Contacts of the strand formed by residues 86 - 92 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7M PHE* 4.0 16.8 - - + -
76M ILE* 3.1 33.2 + - + +
77M ASN* 2.8 30.2 + - - +
84M ASN* 3.0 9.8 + - - +
85M SER* 1.3 78.6 - - - +
87M ARG* 1.3 78.8 + - - +
99M THR 3.5 3.4 - - - -
100M THR* 3.5 26.6 - - - +
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Residues in contact with ARG 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B A 2.9 47.3 + - - -
7M PHE* 3.4 10.5 - - - -
73M GLU* 3.7 5.6 - - + -
74M ALA 3.2 12.6 - - - +
75M ASP* 3.2 29.9 + - - -
76M ILE* 4.1 1.3 - - - -
83M ARG* 3.6 11.5 - - - +
84M ASN* 3.0 38.6 + - - +
85M SER 3.8 3.8 + - - +
86M ASP* 1.3 91.5 + - - +
88M ILE* 1.3 63.1 + - - +
89M LEU* 4.1 3.6 - - + -
98M LYS* 3.5 0.5 - - - -
99M THR* 3.0 47.2 + - + +
102M HIS* 3.9 5.7 - - + -
103M TYR* 3.2 30.0 + - + +
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Residues in contact with ILE 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M PHE* 3.8 16.4 - - + +
10M VAL* 4.0 15.0 - - + -
11M ALA* 3.8 24.9 - - - +
14M LEU* 4.2 10.8 - - + -
73M GLU* 3.2 6.8 - - - +
74M ALA* 2.9 54.5 + - + +
76M ILE* 3.8 18.5 - - + +
87M ARG* 1.3 75.8 - - - +
89M LEU* 1.3 64.2 + - - +
90M TYR* 4.3 2.5 + - + -
96M ILE* 3.7 25.1 - - + -
97M TYR 3.5 9.6 - - - +
109M ILE* 3.9 9.2 - - + -
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Residues in contact with LEU 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56M PHE* 3.6 40.8 - - + -
63M LEU* 3.9 4.9 - - + -
71M TRP* 4.1 11.6 - - + -
72M ARG 3.4 5.6 - - - +
73M GLU* 3.7 14.8 - - + -
87M ARG* 3.9 8.5 - - + +
88M ILE* 1.3 80.7 - - - +
90M TYR* 1.3 61.9 + - - +
95M LEU 3.8 0.3 - - - +
96M ILE* 3.4 5.4 - - - +
97M TYR* 2.7 49.7 + - + +
99M THR* 3.7 30.5 - - + +
103M TYR* 4.2 2.5 - - + -
106M PHE* 3.7 20.0 - - + -
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Residues in contact with TYR 90 (chain M).
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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14M LEU* 3.9 32.1 - - + -
19M LYS* 6.0 1.1 - - - -
20M LEU* 3.5 40.1 - - + +
53M GLY* 3.5 13.3 - - - -
70M THR 4.1 0.2 - - - +
71M TRP* 3.5 4.8 - - - -
72M ARG* 2.8 72.8 + - + +
73M GLU 4.2 10.3 - - - -
74M ALA* 4.6 0.7 - - + -
88M ILE* 4.5 6.7 - - + -
89M LEU* 1.3 77.3 - - - +
91M SER* 1.3 63.2 + - - +
94M TRP* 3.7 28.9 - + + -
95M LEU 3.3 8.7 - - - +
96M ILE* 4.4 6.5 - - + -
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Residues in contact with SER 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69M ARG* 3.7 16.4 - - - -
70M THR 3.1 11.4 - - - -
71M TRP* 3.6 14.8 - - - -
90M TYR* 1.3 77.7 - - - +
92M SER* 1.3 65.2 + - - +
93M ASP* 2.5 26.3 + - - -
94M TRP* 3.0 25.3 + - - -
95M LEU* 2.9 33.4 + - - +
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Residues in contact with SER 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68M GLY 3.8 4.3 + - - -
69M ARG* 3.4 10.7 - - - +
70M THR* 2.8 43.4 + - - -
91M SER* 1.3 72.4 - - - +
93M ASP* 1.3 57.8 + - - +
94M TRP* 3.3 21.0 + - - -
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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