Contacts of the strand formed by residues 86 - 92 (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 ASP 86 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7L PHE* 3.9 17.0 - - + -
76L ILE* 3.1 33.2 + - + +
77L ASN* 2.9 27.8 - - - +
84L ASN* 3.1 10.1 + - - +
85L SER* 1.3 79.0 - - - +
87L ARG* 1.3 79.7 + - - +
99L THR 3.6 3.1 - - - -
100L THR* 3.5 27.0 - - - +
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Residues in contact with ARG 87 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A A 2.9 45.3 + - - -
7L PHE* 3.4 13.9 - - - -
73L GLU* 3.8 8.3 - - + -
74L ALA 3.2 11.2 - - - +
75L ASP* 3.2 27.1 + - - -
76L ILE* 4.3 0.4 - - - -
83L ARG* 3.4 14.8 - - - +
84L ASN* 3.0 38.8 + - - +
85L SER 4.4 6.1 - - - +
86L ASP* 1.3 91.6 + - - +
88L ILE* 1.3 61.5 + - - +
89L LEU* 3.9 15.3 - - + -
98L LYS* 3.6 10.0 - - - -
99L THR* 3.1 26.7 + - + +
102L HIS* 4.1 4.4 - - - -
103L TYR* 3.4 25.5 - - + +
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Residues in contact with ILE 88 (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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7L PHE* 3.9 13.2 - - + +
10L VAL* 4.0 10.8 - - + -
11L ALA* 3.7 30.1 - - + +
14L LEU* 3.9 15.5 - - + -
73L GLU* 3.2 5.2 - - - -
74L ALA* 2.9 55.5 + - + +
76L ILE* 3.8 19.4 - - + +
87L ARG* 1.3 72.2 - - - +
89L LEU* 1.3 68.9 + - - +
90L TYR* 4.3 2.8 + - + -
96L ILE* 3.8 23.1 - - + -
97L TYR 3.5 11.2 - - - +
109L ILE* 4.5 5.6 - - + -
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Residues in contact with LEU 89 (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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56L PHE* 3.5 48.5 - - + -
63L LEU* 3.8 17.0 - - + -
71L TRP* 4.1 4.7 - - + -
72L ARG 3.4 3.6 - - - +
73L GLU* 3.8 8.7 - - + -
87L ARG* 3.9 24.5 - - + +
88L ILE* 1.3 82.8 - - - +
90L TYR* 1.3 61.2 + - - +
96L ILE* 3.4 5.7 - - - +
97L TYR* 2.7 43.3 + - + +
99L THR* 4.1 2.5 - - + -
103L TYR* 4.1 6.1 - - + -
106L PHE* 3.8 26.0 - - + -
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Residues in contact with TYR 90 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14L LEU* 4.0 20.9 - - + -
19L LYS* 6.0 1.1 - - - -
20L LEU* 3.5 29.3 - - + +
53L GLY* 3.4 24.8 - - - -
70L THR 4.0 0.2 - - - +
71L TRP* 3.5 5.7 - - - -
72L ARG* 2.9 71.0 + - + +
73L GLU 4.2 9.6 - - - -
74L ALA* 4.4 1.1 - - + -
88L ILE* 4.4 6.3 - - + -
89L LEU* 1.3 77.2 - - - +
91L SER* 1.3 65.6 + - - +
94L TRP* 3.8 27.1 - + + -
95L LEU 3.2 8.7 - - - +
96L ILE* 3.9 19.5 - - + -
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Residues in contact with SER 91 (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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69L ARG* 3.9 15.3 - - - -
70L THR 3.2 11.0 - - - -
71L TRP* 3.6 17.0 - - - -
90L TYR* 1.3 77.7 - - - +
92L SER* 1.3 60.8 + - - +
93L ASP* 2.6 25.0 + - - -
94L TRP* 3.0 29.6 + - - -
95L LEU* 2.9 30.3 + - - +
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Residues in contact with SER 92 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68L GLY 4.0 4.4 + - - -
69L ARG* 3.6 8.5 - - - +
70L THR* 2.9 40.9 + - - -
91L SER* 1.3 72.2 - - - +
93L ASP* 1.3 57.9 + - - +
94L TRP* 3.0 25.6 + - - -
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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