Contacts of the strand formed by residues 117 - 123 (chain C) in PDB entry 2BME
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 VAL 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C ALA 3.0 9.7 + - - +
85C GLY* 3.1 1.9 - - - -
86C ALA 2.8 26.5 + - - +
115C ASN 3.4 1.5 + - - +
116C ILE* 1.3 71.2 - - - +
118C ILE* 1.3 63.0 + - - +
119C ILE* 4.4 4.5 - - + -
167C CYS* 3.6 20.0 - - - +
170C LYS* 3.7 40.2 - - + -
171C ILE* 3.7 28.7 - - + +
174C LYS* 3.7 28.0 - - + +
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Residues in contact with ILE 118 (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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16C ILE* 5.9 0.7 - - + -
86C ALA* 3.3 13.5 - - + +
88C LEU* 3.7 33.0 - - + -
105C LEU* 3.4 26.2 - - + -
108C ALA* 4.0 18.2 - - + -
109C ARG* 4.2 9.2 - - + +
116C ILE* 3.6 31.8 + - + +
117C VAL* 1.3 78.9 - - - +
119C ILE* 1.3 70.5 + - - +
120C LEU 4.6 0.4 - - - +
146C GLU 4.9 1.4 + - - +
147C LEU* 3.9 26.5 - - + +
148C MET 3.7 17.8 + - - -
170C LYS* 5.8 0.3 - - - +
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Residues in contact with ILE 119 (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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86C ALA 3.0 9.4 + - - +
87C LEU* 3.5 8.6 - - + -
88C LEU 2.9 24.8 + - - +
117C VAL* 4.4 1.6 - - + -
118C ILE* 1.3 78.6 - - - +
120C LEU* 1.3 69.0 + - - +
121C CYS* 3.6 3.9 + - - -
148C MET* 3.5 30.5 - - + +
150C LEU* 4.2 13.9 - - + -
163C ALA* 3.6 39.9 - - + +
166C GLN* 4.0 9.2 - - + -
167C CYS* 3.7 33.4 - - + +
170C LYS* 4.1 11.4 - - + -
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Residues in contact with LEU 120 (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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88C LEU* 3.5 26.5 - - + +
90C TYR* 3.9 15.9 - - + -
101C LEU* 3.8 32.1 - - + -
118C ILE* 4.0 2.8 + - - +
119C ILE* 1.3 74.4 - - - +
121C CYS* 1.3 60.0 + - - +
138C ALA* 4.3 6.5 - - + +
141C PHE* 4.2 17.3 - - + -
142C ALA* 4.1 17.0 - - + -
147C LEU* 4.1 17.9 - - + +
148C MET 2.9 14.9 + - - +
149C PHE* 3.5 23.5 - - + -
150C LEU 3.0 27.0 + - - +
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Residues in contact with CYS 121 (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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26C LEU* 4.8 3.6 - - + -
87C LEU* 4.0 24.9 - - - -
88C LEU 2.8 13.2 + - - +
89C VAL* 3.4 14.0 - - + +
90C TYR* 3.0 29.3 + - - +
119C ILE* 4.0 7.6 - - - -
120C LEU* 1.3 77.6 - - - +
122C GLY* 1.3 58.5 + - - +
123C ASN 3.4 2.8 + - - -
150C LEU* 3.3 4.9 - - - -
152C THR* 4.1 20.2 - - + +
163C ALA* 3.9 28.9 - - - -
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Residues in contact with GLY 122 (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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90C TYR* 3.4 32.9 - - - -
92C ILE* 3.6 11.7 - - - +
121C CYS* 1.3 67.7 - - - +
123C ASN* 1.3 64.4 + - - -
125C LYS 4.5 0.5 + - - -
149C PHE* 3.9 4.9 - - - -
150C LEU 3.0 13.2 + - - -
151C GLU* 3.1 10.2 - - - +
152C THR 2.8 22.8 + - - +
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Residues in contact with ASN 123 (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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21C THR 2.9 23.7 + - - +
22C GLY* 3.5 10.9 + - - -
26C LEU* 3.4 9.5 - - - +
89C VAL* 3.9 10.1 - - + -
90C TYR 2.8 18.6 + - - +
91C ASP* 3.7 0.3 - - - -
92C ILE* 3.0 25.6 + - - +
121C CYS 3.4 0.2 + - - -
122C GLY* 1.3 73.9 - - - +
124C LYS* 1.3 79.8 + - - +
125C LYS 3.3 0.9 - - - -
152C THR* 2.9 28.9 + - - +
154C ALA 3.2 16.8 + - - -
1178C GNP 3.3 24.4 + - - -
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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