Contacts of the helix formed by residues 38 - 50 (chain J) in PDB entry 3KDO
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 THR 38 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33J PRO* 4.3 1.3 - - - -
36J GLY 6.1 0.2 - - - -
37J TYR* 1.3 78.0 - - - +
39J ILE* 1.3 64.6 + - - +
40J GLU* 3.3 17.3 + - - +
41J GLN* 2.8 41.8 + - - +
42J ALA* 3.0 21.8 + - - +
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Residues in contact with ILE 39 (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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31J VAL* 3.8 29.6 - - + +
33J PRO* 3.8 11.9 - - + +
38J THR* 1.3 73.9 - - - +
40J GLU* 1.3 75.4 + - - +
42J ALA* 3.2 0.6 + - - -
43J ALA* 2.7 34.5 + - - +
77J PHE* 3.7 22.0 - - + -
85J TRP* 3.3 67.8 - - + +
87J VAL* 4.0 4.3 - - + -
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Residues in contact with GLU 40 (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 ASP* 5.1 2.3 - - - +
13J VAL* 3.5 22.5 - - + +
15J LYS* 3.0 37.9 + - - +
38J THR* 3.3 18.6 + - - +
39J ILE* 1.3 95.0 - - + +
41J GLN* 1.3 57.1 + - + +
44J GLY* 2.8 24.8 + - - -
77J PHE* 4.2 10.9 - - + -
85J TRP* 5.9 0.3 - - - -
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Residues in contact with GLN 41 (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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9J TYR* 4.7 0.7 - - - +
10J ASP* 4.7 15.3 - - - +
36J GLY 4.1 3.7 + - - +
37J TYR* 3.3 25.5 - - + -
38J THR* 2.8 50.2 + - - +
39J ILE 3.2 0.2 - - - -
40J GLU* 1.3 78.0 - - + +
42J ALA* 1.3 60.9 + - - +
44J GLY* 4.0 0.9 - - - -
45J ALA 3.3 13.0 + - - -
117J ARG* 3.2 33.3 + - - +
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Residues in contact with ALA 42 (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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31J VAL* 3.8 22.0 - - + -
33J PRO* 4.0 19.1 - - + -
37J TYR* 5.3 0.4 - - + -
38J THR 3.0 15.2 + - - +
39J ILE 3.7 3.4 - - - +
41J GLN* 1.3 76.4 - - - +
43J ALA* 1.3 65.1 + - - +
45J ALA* 3.2 5.5 + - - +
46J VAL* 3.1 26.6 + - - +
117J ARG* 3.9 20.1 - - + +
118J VAL* 4.3 5.7 - - + +
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Residues in contact with ALA 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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31J VAL* 4.8 4.2 - - - +
39J ILE* 2.7 22.1 + - + +
40J GLU 4.0 0.9 - - - +
42J ALA* 1.3 70.6 - - - +
44J GLY* 1.3 66.1 + - - +
46J VAL* 3.1 10.0 + - - +
47J ALA* 2.9 25.1 + - - +
74J ALA* 4.1 6.3 - - + +
77J PHE* 3.6 29.8 - - + -
87J VAL* 3.9 22.4 - - + -
89J ILE* 4.5 1.3 - - - +
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Residues in contact with GLY 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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9J TYR* 3.5 27.7 - - - +
10J ASP* 5.9 0.2 - - - -
12J TYR* 3.8 6.5 - - - +
13J VAL* 3.7 11.6 - - - +
40J GLU 2.8 19.6 + - - -
41J GLN 4.0 1.3 - - - -
43J ALA* 1.3 75.9 - - - +
45J ALA* 1.3 56.6 + - - +
47J ALA* 3.4 0.8 + - - -
48J ALA* 2.9 30.3 + - - +
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Residues in contact with ALA 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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9J TYR* 3.7 36.0 - - + +
41J GLN 3.3 10.9 + - - +
42J ALA 3.2 8.4 + - - +
43J ALA 3.2 0.4 - - - -
44J GLY* 1.3 75.0 - - - +
46J VAL* 1.3 58.9 + - - +
49J GLU* 2.9 35.9 + - - +
115J MET* 4.0 17.0 - - + -
117J ARG* 3.8 13.5 - - + +
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Residues in contact with VAL 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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29J PHE* 3.9 24.7 - - + -
31J VAL* 4.8 4.9 - - + -
42J ALA 3.1 17.3 + - - +
43J ALA* 3.1 9.8 + - - +
45J ALA* 1.3 76.9 - - - +
47J ALA* 1.3 60.6 + - - +
50J SER* 2.8 30.9 + - - +
89J ILE* 3.6 21.3 - - + -
112J ILE* 3.7 12.7 - - + +
115J MET* 3.6 21.8 - - + -
118J VAL* 4.3 5.8 - - + -
121J LEU* 4.1 22.4 - - + -
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Residues in contact with ALA 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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12J TYR* 3.7 30.7 - - + +
43J ALA 2.9 14.8 + - - +
46J VAL* 1.3 76.4 - - - +
48J ALA* 1.3 55.9 + - - +
50J SER* 3.2 7.7 + - - -
51J SER* 2.6 34.9 + - - -
72J ALA* 4.0 6.8 - - + +
74J ALA* 4.2 3.1 - - + +
89J ILE* 3.9 28.2 - - + +
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Residues in contact with ALA 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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165D LYS* 3.9 0.2 - - - +
9J TYR* 3.4 28.5 - - + -
12J TYR* 3.4 33.3 - - + -
44J GLY 2.9 18.6 + - - +
46J VAL 3.3 0.2 - - - -
47J ALA* 1.3 76.5 - - - +
49J GLU* 1.3 58.4 + - - +
51J SER 3.0 15.4 + - - -
52J THR 3.3 0.3 + - - -
53J GLY* 2.9 27.7 + - - +
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Residues in contact with GLU 49 (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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163D LYS* 5.3 0.3 + - - -
165D LYS* 3.3 27.0 + - - +
192D GLU* 4.8 1.6 - - - +
322D LYS* 2.8 37.6 + - + -
323D LEU* 6.3 0.2 - - - -
600D CAP 3.5 10.0 - - - +
9J TYR* 2.8 27.2 + - + +
45J ALA 2.9 22.9 + - - +
48J ALA* 1.3 74.7 - - - +
50J SER* 1.3 56.4 + - - +
51J SER 3.5 0.2 - - - -
53J GLY 3.9 11.8 - - - +
54J THR* 3.7 7.7 + - - -
107J SER* 4.7 1.2 - - - +
111J ASN* 5.3 10.7 + - + +
112J ILE* 4.1 14.1 - - + +
115J MET* 3.6 25.4 - - + -
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Residues in contact with SER 50 (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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193D ASN* 4.6 1.8 - - - -
46J VAL* 2.8 21.5 + - - +
47J ALA* 3.2 7.1 + - - -
48J ALA 3.0 0.4 - - - -
49J GLU* 1.3 78.8 - - - +
51J SER* 1.3 59.1 + - - +
91J TYR* 2.8 35.9 + - - -
96J PHE* 5.3 0.9 - - - -
107J SER* 3.1 48.8 + - - +
108J ILE* 4.5 0.2 - - - -
112J ILE* 3.9 13.2 - - - -
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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