Contacts of the helix formed by residues 108 - 115 (chain D) in PDB entry 5B6N
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 ARG 108 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73D ILE* 3.6 28.1 - - + +
106D ARG* 3.1 24.0 + - - +
107D ASN* 1.3 69.3 - - - +
109D GLU* 1.3 65.9 + - - +
110D LEU 3.3 0.2 - - - -
111D ALA* 3.0 27.6 + - + +
112D ILE* 3.4 12.1 + - + +
117D LEU* 5.0 3.3 - - + +
125D LYS* 4.1 24.7 - - - +
127D MET* 3.1 40.9 + - - +
128D PRO* 3.4 39.9 + - + +
129D VAL 4.8 1.1 - - - +
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Residues in contact with GLU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLU* 5.6 5.9 + - - +
107D ASN* 3.9 18.5 + - + +
108D ARG* 1.3 78.8 - - - +
110D LEU* 1.3 58.3 + - - +
111D ALA 3.1 0.5 + - - -
112D ILE* 3.6 7.1 + - - +
113D LEU* 3.0 54.1 + - + +
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Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PRO 5.8 0.9 - - - +
13D ASN 5.7 0.2 - - - +
14D PHE* 3.5 48.5 - - + -
16D ALA* 6.1 1.1 - - + -
71D LEU* 4.9 7.6 - - + -
103D ILE* 6.4 0.7 - - + -
105D ASP* 3.4 25.8 - - - +
107D ASN* 3.3 12.9 + - + +
108D ARG 3.3 0.6 - - - -
109D GLU* 1.3 77.6 - - - +
111D ALA* 1.3 65.2 + - - +
113D LEU* 3.6 25.8 - - + -
114D LEU* 3.1 46.9 + - + +
116D MET* 3.9 4.6 - - + +
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Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ASN 3.9 2.6 + - - +
108D ARG* 3.0 21.6 + - - +
110D LEU* 1.3 77.4 - - - +
112D ILE* 1.3 55.8 - - - +
113D LEU 3.0 0.4 - - - -
114D LEU 2.8 4.7 + - - -
115D GLY* 2.2 37.8 + - - -
116D MET* 3.7 16.6 - - + -
117D LEU* 3.6 36.6 - - + +
129D VAL 4.9 2.2 - - - +
130D THR* 5.9 1.1 - - - -
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Residues in contact with ILE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 5.7 10.1 - - + -
108D ARG* 3.6 15.5 - - + +
109D GLU* 3.9 6.7 - - - +
111D ALA* 1.3 71.2 - - + +
113D LEU* 1.3 69.3 + - + +
114D LEU 4.4 0.7 - - - -
115D GLY* 4.2 6.0 + - - +
117D LEU* 3.6 28.5 - - + -
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Residues in contact with LEU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PRO* 5.9 6.7 - - + -
13D ASN 5.3 7.9 - - - +
14D PHE* 5.8 0.9 - - + -
109D GLU* 3.0 46.0 + - + +
110D LEU* 3.6 30.7 - - + -
111D ALA 3.0 0.2 - - - -
112D ILE* 1.3 82.4 - - + +
114D LEU* 1.3 66.6 + - + +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ALA* 6.5 0.9 - - + -
12D PRO* 5.4 16.6 - - + +
14D PHE* 5.4 7.2 - - + -
36D LEU* 5.1 7.4 - - + -
110D LEU* 3.2 42.4 - - + +
111D ALA 2.8 3.0 + - - -
112D ILE 4.4 1.3 - - - -
113D LEU* 1.3 87.7 - - + +
115D GLY* 1.3 58.8 + - - +
116D MET* 3.8 32.1 - - + -
135D PHE* 4.6 21.5 - - + -
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Residues in contact with GLY 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 4.2 23.5 - - - +
111D ALA 2.2 22.4 + - - -
112D ILE* 4.7 5.2 - - - -
113D LEU 3.8 0.2 - - - -
114D LEU* 1.3 69.6 - - - +
116D MET* 1.3 53.5 + - - +
117D LEU* 2.7 27.9 + - - +
133D VAL* 5.2 5.3 - - - +
135D PHE* 5.6 1.8 - - - -
148D LEU* 5.0 11.6 - - - +
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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