Contacts of the strand formed by residues 95 - 99 (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 LEU 95 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64M PRO* 4.6 12.1 - - + -
69M ARG* 3.5 38.8 - - - +
71M TRP* 3.7 22.8 - - + -
90M TYR* 3.3 5.2 - - - -
91M SER* 2.9 38.8 + - - +
93M ASP* 4.0 10.3 - - - +
94M TRP* 1.3 75.7 - - - +
96M ILE* 1.3 59.9 + - - +
97M TYR* 4.1 10.3 - - + +
108M LYS* 5.8 3.4 - - + -
110M ARG 3.8 9.0 - - - +
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Residues in contact with ILE 96 (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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11M ALA* 3.6 27.1 - - + +
14M LEU* 4.1 15.7 - - + -
15M GLN* 4.4 10.3 - - + +
88M ILE* 3.7 21.3 - - + -
89M LEU 3.4 3.1 - - - +
90M TYR* 4.4 9.9 - - + -
94M TRP* 3.9 14.8 - - + +
95M LEU* 1.3 78.1 - - - +
97M TYR* 1.3 65.4 + - - +
108M LYS* 3.6 4.7 - - - +
109M ILE* 2.8 46.2 + - + +
110M ARG* 3.1 35.9 + - + -
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Residues in contact with TYR 97 (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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62M LYS 5.8 1.1 - - - -
63M LEU* 3.8 22.7 - - + -
64M PRO* 3.2 32.5 - - + +
71M TRP* 3.7 28.7 - + - -
88M ILE* 3.5 6.6 - - - +
89M LEU* 2.7 43.0 + - + +
95M LEU* 4.1 12.8 - - + +
96M ILE* 1.3 80.5 - - - +
98M LYS* 1.3 60.6 + - - +
106M PHE* 4.1 12.8 - - + -
107M THR* 3.3 7.2 - - - +
108M LYS* 3.5 55.5 - - + -
109M ILE* 3.9 3.4 - - - -
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Residues in contact with LYS 98 (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* 2.9 63.1 - - + -
87M ARG 3.5 5.4 - - - -
89M LEU* 4.9 0.2 - - - -
97M TYR* 1.3 75.2 - - - +
99M THR* 1.3 61.6 + - - +
100M THR* 2.9 24.7 - - - +
106M PHE* 3.2 8.9 - - - +
107M THR* 2.7 58.9 + - + +
109M ILE* 3.9 19.9 - - + +
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Residues in contact with THR 99 (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* 3.6 2.1 - - - -
85M SER 4.1 1.3 - - - +
86M ASP* 3.5 2.3 - - - -
87M ARG* 3.0 49.6 + - + +
89M LEU* 3.7 19.3 - - + -
98M LYS* 1.3 74.8 - - - +
100M THR* 1.3 64.9 + - - +
101M ASP* 2.8 27.0 + - - -
103M TYR* 3.0 25.2 + - + +
105M THR 2.9 15.0 + - - -
106M PHE* 3.7 9.4 - - + -
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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