Contacts of the strand formed by residues 70 - 76 (chain L) in PDB entry 1BRN
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 THR 70 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55L ILE* 3.3 31.3 - - + +
68L GLY 3.7 4.3 + - - -
69L ARG* 1.3 74.6 + - - +
71L TRP* 1.3 66.7 + - - +
72L ARG* 4.2 16.2 - - + +
90L TYR 4.0 0.2 - - - +
91L SER* 3.2 5.2 - - - -
92L SER* 2.9 42.1 + - - +
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Residues in contact with TRP 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L ILE* 3.5 9.3 - - - +
56L PHE* 2.8 50.8 + + + +
58L ASN* 4.0 22.5 - - + +
63L LEU* 3.8 32.3 - - + -
64L PRO* 3.2 32.9 + - + -
65L GLY* 5.0 1.0 - - - -
69L ARG* 3.4 25.5 - - + +
70L THR* 1.3 78.9 - - - +
72L ARG* 1.3 61.8 + - - +
89L LEU* 4.1 4.3 - - + -
90L TYR* 3.5 29.4 - - - -
91L SER* 3.6 15.3 - - - -
95L LEU* 3.9 21.3 - - + -
97L TYR* 3.6 31.4 - + - -
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Residues in contact with ARG 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53L GLY 3.0 25.3 + - - +
54L ASP* 3.2 13.4 - - - +
55L ILE* 3.6 32.2 - - + +
56L PHE* 4.1 2.5 - - - +
70L THR* 4.2 11.5 - - + +
71L TRP* 1.3 78.8 - - - +
73L GLU* 1.3 63.6 + - - +
89L LEU* 3.4 5.9 - - - +
90L TYR* 2.9 67.0 + - + +
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Residues in contact with GLU 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A G 3.3 30.1 - - - +
3A A 4.2 0.9 + - - -
27L LYS* 5.4 1.0 - - - -
51L ILE* 5.8 2.8 - - - +
52L GLY* 3.8 2.6 - - - -
53L GLY 3.0 20.8 + - - -
54L ASP* 2.9 25.8 + - - +
56L PHE* 4.0 14.1 - - + -
72L ARG* 1.3 75.9 - - - +
74L ALA* 1.3 65.7 + - - +
75L ASP* 4.3 3.5 - - - +
83L ARG* 4.7 2.8 + - - -
87L ARG* 3.8 11.2 + - + -
88L ILE 3.2 11.0 - - - +
89L LEU* 3.8 15.7 - - + -
90L TYR* 4.3 2.7 - - - -
103L TYR* 3.1 30.2 + - + +
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Residues in contact with ALA 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L LEU* 3.8 22.4 - - + -
24L TYR* 3.9 8.1 - - + -
52L GLY* 3.7 18.6 - - - -
53L GLY 4.2 0.9 - - - +
73L GLU* 1.3 78.1 - - - +
75L ASP* 1.3 66.4 + - - +
87L ARG* 3.2 7.2 - - - -
88L ILE* 2.9 48.0 + - + +
90L TYR* 4.4 1.3 - - + -
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Residues in contact with ASP 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L ASN* 5.1 0.3 - - - +
24L TYR* 2.6 31.5 + - - -
50L SER* 4.5 3.3 - - - -
51L ILE* 2.9 31.9 + - - +
73L GLU* 4.3 2.1 - - - +
74L ALA* 1.3 73.0 - - - +
76L ILE* 1.3 57.3 + - - +
78L TYR* 4.5 20.0 - - + +
83L ARG* 2.8 57.0 + - - +
84L ASN* 4.9 1.4 - - - +
86L ASP 3.7 5.2 - - - -
87L ARG* 3.2 18.3 + - - +
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Residues in contact with ILE 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L ASN* 3.3 15.0 - - - +
6L THR 3.8 6.7 - - - +
7L PHE* 3.6 43.1 - - + +
10L VAL* 3.7 29.8 - - + -
24L TYR* 3.8 1.1 - - - +
74L ALA 3.8 0.4 - - - +
75L ASP* 1.3 80.0 - - - +
77L ASN* 1.3 77.4 - - - +
78L TYR* 3.1 6.8 + - - +
84L ASN* 3.0 23.4 + - - +
86L ASP* 3.1 17.1 + - + +
88L ILE* 3.8 35.7 - - + +
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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