Contacts of the strand formed by residues 99 - 103 (chain C) in PDB entry 2BZN
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 99 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ALA* 5.0 5.4 - - + -
73C PHE* 3.6 6.0 - - - -
74C THR* 3.1 17.5 - - - +
76C VAL* 4.0 20.9 - - + -
85C TRP* 4.4 7.4 - - + -
88C PHE* 3.8 28.9 - - + -
95C CYS* 3.6 15.7 - - + +
96C LEU* 3.1 35.4 - - + +
97C GLU 3.5 1.4 + - - -
98C HIS* 1.3 79.9 - - - +
100C ALA* 1.3 61.0 + - - +
123C VAL* 3.8 27.9 - - + +
124C LYS 4.6 0.5 + - - -
125C TYR* 3.4 23.0 + - - +
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Residues in contact with ALA 100 (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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73C PHE* 3.6 12.3 - - + -
74C THR 3.0 4.9 + - - -
75C ALA* 4.2 7.4 - - - -
76C VAL* 3.0 33.5 + - - +
99C LEU* 1.3 76.2 - - - +
101C ALA* 1.3 59.9 + - - +
123C VAL* 4.6 1.8 - - - -
125C TYR* 3.3 24.0 - - + +
127C CYS* 4.1 22.4 - - + +
155C MET* 4.4 5.6 - - - -
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Residues in contact with ALA 101 (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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76C VAL 4.7 0.7 - - - -
85C TRP* 4.1 26.0 - - + -
100C ALA* 1.3 74.7 - - - +
102C SER* 1.3 55.5 + - - +
113C LEU* 3.5 24.4 - - + +
116C ILE* 4.1 16.2 - - + -
117C LEU* 4.5 2.0 - - + -
123C VAL* 4.0 11.8 - - + +
125C TYR 3.1 7.2 + - - +
126C ILE* 3.4 5.9 - - - -
127C CYS 2.8 27.2 + - - -
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Residues in contact with SER 102 (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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54C ASN* 3.5 28.6 - - - +
75C ALA 4.2 0.5 - - - -
76C VAL 2.8 29.4 + - - -
77C HIS 4.9 1.4 + - - -
78C LYS* 3.9 24.2 - - - +
85C TRP* 5.6 0.2 - - - -
100C ALA 4.3 0.2 + - - -
101C ALA* 1.3 77.3 - - - +
103C SER* 1.3 65.7 + - - +
109C ASP 5.0 0.9 - - - +
112C GLN* 6.0 0.3 + - - -
113C LEU* 4.2 9.7 - - - +
116C ILE* 5.9 2.1 - - - +
127C CYS* 3.1 19.9 - - - +
129C ASP* 5.7 0.2 - - - -
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Residues in contact with SER 103 (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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78C LYS* 3.9 9.4 - - - +
102C SER* 1.3 78.3 - - - +
104C GLY* 1.3 81.1 + - - +
109C ASP* 3.3 14.9 - - - +
110C PHE* 3.4 12.1 + - - +
113C LEU* 3.8 28.9 - - - -
127C CYS 2.9 6.3 + - - -
128C LEU* 3.3 13.1 - - - +
129C ASP* 3.1 26.3 + - - +
141C PHE* 4.3 1.9 - - - -
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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