Contacts of the helix formed by residues 104 - 112 (chain F) in PDB entry 3DLL
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 GLN 104 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79F ILE* 5.2 9.0 - - + +
100F LEU* 4.2 19.7 - - + +
101F ASN* 2.7 59.0 + - + +
102F TRP 3.4 0.6 - - - -
103F ASP* 1.3 82.8 - - - +
105F VAL* 1.3 70.6 + - + +
106F LEU 3.2 2.0 + - - -
107F GLU* 3.2 8.1 + - - +
108F ILE* 3.0 35.4 + - + +
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Residues in contact with VAL 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F ASN 5.4 1.1 - - - +
102F TRP* 4.8 10.8 - - + +
104F GLN* 1.3 76.4 - - + +
106F LEU* 1.3 58.5 + - + +
108F ILE* 2.7 13.2 + - + +
109F ALA* 2.3 38.0 + - - +
124F ALA 4.0 3.1 - - - +
125F ALA* 3.8 22.0 - - + +
128F VAL* 3.1 44.6 - - + -
129F ALA* 6.2 1.3 - - - -
132F ALA* 5.7 3.8 - - + -
139F VAL* 4.4 27.8 - - + -
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F TRP* 4.8 7.6 - - + +
103F ASP* 3.1 53.6 - - + +
105F VAL* 1.3 79.7 - - + +
107F GLU* 1.3 52.7 + - + +
109F ALA* 3.1 7.5 + - - +
110F LYS* 2.4 55.1 + - - +
121F VAL* 4.0 27.6 - - + +
124F ALA 5.4 0.4 - - - -
125F ALA* 6.0 4.3 - - + -
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Residues in contact with GLU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ASP 4.8 8.4 - - - +
104F GLN* 3.2 7.6 + - - +
106F LEU* 1.3 76.2 - - + +
108F ILE* 1.3 56.5 + - + +
109F ALA 3.0 1.3 - - - -
110F LYS* 3.4 35.5 + - + +
111F THR* 2.5 51.9 + - + +
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Residues in contact with ILE 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F SER* 3.3 15.5 - - - +
79F ILE* 3.4 41.1 - - + -
80F ARG* 4.5 23.3 - - + +
100F LEU* 5.4 6.1 - - + -
104F GLN* 3.0 31.3 + - + +
105F VAL* 2.7 16.0 + - + +
107F GLU* 1.3 72.2 - - + +
109F ALA* 1.3 59.4 + - - +
111F THR* 2.8 12.4 + - - -
112F LYS* 2.8 35.1 - - + +
128F VAL* 5.6 8.7 - - + -
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Residues in contact with ALA 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F VAL* 2.3 28.5 + - + +
106F LEU* 3.1 10.1 - - - +
108F ILE* 1.3 66.2 - - - +
110F LYS* 1.3 54.3 + - - +
112F LYS* 2.5 42.4 + - - +
113F MET* 2.8 10.1 - - + +
121F VAL* 5.5 3.1 - - + -
124F ALA* 3.0 41.1 - - + +
128F VAL* 4.8 6.3 - - + -
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Residues in contact with LYS 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU* 2.4 47.8 + - - +
107F GLU* 3.4 41.7 + - + +
109F ALA* 1.3 65.6 - - - +
111F THR* 1.3 59.2 + - + +
112F LYS 2.8 18.4 - - - +
113F MET* 3.1 19.3 - - + +
121F VAL* 4.9 12.6 - - + -
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Residues in contact with THR 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F PRO* 4.7 7.6 - - - +
75F MET 5.3 1.3 - - - -
76F SER* 2.9 41.2 + - - +
107F GLU* 2.5 44.0 + - + +
108F ILE* 2.8 15.2 + - - -
110F LYS* 1.3 76.4 - - + +
112F LYS* 1.3 55.9 + - - +
114F PRO* 4.8 2.6 - - - +
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Residues in contact with LYS 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F LYS* 4.6 5.8 - - - -
72F THR* 3.6 11.8 + - - +
73F PRO* 3.4 16.4 - - + -
76F SER* 3.2 30.9 + - - +
77F TYR* 2.8 40.7 - - - +
80F ARG* 5.6 3.0 - - - +
108F ILE* 2.8 28.7 + - + +
109F ALA* 2.5 23.1 + - - +
110F LYS 2.8 10.4 - - - +
111F THR* 1.3 72.8 - - - +
113F MET* 1.3 66.0 + - - +
114F PRO* 3.0 14.2 - - + +
115F ASP* 6.1 0.9 - - + +
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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