Contacts of the helix formed by residues 42 - 51 (chain T) in PDB entry 3EXG
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 GLY 42 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34T ASP* 3.8 13.3 + - - -
40T SER 3.4 0.8 + - - -
41T ARG* 1.3 76.4 - - - +
43T LEU* 1.3 63.6 + - - +
44T TRP 3.3 3.3 - - - +
45T LYS* 3.3 32.8 - - - +
46T LYS* 3.4 11.6 + - - +
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Residues in contact with LEU 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10T ASN* 3.6 19.5 - - - +
13T MET* 4.0 20.6 - - + -
14T ASP* 4.5 19.5 - - + +
17T LEU* 4.3 19.1 - - + -
25T LEU* 4.3 8.7 - - + -
40T SER* 3.1 33.5 + - - +
41T ARG 3.0 18.1 + - - +
42T GLY* 1.3 76.3 - - - +
44T TRP* 1.3 61.5 + - - +
46T LYS* 3.1 2.5 + - + -
47T TYR* 2.9 45.6 + - + +
52T ILE* 3.9 13.5 - - + -
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Residues in contact with TRP 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30T VAL 5.6 0.2 + - - -
31T ALA* 3.7 42.2 + - + +
32T GLN* 3.3 50.0 - - + -
34T ASP* 6.0 0.9 - - - -
40T SER 4.6 1.4 + - - -
42T GLY* 3.3 0.8 - - - +
43T LEU* 1.3 74.9 - - - +
45T LYS* 1.3 78.9 + - + +
46T LYS 2.9 5.9 + - - -
48T GLY* 3.0 29.8 + - - -
49T ASP* 2.5 34.9 + - - +
52T ILE* 3.7 21.8 - - + +
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Residues in contact with LYS 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42T GLY* 3.3 23.7 - - - +
44T TRP* 1.3 92.0 - - + +
46T LYS* 1.3 56.1 + - + +
48T GLY 4.9 0.2 - - - -
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Residues in contact with LYS 46 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T ASP* 3.0 27.5 + - - +
18T GLU* 3.4 22.7 + - - -
42T GLY 3.4 12.8 + - - +
43T LEU* 3.1 5.7 + - + +
44T TRP 2.9 0.6 - - - -
45T LYS* 1.3 82.4 - - + +
47T TYR* 1.3 94.2 + - + +
48T GLY 3.7 0.4 - - - -
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Residues in contact with TYR 47 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T ASP* 2.9 35.7 + - - -
17T LEU* 3.6 39.9 - - + -
18T GLU* 3.5 13.0 + - + +
43T LEU* 2.9 33.3 + - + +
46T LYS* 1.3 114.2 + - + +
48T GLY* 1.3 66.6 + - - +
50T LYS* 4.5 2.6 + - - +
51T ARG* 3.4 50.7 + - + +
52T ILE* 4.0 5.8 - - + -
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Residues in contact with GLY 48 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T TRP* 3.0 25.2 + - - +
45T LYS 4.9 0.2 - - - -
46T LYS 3.7 1.0 - - - -
47T TYR* 1.3 76.4 - - - +
49T ASP* 1.3 59.4 + - - -
50T LYS 3.1 5.2 - - - -
51T ARG 2.9 19.2 + - - -
52T ILE* 3.0 12.8 + - - +
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Residues in contact with ASP 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T TRP* 2.5 40.0 + - - -
48T GLY* 1.3 69.1 - - - -
50T LYS* 1.3 67.2 + - - +
51T ARG 3.2 0.2 - - - -
52T ILE 4.1 9.3 - - - +
53T ILE* 3.8 16.1 - - - +
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Residues in contact with LYS 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150S LEU* 5.7 0.9 - - - +
153S LYS 5.3 0.7 - - - -
154S TYR* 3.0 72.0 + - + +
21T GLU* 5.9 3.6 - - - +
47T TYR 4.8 2.2 - - - +
48T GLY 3.0 1.0 + - - +
49T ASP* 1.3 83.8 - - - +
51T ARG* 1.3 71.0 + - + +
53T ILE* 3.8 13.3 - - - +
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Residues in contact with ARG 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154S TYR* 3.2 25.8 + - - -
17T LEU* 3.1 34.8 + - + +
20T ASP 3.2 10.1 + - - -
21T GLU* 3.7 15.4 - - - +
23T VAL 2.8 29.9 + - - -
24T PHE* 3.3 8.4 - - + +
25T LEU 2.9 29.1 + - - +
47T TYR* 3.4 49.3 - - + +
48T GLY 2.9 1.8 + - - -
50T LYS* 1.3 90.5 - - + +
52T ILE* 1.3 64.2 + - + +
53T ILE* 3.8 2.0 - - - -
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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