Contacts of the helix formed by residues 43 - 50 (chain C) in PDB entry 2GER
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 43 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C MET* 5.1 5.7 - - - +
38C ASP 3.2 3.1 + - - -
39C LEU* 3.1 44.4 - - - +
41C THR 3.1 0.4 - - - -
42C VAL* 1.3 77.4 - - - +
44C ALA* 1.3 55.9 + - - +
45C LEU 2.8 3.8 - - - -
46C ARG* 2.5 43.2 + - - +
47C LYS* 3.4 2.5 + - - +
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Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C PHE* 3.2 29.0 - - + -
39C LEU 3.8 3.7 + - - +
40C ALA 4.8 11.0 - - - +
41C THR 4.3 0.6 - - - -
43C SER* 1.3 77.3 - - - +
45C LEU* 1.3 55.6 + - - +
47C LYS* 3.5 12.2 + - - +
48C MET* 3.0 23.9 + - - +
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PHE* 6.5 0.4 - - + -
8C ALA* 5.0 13.7 - - + -
9C GLY 5.1 5.2 - - - +
12C ALA* 5.2 2.7 - - + -
13C PHE* 3.2 29.1 - - + +
16C ALA* 5.6 4.3 - - + -
32C ALA* 3.8 19.5 - - + -
34C SER* 6.1 0.2 - - - -
41C THR 2.8 23.2 + - - +
42C VAL* 3.9 17.9 - - + +
44C ALA* 1.3 75.2 - - - +
46C ARG* 1.3 62.5 - - + +
48C MET* 2.6 27.7 - - - +
49C GLY 3.4 1.6 + - - -
50C VAL* 3.3 38.7 + - + +
52C LEU* 6.0 3.1 - - + -
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Residues in contact with ARG 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C MET* 3.7 25.8 - - + +
42C VAL 3.6 13.7 - - - +
43C SER* 2.5 26.4 + - - +
45C LEU* 1.3 73.3 - - + +
47C LYS* 1.3 52.1 + - - +
48C MET 2.7 2.2 - - - -
49C GLY* 2.4 35.0 + - - -
50C VAL 3.5 7.6 + - - -
51C LYS* 5.7 1.2 - - - +
52C LEU* 3.8 51.3 + - + +
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Residues in contact with LYS 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C SER 3.4 2.2 + - - +
44C ALA* 3.5 14.1 + - - +
46C ARG* 1.3 76.8 - - - +
48C MET* 1.3 63.8 + - - +
49C GLY* 3.2 1.0 - - - -
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Residues in contact with MET 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C PHE* 5.1 7.0 - - + -
16C ALA* 5.4 7.4 - - + -
17C LYS* 5.1 18.8 - - - +
20C THR* 4.3 31.2 - - + +
27C ALA* 4.5 13.0 - - + +
44C ALA 3.0 9.7 + - - +
45C LEU* 2.6 25.4 - - + +
46C ARG 2.5 5.9 + - - -
47C LYS* 1.3 76.1 - - - +
49C GLY* 1.3 54.5 + - - +
50C VAL* 3.2 19.7 - - + -
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Residues in contact with GLY 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ALA* 2.5 31.4 - - - +
28C HIS* 3.2 19.1 + - - -
46C ARG 2.4 16.5 + - - -
47C LYS 3.2 1.5 - - - -
48C MET* 1.3 75.2 - - - +
50C VAL* 1.3 54.4 + - - +
51C LYS* 3.9 3.0 + - - -
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ALA* 5.3 11.0 - - + -
27C ALA* 3.7 17.3 - - + +
30C ILE* 3.7 26.2 - - + +
31C MET 4.8 0.7 - - - +
32C ALA* 3.8 11.2 - - + +
45C LEU* 3.3 34.1 - - + +
46C ARG* 3.5 11.1 + - - -
48C MET* 3.2 34.5 - - + -
49C GLY* 1.3 78.1 - - - +
51C LYS* 1.3 68.9 + - - +
52C LEU* 3.5 2.8 + - - +
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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