Contacts of the helix formed by residues 87 - 95 (chain C) in PDB entry 3LBF
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 GLY 87 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C PHE* 3.4 11.9 - - - -
84C THR* 2.8 17.2 + - - -
85C GLY 3.2 0.4 - - - -
86C SER* 1.3 76.9 - - - +
88C TYR* 1.3 58.6 + - - +
89C GLN 3.5 1.8 - - - -
90C THR* 3.2 16.5 + - - -
91C ALA* 2.8 26.0 + - - +
113C ALA* 4.0 11.7 - - - -
117C LEU* 3.6 6.5 - - - +
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Residues in contact with TYR 88 (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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27C LEU* 3.5 29.6 + - - +
30C VAL* 3.7 31.3 + - + -
32C ARG* 3.5 55.8 - - + +
35C PHE* 3.4 20.6 - + + -
45C TRP* 5.2 1.2 - - - -
58C ILE* 3.6 13.0 - - + -
59C SER 5.7 0.2 - - - -
61C PRO* 4.7 4.6 - - + +
64C VAL* 4.0 22.0 - - + -
86C SER* 3.1 17.4 + - - +
87C GLY* 1.3 74.4 - - - +
89C GLN* 1.3 68.9 + - - +
90C THR 3.2 0.5 + - - -
91C ALA* 3.2 4.0 + - - +
92C ILE* 3.2 39.8 + - + +
300C SAH 3.4 5.9 + - - +
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Residues in contact with GLN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C VAL* 3.4 29.9 - - + +
67C MET* 4.6 9.2 - - - +
68C THR* 2.9 28.4 + - - -
81C GLU* 3.2 21.5 - - - +
88C TYR* 1.3 78.8 - - - +
90C THR* 1.3 62.1 + - - +
92C ILE* 3.3 16.9 + - - +
93C LEU* 3.0 36.2 + - + +
146C ILE* 4.7 9.0 - - + +
148C THR* 4.2 13.7 - - + +
300C SAH 3.2 18.8 + - - +
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Residues in contact with THR 90 (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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81C GLU* 2.6 28.8 + - - +
84C THR* 3.5 8.8 + - + +
87C GLY* 3.3 22.8 - - - -
88C TYR 3.0 0.4 - - - -
89C GLN* 1.3 79.4 - - - +
91C ALA* 1.3 57.4 + - - +
93C LEU* 3.3 6.9 + - - +
94C ALA* 2.9 27.8 + - - +
100C VAL* 4.1 8.5 - - + +
102C SER* 4.1 8.7 - - - -
117C LEU* 4.1 10.8 - - + -
125C VAL* 3.7 32.3 - - + -
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Residues in contact with ALA 91 (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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30C VAL* 3.8 23.8 - - + -
35C PHE* 4.0 9.2 - - + -
87C GLY 2.8 16.3 + - - +
88C TYR 3.2 4.9 + - - +
90C THR* 1.3 75.4 - - - +
92C ILE* 1.3 62.2 + - - +
94C ALA* 3.2 12.4 + - - +
95C HIS* 3.2 21.0 + - - -
117C LEU* 4.2 6.9 - - + +
120C LEU* 4.4 0.7 - - + -
122C LEU* 3.7 24.7 - - + -
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Residues in contact with ILE 92 (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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23C VAL* 4.8 5.8 - - + +
26C ALA* 3.9 14.5 - - + +
27C LEU* 4.1 21.1 - - + +
30C VAL* 3.9 18.2 - - + -
64C VAL* 3.4 28.9 - - + -
68C THR* 4.3 8.7 - - + +
88C TYR* 3.2 40.5 + - + +
89C GLN* 3.3 16.1 + - - +
91C ALA* 1.3 73.8 - - - +
93C LEU* 1.3 65.7 + - - +
95C HIS* 3.3 14.2 + - - +
96C LEU* 3.4 23.3 + - + +
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Residues in contact with LEU 93 (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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68C THR* 4.4 4.7 - - + -
71C LEU* 3.9 17.9 - - + -
73C LEU* 4.0 15.7 - - + -
79C VAL* 4.1 12.6 - - + -
81C GLU* 4.0 15.9 - - + -
89C GLN* 3.0 35.5 + - + +
90C THR* 3.3 6.0 + - - +
92C ILE* 1.3 75.4 - - - +
94C ALA* 1.3 57.2 + - - +
96C LEU* 2.8 22.0 + - - +
97C VAL* 3.1 17.4 + - + +
100C VAL* 3.7 19.5 - - + -
146C ILE* 2.9 38.8 - - + -
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Residues in contact with ALA 94 (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 THR 2.9 13.8 + - - +
91C ALA* 3.2 11.8 + - - +
93C LEU* 1.3 75.8 - - - +
95C HIS* 1.3 60.4 + - - +
96C LEU 3.3 0.9 + - - -
97C VAL 3.5 4.5 - - - +
100C VAL* 3.8 6.0 - - - +
122C LEU* 3.9 19.7 - - + -
124C ASN* 3.0 42.6 + - - +
125C VAL* 3.9 14.6 - - + -
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Residues in contact with HIS 95 (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 ALA* 3.8 18.6 - - + +
29C ALA* 3.9 27.1 + - + +
30C VAL* 3.6 24.9 - - + +
91C ALA 3.2 22.3 + - - -
92C ILE* 3.6 8.3 - - - +
93C LEU 3.2 0.6 - - - -
94C ALA* 1.3 75.9 - - - +
96C LEU* 1.3 62.6 + - - +
97C VAL 5.1 0.2 - - - -
122C LEU* 3.8 28.8 - - + +
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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