Contacts of the helix formed by residues 42 - 48 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34J ASP* 2.5 17.2 + - - -
40J SER 3.4 0.4 + - - -
41J ARG* 1.3 73.1 - - - +
43J LEU* 1.3 64.9 + - - +
44J TRP* 3.2 2.9 - - - -
45J LYS* 2.9 29.8 + - - +
46J LYS* 3.1 12.3 + - - +
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Residues in contact with LEU 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J ASN* 3.4 28.5 - - - +
13J MET* 4.2 28.7 - - + -
14J ASP* 4.7 14.1 - - + +
17J LEU* 3.8 20.4 - - + -
25J LEU* 4.9 3.6 - - + -
40J SER* 3.0 16.2 + - - +
41J ARG 3.3 15.3 - - - +
42J GLY* 1.3 76.7 - - - +
44J TRP* 1.3 55.4 + - - +
46J LYS* 3.2 5.3 + - + -
47J TYR* 2.9 50.3 + - + +
52J ILE* 4.0 14.8 - - + -
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Residues in contact with TRP 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J VAL 5.3 0.4 + - - -
31J ALA* 3.6 53.0 + - + +
32J GLN* 4.0 28.8 - - + +
40J SER 4.6 1.4 + - - -
42J GLY 3.0 1.0 + - - -
43J LEU* 1.3 74.0 - - - +
45J LYS* 1.3 99.9 + - + +
48J GLY* 2.7 39.1 + - - -
49J ASP* 2.8 29.0 + - - +
52J ILE* 3.8 21.6 - - + +
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Residues in contact with LYS 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J ASP* 5.1 11.2 - - - +
42J GLY* 2.9 20.4 + - - +
44J TRP* 1.3 105.4 - - + +
46J LYS* 1.3 62.5 + - - +
47J TYR 3.5 0.2 + - - -
48J GLY* 4.4 1.9 + - - -
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Residues in contact with LYS 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J ASP* 3.3 26.2 + - - +
18J GLU* 3.2 31.3 + - - -
42J GLY 3.1 8.7 + - - +
43J LEU* 3.6 11.9 - - + +
44J TRP 3.1 0.2 - - - -
45J LYS* 1.3 83.0 - - - +
47J TYR* 1.3 81.4 + - + +
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Residues in contact with TYR 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J ASP* 2.8 32.8 + - - -
17J LEU* 3.6 40.6 - - + -
18J GLU* 3.2 22.0 + - + +
43J LEU* 2.9 35.5 + - + +
46J LYS* 1.3 101.4 - - + +
48J GLY* 1.3 64.0 + - - +
50J LYS* 4.8 2.8 + - - +
51J ARG* 3.7 49.3 + - + +
52J ILE* 3.9 4.9 - - + -
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Residues in contact with GLY 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44J TRP* 2.7 28.3 + - - -
45J LYS 4.4 1.7 + - - -
46J LYS 3.9 0.4 - - - -
47J TYR* 1.3 73.0 - - - +
49J ASP* 1.3 68.3 + - - -
50J LYS 3.2 3.7 + - - -
51J ARG 3.5 0.3 + - - -
52J ILE* 3.2 24.9 + - - +
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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