Contacts of the strand formed by residues 106 - 112 (chain C) in PDB entry 3BPL
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 PHE 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C CYS* 4.0 8.5 - - - -
48C MET* 3.7 28.7 - - + -
50C CYS* 5.1 0.7 - - - -
65C LEU* 6.0 0.2 - - + -
67C TYR* 3.8 37.2 - + + -
68C TRP 4.5 2.0 - - - -
69C TYR* 3.5 33.2 - + + -
95C LEU* 4.3 3.8 - - + -
104C GLN 3.0 2.1 + - - +
105C THR* 1.3 70.3 - - - +
107C VAL* 1.3 66.5 + - - +
108C VAL* 3.3 33.0 - - + -
122C GLN 3.8 0.2 - - - +
123C MET* 2.9 4.0 - - - -
124C LEU* 2.5 53.6 + - + +
126C LEU* 3.5 32.1 - - + -
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Residues in contact with VAL 107 (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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66C HIS 3.8 0.2 - - - +
67C TYR* 3.2 6.0 - - - -
68C TRP* 2.9 82.6 + - + +
70C LYS* 4.2 21.8 - - + -
105C THR 4.3 0.9 - - - +
106C PHE* 1.3 80.8 - - - +
108C VAL* 1.3 61.8 + - - +
121C THR* 3.6 13.7 - - - +
122C GLN 3.0 15.5 - - - +
123C MET* 3.8 16.4 - - + -
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Residues in contact with VAL 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C VAL* 4.3 21.8 - - + -
40C CYS* 4.0 13.5 - - - -
50C CYS* 4.9 0.7 - - - -
65C LEU* 4.6 11.9 - - + -
66C HIS 3.4 4.3 - - - +
67C TYR* 4.4 4.7 - - + +
106C PHE* 3.3 36.9 - - + -
107C VAL* 1.3 73.6 - - - +
109C GLN* 1.3 61.3 + - - +
120C ALA 4.1 0.7 - - - +
121C THR* 3.6 3.1 + - - -
122C GLN* 2.7 66.6 + - + +
124C LEU* 4.8 8.1 - - + -
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Residues in contact with GLN 109 (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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38C VAL* 5.7 0.4 - - - -
64C THR 3.4 1.6 - - - +
65C LEU* 3.3 11.0 - - - +
66C HIS* 2.6 69.0 + - + +
68C TRP* 3.6 27.0 - - + -
108C VAL* 1.3 75.8 - - - +
110C LEU* 1.3 65.1 + - - +
111C GLN* 3.7 15.0 + - - +
119C GLN* 4.0 23.2 + - + +
120C ALA 3.8 4.3 - - - +
121C THR* 4.9 4.6 - - - -
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Residues in contact with LEU 110 (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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35C LEU* 3.3 23.8 - - + +
36C PRO* 3.2 36.3 - - + +
38C VAL* 3.8 24.5 - - + +
52C TRP* 3.6 45.3 - - + -
63C LEU* 4.5 20.2 - - + -
64C THR 3.7 6.7 - - - +
65C LEU* 4.7 3.4 - - + -
108C VAL* 4.3 0.4 - - - +
109C GLN* 1.3 73.6 - - - +
111C GLN* 1.3 58.0 + - - +
119C GLN* 3.3 18.3 - - - +
120C ALA* 3.2 15.8 + - + +
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Residues in contact with GLN 111 (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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35C LEU* 4.9 0.2 - - - -
63C LEU* 3.1 13.4 - - - +
64C THR* 2.9 49.6 + - - +
66C HIS* 4.0 14.3 - - + +
109C GLN* 3.7 14.0 + - + +
110C LEU* 1.3 73.2 - - - +
112C ASP* 1.3 69.5 + - - +
113C PRO* 4.7 2.5 - - + -
115C GLU 3.0 26.3 + - - -
116C PRO* 3.3 21.8 + - - +
118C ARG 4.5 0.2 - - - -
119C GLN* 3.5 25.2 - - - +
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Residues in contact with ASP 112 (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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35C LEU* 4.8 0.4 - - + -
57C GLU* 5.0 2.3 - - - +
61C THR* 3.6 14.1 + - - +
63C LEU* 3.6 17.0 - - + -
111C GLN* 1.3 83.1 + - - +
113C PRO* 1.3 70.0 - - - +
114C ARG* 3.1 20.5 + - - +
115C GLU* 2.5 58.3 + - - +
116C PRO* 4.4 0.5 - - - +
118C ARG* 3.7 27.2 + - + +
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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