Contacts of the helix formed by residues 117 - 122 (chain E) in PDB entry 6B0B
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 LYS 117 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A TRP* 3.5 38.0 - - + -
125A LEU* 5.8 0.6 - - - +
116E CYS* 1.3 78.5 - - - +
118E PRO* 1.3 69.8 - - + +
120E GLN* 3.0 17.7 + - - +
121E ASP* 3.0 13.6 - - - +
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Residues in contact with PRO 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A SER* 4.5 8.3 - - - +
87A SER* 4.1 10.3 - - - -
90A TRP* 3.3 44.6 - - + +
118A PRO* 5.6 4.8 - - + +
86E SER* 3.7 19.5 - - - +
90E TRP* 5.6 0.3 + - - -
116E CYS* 3.6 15.0 - - - -
117E LYS* 1.3 92.7 - - + +
119E GLN* 1.3 58.8 + - + +
121E ASP* 2.9 18.7 - - - +
122E GLY* 3.1 14.0 + - - -
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Residues in contact with GLN 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A SER* 3.2 31.8 + - - -
84E PRO 4.0 1.5 - - - +
85E CYS* 3.2 36.4 - - - +
86E SER* 3.7 19.7 - - - +
112E TYR* 3.4 9.2 + - - +
113E TYR* 3.1 44.0 - - + +
114E HIS* 4.0 21.2 + - - +
116E CYS* 4.4 4.8 + - - +
117E LYS 3.4 0.8 - - - -
118E PRO* 1.3 76.3 - - + +
120E GLN* 1.3 62.8 + - - +
122E GLY* 3.9 2.9 - - - +
123E LEU* 3.8 22.1 + - + +
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Residues in contact with GLN 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E TYR* 4.7 9.4 - - - -
116E CYS 4.2 8.3 + - - +
117E LYS* 3.0 19.2 + - - +
119E GLN* 1.3 81.2 - - - +
121E ASP* 1.3 64.1 + - + +
122E GLY 3.5 0.7 + - - -
123E LEU* 3.7 11.5 - - - +
124E ARG* 3.7 34.3 + - - +
176E ARG* 4.3 10.0 + - - +
180E ILE* 3.7 42.1 - - - +
7F A 5.5 5.6 + - - -
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Residues in contact with ASP 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E TRP* 4.9 12.1 + - - -
117E LYS 3.0 11.4 - - - +
118E PRO* 2.9 19.2 - - - +
120E GLN* 1.3 74.5 - - + +
122E GLY* 1.3 62.4 + - - +
123E LEU 3.1 2.9 - - - -
124E ARG* 3.2 24.4 + - + +
125E LEU* 3.5 14.2 + - - +
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Residues in contact with GLY 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E CYS 5.1 1.6 - - - -
86E SER* 4.4 12.6 - - - -
89E ALA* 3.2 25.1 - - - +
90E TRP* 4.0 20.7 + - - -
118E PRO 3.1 18.9 + - - -
119E GLN 3.9 2.7 - - - -
120E GLN 3.2 1.6 - - - -
121E ASP* 1.3 77.7 - - - +
123E LEU* 1.3 56.3 + - - +
125E LEU* 4.7 2.4 + - - +
126E LEU* 3.8 9.4 - - - +
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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