Contacts of the helix formed by residues 103 - 110 (chain B) in PDB entry 2CMG
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 ASP 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B SER* 2.5 31.5 + - - -
28B HIS 5.0 0.3 + - - -
29B ASN* 2.8 17.8 - - - +
82B PHE* 3.7 7.7 - - + -
101B GLN* 2.9 22.5 - - - +
102B ALA* 1.3 76.9 - - + +
104B GLU* 1.3 60.6 + - - +
105B LYS* 3.5 10.7 + - - +
106B ILE* 3.1 28.1 + - - +
107B LEU* 3.1 21.3 + - - +
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Residues in contact with GLU 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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101B GLN 4.6 0.2 + - - -
102B ALA 3.5 2.5 + - - +
103B ASP* 1.3 70.2 - - - +
105B LYS* 1.3 66.6 + - - +
106B ILE 3.1 0.2 + - - -
107B LEU* 3.2 6.2 + - - +
108B ASP* 2.9 40.3 + - - +
128B HIS* 3.3 35.8 - - + +
130B LYS* 2.7 43.8 + - + +
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Residues in contact with LYS 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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24B VAL* 3.3 19.4 - - + +
25B ARG 2.5 40.5 + - - -
26B SER* 3.1 20.4 - - - +
103B ASP* 3.3 6.0 - - - +
104B GLU* 1.3 79.3 - - - +
106B ILE* 1.3 53.2 + - - +
108B ASP* 4.3 4.5 - - - +
109B SER* 2.4 31.7 + - - -
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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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24B VAL* 3.6 41.7 - - + +
26B SER* 3.8 8.1 - - - +
29B ASN* 4.0 10.3 - - + +
31B LEU* 4.3 10.3 - - + -
45B LEU* 4.1 13.7 - - + -
82B PHE* 3.4 30.7 - - + -
103B ASP* 3.1 28.2 + - - +
104B GLU 3.1 0.6 - - - -
105B LYS* 1.3 83.3 - - - +
107B LEU* 1.3 58.8 + - - +
109B SER* 2.8 29.0 + - - -
110B PHE* 3.5 17.1 - - + -
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Residues in contact with LEU 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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82B PHE* 3.4 52.6 - - + +
84B LEU* 4.1 16.3 - - + +
99B PHE* 3.9 19.1 - - + -
101B GLN* 4.4 2.5 - - + -
103B ASP 3.1 15.7 + - - +
104B GLU* 3.8 5.6 - - - +
106B ILE* 1.3 77.5 - - - +
108B ASP* 1.3 61.6 + - - +
110B PHE* 3.3 21.6 + - + +
117B PHE* 3.7 8.2 - - - -
121B LYS* 4.5 17.7 - - - +
126B PHE* 5.3 0.9 - - + -
128B HIS* 3.9 33.9 - - + +
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Residues in contact with ASP 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 GLU* 2.9 32.3 + - - +
105B LYS* 4.3 4.5 - - - +
107B LEU* 1.3 72.4 - - - +
109B SER* 1.3 57.7 + - - +
110B PHE 3.0 6.1 - - - -
111B ILE* 3.0 31.8 + - - +
117B PHE* 4.0 10.0 - - + -
121B LYS* 2.9 30.8 + - - -
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Residues in contact with SER 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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22B LEU* 3.6 20.8 - - - +
24B VAL* 3.5 27.1 - - - +
31B LEU* 3.6 20.2 - - - -
33B ILE* 4.1 6.9 - - - +
105B LYS* 2.4 27.4 + - - +
106B ILE* 2.8 15.2 + - - -
108B ASP* 1.3 78.1 - - - +
110B PHE* 1.3 56.3 + - - +
111B ILE* 3.2 11.2 + - - +
112B SER 5.0 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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31B LEU* 3.5 34.5 - - + -
33B ILE* 5.5 1.3 - - + -
43B ALA* 4.0 8.7 - - + -
45B LEU* 4.2 15.0 - - + -
50B LEU* 4.0 22.2 - - + -
82B PHE* 3.6 30.1 - + + -
106B ILE* 3.5 28.9 - - + -
107B LEU* 3.4 10.8 - - - +
108B ASP 3.0 1.6 - - - -
109B SER* 1.3 77.0 - - - +
111B ILE* 1.3 62.8 + - - +
112B SER 3.3 2.7 - - - -
113B PHE* 3.0 38.2 + + + -
114B PHE* 3.1 41.6 + + + +
117B PHE* 4.1 4.5 - - + -
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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