Contacts of the helix formed by residues 106 - 117 (chain K) in PDB entry 6R1U
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 106 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98K HIS* 2.9 39.0 + - - -
99K TYR* 2.9 27.3 - - - -
105K ASP* 1.3 74.7 - - - +
107K TYR* 1.3 63.2 + - - +
108K ASP 3.4 1.8 - - - -
109K LYS* 3.6 7.4 + - - -
110K TYR 3.3 10.7 + - - -
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Residues in contact with TYR 107 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24F ASP* 5.6 4.2 + - - -
98K HIS 3.4 1.0 + - - -
99K TYR 3.3 24.7 - - - -
100K TYR 3.7 12.1 - - - -
101K ARG 3.2 29.2 - - - +
102K SER* 3.4 32.3 - - - +
104K LYS 3.2 11.4 + - - +
105K ASP 3.3 0.2 - - - -
106K GLY* 1.3 75.3 - - - +
108K ASP* 1.3 60.8 + - - +
110K TYR* 3.1 6.2 + + - +
111K THR* 2.7 62.2 + - + +
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Residues in contact with ASP 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104K LYS 4.8 0.2 + - - -
105K ASP 4.4 8.8 + - - +
107K TYR* 1.3 80.5 - - - +
109K LYS* 1.3 63.9 + - - +
111K THR* 2.8 20.9 + - - -
112K THR* 2.9 27.6 + - - -
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Residues in contact with LYS 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K TYR* 4.2 14.4 - - + +
105K ASP 5.2 0.6 + - - +
106K GLY* 3.6 13.1 + - - +
107K TYR 3.3 0.4 - - - -
108K ASP* 1.3 79.7 - - - +
110K TYR* 1.3 59.8 + - - +
112K THR* 4.2 5.4 - - - -
113K TRP* 3.4 23.9 + - - +
130K PHE* 3.6 8.9 - - + -
134K GLN* 4.4 12.4 + - + +
135K GLN* 3.0 30.3 - - - +
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Residues in contact with TYR 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K TYR* 3.7 31.6 - - + +
100K TYR* 4.4 18.7 - + - -
106K GLY 3.3 13.7 + - - +
107K TYR* 3.1 8.0 + + - +
108K ASP 3.1 0.8 - - - -
109K LYS* 1.3 79.2 - - - +
111K THR* 1.3 67.0 + - + +
113K TRP* 3.6 10.6 - + - -
114K LYS* 3.1 48.1 + - + +
125K PRO 3.0 23.3 + - - -
127K PRO* 3.2 31.5 - - + +
130K PHE* 3.5 45.0 - + + -
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Residues in contact with THR 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K TYR* 2.7 58.0 + - + +
108K ASP* 2.8 16.8 + - - -
110K TYR* 1.3 79.2 - - + +
112K THR* 1.3 63.2 + - - +
114K LYS* 3.2 12.8 + - + +
115K LYS* 3.0 22.0 + - - +
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Residues in contact with THR 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K ASP* 2.9 28.2 + - - -
109K LYS* 4.2 5.3 - - - -
111K THR* 1.3 74.1 + - - +
113K TRP* 1.3 60.9 + - - +
115K LYS* 2.9 39.7 + - + +
116K ILE* 3.1 22.8 + - + +
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Residues in contact with TRP 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K LYS 3.4 18.2 + - - +
110K TYR* 3.6 17.5 - + - +
112K THR* 1.3 79.2 - - - +
114K LYS* 1.3 76.2 + - - +
116K ILE* 3.9 9.0 - - - +
117K TRP* 2.9 64.0 + + - +
125K PRO* 3.4 40.2 - - + -
126K SER 3.6 1.8 - - - -
129K ALA* 3.9 5.6 - - + -
130K PHE* 3.3 58.5 - + + -
133K ASP* 2.8 21.3 + - - +
134K GLN* 3.5 23.5 - - - +
233K SER* 4.3 11.4 - - - -
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Residues in contact with LYS 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K TYR* 6.0 3.4 - - - -
110K TYR* 3.1 43.2 + - + +
111K THR* 3.4 14.6 - - + +
112K THR 3.1 0.4 - - - -
113K TRP* 1.3 87.0 - - + +
115K LYS* 1.3 49.9 + - - +
117K TRP* 4.0 2.4 - - - +
118K THR* 2.6 32.5 + - + +
125K PRO* 3.5 39.2 + - + +
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Residues in contact with LYS 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111K THR 3.0 10.4 + - - +
112K THR* 2.9 25.2 + - + +
114K LYS* 1.3 74.2 - - - +
116K ILE* 1.3 93.5 + - + +
117K TRP 3.2 0.2 - - - -
118K THR* 2.4 27.9 + - - -
119K SER* 3.0 19.7 + - - +
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Residues in contact with ILE 116 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112K THR* 3.1 17.5 + - + +
113K TRP* 3.9 11.4 - - + +
115K LYS* 1.3 104.7 - - + +
117K TRP* 1.3 60.3 + - - +
118K THR 3.0 5.0 + - - -
119K SER* 3.3 8.1 + - - -
120K ASN* 3.1 37.8 + - - +
232K PRO 4.0 16.8 - - - +
233K SER* 4.0 19.1 - - - +
234K CYS 5.7 0.9 - - - +
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Residues in contact with TRP 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K TRP* 2.9 54.2 + + + +
114K LYS* 4.0 6.3 - - - +
115K LYS 3.2 0.2 - - - -
116K ILE* 1.3 76.4 - - - +
118K THR* 1.3 57.9 + - - +
121K GLY* 3.3 20.0 + - - +
123K THR* 3.0 46.7 + - - +
124K GLU 4.1 0.8 - - - -
125K PRO* 3.4 22.3 - - + +
129K ALA* 4.6 12.6 - - + -
133K ASP* 3.4 33.0 - - + -
210K LEU* 3.7 28.5 - - + -
226K ASP* 4.3 1.6 + - - -
231K SER* 4.0 1.8 - - - -
232K PRO* 3.8 34.8 - - + -
233K SER* 4.4 4.9 - - - -
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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