Contacts of the helix formed by residues 42 - 51 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34H ASP* 3.0 15.0 + - - -
40H SER 3.4 0.6 + - - -
41H ARG* 1.3 75.1 - - - +
43H LEU* 1.3 65.2 + - - +
44H TRP 3.3 3.1 - - - +
45H LYS* 3.0 24.5 + - - +
46H LYS* 3.1 13.9 + - - +
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Residues in contact with LEU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H ASN* 4.3 13.7 - - - +
13H MET* 4.1 31.6 - - + -
14H ASP* 4.0 34.1 - - + +
17H LEU* 3.8 27.4 - - + -
25H LEU* 4.6 6.5 - - + -
40H SER* 3.2 23.1 + - - +
41H ARG 2.8 7.5 + - - +
42H GLY* 1.3 75.5 - - - +
44H TRP* 1.3 63.0 + - - +
46H LYS* 3.0 12.6 + - + +
47H TYR* 3.1 26.0 + - + -
52H ILE* 3.8 11.8 - - + +
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Residues in contact with TRP 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H VAL 5.3 0.6 + - - -
31H ALA* 3.7 32.9 - - + +
32H GLN* 4.3 36.1 - - + -
34H ASP* 5.8 0.2 + - - -
40H SER 4.5 1.6 + - - -
42H GLY 3.3 1.0 - - - +
43H LEU* 1.3 77.9 - - - +
45H LYS* 1.3 97.9 + - + +
48H GLY* 2.7 40.3 + - - -
49H ASP* 2.6 34.9 + - - +
52H ILE* 3.4 34.4 + - + +
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Residues in contact with LYS 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H GLY* 3.0 14.6 + - - +
44H TRP* 1.3 107.0 - - + +
46H LYS* 1.3 57.5 + - - +
48H GLY 5.0 0.2 + - - -
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Residues in contact with LYS 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H ASP* 3.1 29.0 + - - +
18H GLU* 3.6 21.3 + - - -
42H GLY 3.1 9.2 + - - +
43H LEU* 3.0 11.3 + - + +
45H LYS* 1.3 79.2 - - - +
47H TYR* 1.3 94.4 + - + +
48H GLY 3.8 0.2 - - - -
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Residues in contact with TYR 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H ASP* 3.0 34.7 + - - -
17H LEU* 3.9 27.6 - - + -
18H GLU* 3.4 20.9 + - - +
43H LEU* 3.1 23.1 + - + +
46H LYS* 1.3 110.0 + - + +
48H GLY* 1.3 68.2 + - - +
50H LYS* 4.4 2.9 + - - +
51H ARG* 3.5 55.9 + - + +
52H ILE* 4.5 3.4 - - + -
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Residues in contact with GLY 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H TRP* 2.7 35.7 + - - +
45H LYS 4.8 0.6 - - - -
46H LYS 3.8 0.4 - - - -
47H TYR* 1.3 78.7 - - - +
49H ASP* 1.3 63.0 + - - -
50H LYS 2.9 6.7 + - - -
51H ARG 3.2 7.1 + - - -
52H ILE 3.2 9.0 + - - -
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Residues in contact with ASP 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A THR* 5.1 15.2 - - - +
276A GLU* 5.8 1.6 - - - +
44H TRP* 2.6 39.6 + - - +
48H GLY* 1.3 69.4 - - - -
50H LYS* 1.3 63.4 + - - +
51H ARG 3.3 0.4 - - - -
52H ILE 3.8 12.7 - - - +
53H ILE* 3.5 20.1 - - - +
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Residues in contact with LYS 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLU* 3.9 31.1 + - - +
153G LYS 5.5 0.2 - - - -
154G TYR* 3.3 76.3 + - + +
21H GLU* 5.9 5.1 - - - +
24H PHE* 4.3 0.2 - - - +
47H TYR 4.9 2.7 - - - +
48H GLY 2.9 1.6 + - - -
49H ASP* 1.3 79.8 - - - +
51H ARG* 1.3 70.8 + - + +
53H ILE* 3.9 12.0 - - - +
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Residues in contact with ARG 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G TYR* 3.1 26.5 + - - -
17H LEU* 2.7 34.1 + - + +
20H ASP 2.9 15.4 + - - -
21H GLU* 3.4 18.9 + - - +
23H VAL 2.8 23.5 + - - -
24H PHE* 3.3 7.2 - - - +
25H LEU 2.8 28.8 + - - +
47H TYR* 3.5 55.8 - - + +
48H GLY 3.2 1.2 + - - -
50H LYS* 1.3 92.4 - - + +
52H ILE* 1.3 64.2 + - + +
53H ILE* 3.9 1.3 - - - -
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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