Contacts of the helix formed by residues 40 - 47 (chain B) in PDB entry 2G9I
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 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B VAL 3.6 0.6 + - - -
39B CYS* 1.3 71.3 - - - +
41B THR* 1.3 66.5 + - - +
42B VAL 3.2 0.2 - - - -
43B ILE* 3.3 4.5 + - - +
44B SER* 2.8 33.2 + - - -
121B PRO* 5.9 0.3 - - - +
122B PRO* 4.3 10.2 - - - +
148B ILE* 3.8 11.7 - - - -
149B THR 2.8 22.2 + - - -
150B ASP* 3.9 17.8 + - - -
165B ILE* 3.7 23.4 - - - +
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Residues in contact with THR 41 (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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39B CYS* 3.2 19.8 - - - -
40B SER* 1.3 82.0 - - - +
42B VAL* 1.3 65.5 + - - +
44B SER* 3.4 0.6 + - - -
45B LYS* 2.9 33.9 + - - +
109B ASP* 3.9 15.7 - - + +
112B ASN* 3.8 28.7 + - - +
119B LEU* 3.6 22.6 - - + +
150B ASP* 5.6 4.7 - - - +
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Residues in contact with VAL 42 (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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14B ILE* 3.7 29.5 - - + +
20B LEU* 3.9 12.3 - - + +
38B VAL* 3.5 20.9 - - + -
39B CYS* 3.2 19.3 + - + +
41B THR* 1.3 86.6 + - - +
43B ILE* 1.3 56.0 + - - +
45B LYS* 3.4 9.1 + - + -
46B ALA* 2.9 30.5 + - - +
214B PRO* 3.7 31.9 - - + +
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Residues in contact with ILE 43 (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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20B LEU* 4.0 21.1 - - + -
38B VAL* 4.0 13.9 - - + -
39B CYS 3.7 14.6 - - - +
40B SER 3.3 5.5 + - - +
42B VAL* 1.3 76.9 - - - +
44B SER* 1.3 61.9 + - - +
46B ALA* 3.2 2.3 + - - +
47B GLU* 3.0 42.5 + - + +
122B PRO* 4.0 13.5 - - + -
128B SER* 3.6 29.4 - - - +
132B LEU* 4.3 13.2 - - + -
148B ILE* 3.8 31.0 - - + -
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Residues in contact with SER 44 (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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40B SER* 2.8 21.7 + - - -
41B THR* 3.6 1.6 - - - -
43B ILE* 1.3 72.8 - - - +
45B LYS* 1.3 61.3 + - - +
47B GLU* 3.5 0.8 + - - -
48B GLY 3.2 3.6 + - - -
49B ARG* 2.9 37.1 + - - +
119B LEU* 3.5 20.8 - - - +
120B LEU 2.5 29.1 + - - -
121B PRO* 3.5 0.9 - - - +
122B PRO* 3.4 19.1 - - - +
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Residues in contact with LYS 45 (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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13B LEU* 6.5 0.9 - - - -
14B ILE* 4.1 31.4 - - + +
15B LYS* 4.3 3.8 - - - -
16B GLU* 3.4 15.4 + - - +
41B THR* 2.9 25.5 + - - +
42B VAL* 3.7 9.6 - - + +
44B SER* 1.3 72.6 - - - +
46B ALA* 1.3 66.6 + - - +
48B GLY* 3.1 12.1 + - - -
49B ARG 5.0 0.4 - - - +
50B ILE* 4.9 12.5 - - + +
112B ASN* 2.8 44.5 + - - +
113B VAL* 4.3 8.3 - - - +
114B GLU* 6.0 0.9 - - - -
119B LEU* 4.1 17.0 - - + +
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Residues in contact with ALA 46 (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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14B ILE* 3.7 6.1 - - + +
15B LYS 3.8 10.8 - - - -
16B GLU* 3.5 1.9 - - - +
17B GLY* 2.9 25.8 + - - -
18B ASP 3.8 15.9 - - - +
20B LEU* 3.6 22.9 - - + -
42B VAL 2.9 17.9 + - - +
43B ILE* 3.6 4.5 - - + +
45B LYS* 1.3 75.5 - - - +
47B GLU* 1.3 63.4 + - + +
48B GLY 3.3 0.2 - - - -
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Residues in contact with GLU 47 (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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16B GLU* 4.5 5.1 - - - +
43B ILE* 3.0 26.9 + - - +
44B SER 4.4 2.0 - - - +
45B LYS 3.1 0.4 - - - -
46B ALA* 1.3 83.0 - - + +
48B GLY* 1.3 64.0 + - - +
49B ARG* 3.5 14.7 - - + +
122B PRO* 3.9 15.8 - - - +
123B LEU 4.6 3.6 + - - -
124B ASP 5.6 0.2 + - - -
128B SER* 2.6 34.8 + - - -
131B LYS* 6.1 0.7 - - - +
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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