Contacts of the helix formed by residues 105 - 115 (chain D) in PDB entry 3S52
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 105 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66D SER* 3.4 6.2 + - - +
68D HIS* 3.7 38.8 - - + +
103D THR* 3.2 11.6 + - + +
104D LEU* 1.3 70.9 - - - +
106D GLU* 1.3 62.2 + - + +
108D GLN* 3.2 10.6 + - - +
109D ALA* 2.8 29.3 + - - +
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Residues in contact with GLU 106 (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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3C GLN* 3.0 38.9 + - - +
5C ARG* 4.2 8.4 + - - +
11C LEU* 3.7 22.4 + - + +
64D PHE 5.7 0.2 + - - -
65D GLY* 3.8 0.6 - - - -
66D SER* 3.0 42.3 + - - +
105D ARG* 1.3 74.9 - - + +
107D LEU* 1.3 67.7 + - - +
109D ALA* 3.4 9.0 + - - +
110D GLY* 3.1 17.7 + - - -
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Residues in contact with LEU 107 (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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178A PHE* 4.0 29.4 - - + -
11C LEU* 3.5 37.2 - - + +
12C LEU 4.7 7.0 - - - -
13C ASP* 4.9 5.4 - - + +
64D PHE* 3.6 22.1 + - + +
104D LEU* 3.5 27.9 + - + +
105D ARG 3.3 0.2 - - - -
106D GLU* 1.3 78.9 - - - +
108D GLN* 1.3 62.1 + - - +
110D GLY* 3.1 5.8 + - - -
111D PHE* 3.0 55.9 + - + -
120D LYS* 4.5 2.7 - - + +
121D ALA* 4.2 0.9 - - + -
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Residues in contact with GLN 108 (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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103D THR* 3.7 17.7 - - + +
104D LEU 2.9 19.4 + - - +
105D ARG* 3.5 7.9 - - - +
107D LEU* 1.3 75.3 - - - +
109D ALA* 1.3 64.6 + - - +
111D PHE* 3.1 6.3 + - - +
112D LYS* 2.9 40.8 + - + +
118D TRP* 3.1 54.1 - - + +
121D ALA* 3.7 15.7 - - + +
122D LYS* 3.8 9.2 - - + +
219D SO4 3.7 14.7 + - - -
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Residues in contact with ALA 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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105D ARG 2.8 19.6 + - - +
106D GLU* 3.6 9.6 - - - +
107D LEU 3.3 0.2 - - - -
108D GLN* 1.3 71.7 - - - +
110D GLY* 1.3 62.2 - - - +
112D LYS* 3.5 12.2 + - - +
113D LYS* 3.3 22.5 + - - +
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Residues in contact with GLY 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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10C ALA* 4.0 31.4 - - - +
11C LEU 4.9 1.6 - - - -
106D GLU 3.1 10.0 + - - -
107D LEU 3.1 8.6 + - - -
109D ALA* 1.3 75.5 - - - +
111D PHE* 1.3 63.3 - - - +
113D LYS* 3.3 6.7 + - - +
114D ALA* 3.1 24.1 + - - +
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Residues in contact with PHE 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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11C LEU 5.7 2.0 - - - -
107D LEU* 3.0 36.1 + - + -
108D GLN* 3.6 11.4 - - - +
110D GLY* 1.3 72.7 - - - +
112D LYS* 1.3 56.2 + - - +
114D ALA* 4.5 0.9 - - - +
115D GLY* 2.7 30.3 + - - -
116D GLN* 2.7 56.3 + - + +
117D PRO 3.5 18.2 - - - +
118D TRP* 4.2 9.6 - - + -
120D LYS* 3.8 45.5 - - + -
121D ALA* 3.8 18.8 - - + -
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Residues in contact with LYS 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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112A LYS 4.6 0.9 - - - +
115A GLY* 3.2 46.2 + - - +
108D GLN* 2.9 44.0 + - + +
109D ALA* 3.8 9.4 - - - +
111D PHE* 1.3 76.2 - - - +
113D LYS* 1.3 63.4 + - - +
115D GLY* 3.2 5.0 + - - -
118D TRP* 3.8 18.8 - - + +
219D SO4 5.2 5.9 + - - -
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Residues in contact with LYS 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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112A LYS 5.5 0.5 - - - +
109D ALA 3.3 11.7 + - - +
110D GLY* 3.7 8.7 - - - +
112D LYS* 1.3 80.9 - - - +
114D ALA* 1.3 62.7 + - + +
115D GLY 3.5 0.3 + - - -
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Residues in contact with ALA 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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112A LYS* 4.9 2.3 - - - +
6C ASP* 5.7 4.0 - - - +
8C GLN* 6.4 2.2 - - + -
110D GLY 3.1 15.9 + - - +
113D LYS* 1.3 76.9 - - + +
115D GLY* 1.3 63.8 + - - +
116D GLN* 3.5 28.2 + - + +
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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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112A LYS* 3.3 39.6 + - - +
115A GLY* 4.4 4.9 - - - -
116A GLN 5.6 0.4 - - - -
118A TRP* 3.2 26.6 + - - -
111D PHE 2.7 8.9 + - - -
112D LYS 3.2 9.0 + - - -
113D LYS 3.3 0.8 + - - -
114D ALA* 1.3 79.8 - - - +
116D GLN* 1.3 59.2 + - - -
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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