Contacts of the helix formed by residues 38 - 50 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33I PRO* 4.3 1.8 - - - -
37I TYR* 1.3 76.4 - - - +
39I ILE* 1.3 63.7 - - - +
40I GLU* 3.4 17.6 + - - +
41I GLN* 3.0 37.7 + - - +
42I ALA* 2.9 21.8 + - - +
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Residues in contact with ILE 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I VAL* 3.7 32.1 - - + +
33I PRO* 3.9 12.9 - - + +
38I THR* 1.3 73.4 - - - +
40I GLU* 1.3 75.4 + - - +
43I ALA* 2.6 39.2 + - + +
77I PHE* 3.7 22.2 - - + -
85I TRP* 3.5 69.8 - - + +
87I VAL* 3.9 5.8 - - + -
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Residues in contact with GLU 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I TYR* 5.0 1.9 - - - +
13I VAL* 3.7 19.3 - - + +
15I LYS* 3.1 37.9 + - - +
38I THR* 3.4 18.1 + - - +
39I ILE* 1.3 96.0 - - + +
41I GLN* 1.3 57.3 + - + +
44I GLY* 2.8 27.7 + - - -
77I PHE* 4.3 10.4 - - + -
85I TRP* 5.9 0.7 - - - -
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Residues in contact with GLN 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I TYR* 4.4 6.4 - - - -
36I GLY 4.0 3.5 - - - +
37I TYR* 3.3 29.7 - - + -
38I THR* 3.0 41.9 + - - +
40I GLU* 1.3 77.2 - - + +
42I ALA* 1.3 62.7 + - - +
44I GLY* 4.1 0.6 - - - -
45I ALA* 3.2 15.9 + - - +
117I ARG* 3.3 24.7 + - - +
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Residues in contact with ALA 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I VAL* 3.8 21.5 - - + -
33I PRO* 3.8 22.2 - - + -
37I TYR* 5.3 0.2 - - + -
38I THR 2.9 14.2 + - - +
39I ILE 3.7 3.4 - - - +
41I GLN* 1.3 75.1 - - - +
43I ALA* 1.3 65.0 + - - +
45I ALA* 3.3 4.7 + - - +
46I VAL* 3.1 27.2 + - - +
117I ARG* 4.1 19.7 - - + +
118I VAL* 4.2 4.6 - - + +
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Residues in contact with ALA 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I VAL* 4.8 1.6 - - + -
31I VAL* 4.7 5.3 - - - +
39I ILE* 2.6 22.2 + - + +
40I GLU 4.1 1.1 - - - +
42I ALA* 1.3 72.8 - - - +
44I GLY* 1.3 58.0 + - - +
46I VAL* 3.3 8.4 + - - +
47I ALA* 3.0 29.9 + - - +
74I ALA* 4.3 3.9 - - + +
77I PHE* 3.6 27.6 - - + -
87I VAL* 3.8 23.3 - - + -
89I ILE* 4.3 3.8 - - - +
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Residues in contact with GLY 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I TYR* 3.5 20.5 - - - -
12I TYR* 3.9 7.4 - - - +
13I VAL* 3.9 16.1 - - - +
40I GLU 2.8 19.2 + - - -
43I ALA* 1.3 78.0 - - - +
45I ALA* 1.3 56.8 + - - +
47I ALA* 3.3 3.2 + - - +
48I ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I TYR* 3.8 25.9 + - + +
41I GLN 3.2 18.4 + - - +
42I ALA 3.3 5.4 + - - +
44I GLY* 1.3 75.2 - - - +
46I VAL* 1.3 57.3 + - - +
48I ALA* 3.4 1.4 + - - +
49I GLU* 2.9 33.4 + - - +
115I MET* 3.8 16.7 - - + +
117I ARG* 3.8 20.6 - - + +
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Residues in contact with VAL 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I PHE* 4.1 23.3 - - + -
31I VAL* 5.0 4.5 - - + -
42I ALA 3.1 17.7 + - - +
43I ALA* 3.6 10.3 - - - +
44I GLY 3.3 0.2 - - - -
45I ALA* 1.3 77.1 - - - +
47I ALA* 1.3 61.5 + - - +
49I GLU 3.4 0.2 + - - -
50I SER* 2.9 30.5 + - - +
89I ILE* 3.6 20.0 - - + -
112I ILE* 3.6 12.3 - - + +
115I MET* 3.3 26.9 - - + -
118I VAL* 4.2 5.8 - - + -
121I LEU* 4.0 21.5 - - + -
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Residues in contact with ALA 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I TYR* 3.7 33.2 - - + +
43I ALA 3.0 16.1 + - - +
46I VAL* 1.3 76.6 - - - +
48I ALA* 1.3 59.6 + - - +
50I SER* 3.2 8.3 + - - -
51I SER* 2.8 31.7 + - - -
72I ALA* 4.2 3.2 - - + +
74I ALA* 4.5 1.8 - - + +
89I ILE* 4.1 27.1 - - + -
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Residues in contact with ALA 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E LYS* 3.9 0.9 - - - +
9I TYR* 3.3 36.6 - - + +
12I TYR* 3.6 27.3 - - + -
44I GLY 2.9 9.1 + - - +
45I ALA 3.7 1.8 - - - +
47I ALA* 1.3 76.8 - - - +
49I GLU* 1.3 56.0 + - - +
51I SER 2.9 15.6 + - - -
52I THR 3.4 0.3 + - - -
53I GLY* 3.0 31.0 + - - -
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Residues in contact with GLU 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E LYS* 3.0 31.4 + - - +
192E GLU* 4.8 2.1 - - - +
193E ASN* 4.9 0.2 - - - +
322E LYS* 6.1 2.7 - - - +
45I ALA 2.9 20.6 + - - +
48I ALA* 1.3 73.2 - - - +
50I SER* 1.3 56.9 + - - +
51I SER 3.2 0.7 - - - -
53I GLY 4.9 2.0 - - - -
54I THR* 6.2 0.4 - - - +
107I SER* 4.6 1.4 - - - +
111I ASN* 5.5 7.8 + - + +
112I ILE* 3.7 21.5 - - + +
115I MET* 3.9 14.1 - - + -
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Residues in contact with SER 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E ASN* 4.9 1.1 - - - -
46I VAL* 2.9 21.1 + - - +
47I ALA* 3.2 7.1 + - - -
49I GLU* 1.3 76.9 - - - +
51I SER* 1.3 57.9 + - - +
91I TYR* 2.8 37.8 + - - -
96I PHE* 5.1 1.7 - - - -
107I SER* 2.9 49.3 + - - +
108I ILE* 4.4 3.1 - - - -
112I ILE* 4.0 10.3 - - - -
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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