23.2 + - - +
64C TYR 3.5 3.3 - - - +
65C GLY* 1.3 80.0 - - - +
67C THR* 1.3 86.0 + - - +
68C MET* 4.8 7.2 - - + -
77C PRO* 3.7 20.9 - - + -
78C ILE 3.5 9.4 - - - +
79C TYR* 3.9 23.8 - - + +
2E MAN 2.6 26.2 + - - -
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Residues in contact with THR 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C LEU* 1.3 75.5 - - - +
68C MET* 1.3 72.2 + - - +
69C VAL* 4.5 4.3 - - + -
77C PRO* 3.1 6.1 - - - +
78C ILE* 2.6 56.7 + - + +
80C TRP* 3.7 17.5 - - + -
127C LEU* 4.5 15.0 - - + -
1002C ARC 4.9 8.8 - - + +
2E MAN 3.0 31.0 + - - -
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Residues in contact with MET 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 3.9 37.2 - - + -
5C THR 5.0 4.9 - - - +
66C LEU* 4.8 6.3 - - + -
67C THR* 1.3 89.0 + - - +
69C VAL* 1.3 64.8 + - - +
70C PRO* 4.1 5.0 - - - +
75C GLN* 4.1 35.6 - - + +
76C ASN* 2.9 17.0 - - - +
77C PRO* 3.7 21.3 - - + -
2E MAN 5.1 1.2 + - - -
3E SGA 5.8 4.3 - - - +
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Residues in contact with VAL 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C THR* 4.5 3.1 - - + -
68C MET* 1.3 79.6 - - - +
70C PRO* 1.3 80.2 - - + +
71C PHE* 3.6 16.4 + - + -
75C GLN* 3.6 1.3 - - - -
76C ASN* 2.6 40.5 + - - +
78C ILE* 3.7 23.3 - - + -
126C ALA 4.2 0.7 - - - +
127C LEU* 3.5 55.6 - - + +
128C THR 4.2 2.5 - - - +
129C LYS* 4.8 0.7 - - + -
134C ARG* 4.3 1.8 - - - +
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Residues in contact with PRO 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C MET 4.1 4.7 - - - +
69C VAL* 1.3 87.7 - - + +
71C PHE* 1.3 66.1 + - - +
74C GLU 3.9 6.5 - - - +
75C GLN* 4.2 22.0 - - + +
129C LYS* 3.2 35.0 - - + +
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Residues in contact with PHE 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C VAL* 3.6 15.0 + - + -
70C PRO* 1.3 74.4 - - - +
72C GLY* 1.3 58.5 + - - +
73C GLY 2.4 21.2 + - - -
74C GLU* 2.8 23.6 + - - +
76C ASN* 3.4 34.3 + - + -
78C ILE* 4.8 4.7 - - + -
128C THR 4.0 0.9 - - - +
129C LYS 3.0 24.0 - - - +
131C TYR* 3.7 31.6 - + - +
134C ARG* 3.5 42.2 - - - -
193C SER 4.1 18.6 - - - -
194C GLU 5.0 0.2 - - - -
195C GLY 4.7 4.0 - - - -
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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