Contacts of the helix formed by residues 102 - 111 (chain B) in PDB entry 4RG7
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 SER 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B GLN 3.7 1.4 + - - -
101B LYS* 1.3 79.5 - - - +
103B HIS* 1.3 64.4 + - - +
104B ASP* 2.9 11.9 + - - +
105B ASP* 2.2 56.0 + - - +
106B ILE* 3.3 21.0 + - - +
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Residues in contact with HIS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LYS 4.7 4.1 + - - -
102B SER* 1.3 74.6 + - - +
104B ASP* 1.3 57.4 + - - +
106B ILE* 3.3 15.9 + - + +
107B VAL* 3.2 25.1 + - - +
118B LEU* 4.9 11.8 - - + +
125B TYR* 6.1 1.1 - + - -
133B LYS 5.6 1.1 - - - -
136B GLU* 4.3 31.4 - - + +
137B CYS* 4.5 17.7 - - - -
140B LYS* 5.1 12.1 - - + -
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Residues in contact with ASP 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B SER* 3.3 7.8 - - - +
103B HIS* 1.3 78.0 - - - +
105B ASP* 1.3 64.5 + - - +
107B VAL* 3.4 8.3 + - - +
108B THR* 3.1 22.7 + - - -
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Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LYS* 4.2 10.5 - - + -
102B SER* 2.2 51.7 + - - +
104B ASP* 1.3 67.0 - - - +
106B ILE* 1.3 64.4 + - - +
108B THR* 3.1 9.3 + - - -
109B GLU* 3.0 24.6 + - - +
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Residues in contact with ILE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU 4.1 12.1 - - - +
93B SER* 4.2 12.6 - - - -
101B LYS* 4.0 13.9 - - + +
102B SER 3.3 15.2 + - - +
103B HIS* 3.3 11.6 + - + +
104B ASP 3.3 0.2 - - - -
105B ASP* 1.3 78.3 - - - +
107B VAL* 1.3 59.1 + - - +
109B GLU* 3.3 5.2 + - - +
110B PHE* 3.0 53.8 + - + +
114B ALA 4.9 0.4 - - - +
117B THR* 3.9 12.8 - - + +
118B LEU* 3.7 28.0 - - + -
121B LEU* 3.7 28.7 - - + -
137B CYS* 5.9 0.9 - - - -
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B HIS 3.2 10.0 + - - +
104B ASP* 3.7 11.2 - - - +
105B ASP 3.2 0.2 - - - -
106B ILE* 1.3 79.8 - - - +
108B THR* 1.3 57.7 + - - +
111B GLY* 2.9 31.4 + - - +
114B ALA* 3.8 19.3 - - + -
118B LEU* 5.6 4.9 - - + -
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Residues in contact with THR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ASP 3.1 14.1 + - - -
105B ASP* 3.4 12.6 - - - -
107B VAL* 1.3 80.1 - - - +
109B GLU* 1.3 63.6 + - - +
111B GLY* 3.7 5.9 + - - -
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B THR 5.0 6.4 - - - +
68B THR 5.1 0.2 - - - -
69B PRO* 3.0 38.4 - - + +
72B LYS* 4.9 5.4 - - - +
91B ILE 5.7 0.9 - - - +
92B LEU 4.5 6.4 - - - +
105B ASP 3.0 16.0 + - - +
106B ILE* 3.7 6.1 - - - +
108B THR* 1.3 79.6 - - - +
110B PHE* 1.3 86.5 + - + +
111B GLY 3.7 0.2 + - - -
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Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PRO* 3.5 44.2 - - + +
72B LYS* 4.1 13.2 - - + -
73B TYR* 4.3 8.3 - - + -
91B ILE 5.1 1.1 - - - -
92B LEU* 4.1 26.5 - - + -
106B ILE* 3.0 34.3 + - + +
109B GLU* 1.3 99.8 - - + +
111B GLY* 1.3 54.4 + - - +
112B ASP 2.9 1.0 + - - -
113B SER* 2.7 43.0 + - - -
114B ALA* 3.8 16.2 - - - +
117B THR* 3.6 34.3 - - + -
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Residues in contact with GLY 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B VAL 2.9 16.5 + - - +
108B THR 3.7 4.2 + - - -
109B GLU 3.4 3.6 + - - -
110B PHE* 1.3 71.4 - - - +
112B ASP* 1.3 58.0 + - - -
114B ALA* 3.1 21.0 - - - +
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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