Contacts of the helix formed by residues 48 - 58 (chain D) in PDB entry 3P05
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 48 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D PRO* 4.7 0.9 - - + -
2D ILE* 4.2 12.1 - - + -
12D HIS* 4.0 24.9 + - + +
47D ALA* 1.3 75.6 - - - +
49D PRO* 1.3 75.9 - - - +
50D GLN* 3.5 5.7 + - - +
51D ASP* 3.0 33.5 + - - +
52D LEU* 3.0 22.4 + - - +
111D LEU* 4.2 9.6 - - + +
114D GLN* 3.7 10.5 - - + +
115D ILE* 4.7 3.1 - - + -
118D MET* 3.9 17.9 - - + -
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Residues in contact with PRO 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D THR* 1.3 86.7 - - - +
50D GLN* 1.3 55.9 + - - +
52D LEU* 3.8 2.7 - - + +
53D ASN* 2.9 35.5 + - - -
103D ASP 4.6 0.7 - - - +
104D ILE 3.4 28.3 - - - +
106D GLY* 3.8 12.1 - - - -
114D GLN* 3.6 22.0 - - + +
118D MET* 4.2 0.9 - - - -
126D VAL* 3.9 26.9 - - + +
127D GLY* 3.9 17.9 - - - +
130D TYR* 3.8 13.0 - - + -
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Residues in contact with GLN 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C GLU* 5.9 3.4 + - - -
12D HIS* 4.9 2.3 + - - -
48D THR* 3.1 2.9 - - - +
49D PRO* 1.3 77.0 - - - +
51D ASP* 1.3 71.2 + - - +
53D ASN* 3.3 9.6 + - + +
54D THR* 3.1 26.5 + - - +
106D GLY* 5.7 0.9 - - - -
111D LEU* 3.7 40.8 - - + +
114D GLN* 3.0 24.4 + - - +
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Residues in contact with ASP 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D PRO* 2.5 42.4 - - + +
12D HIS* 4.6 4.0 + - - -
14D ALA* 4.8 1.0 - - - -
15D ILE* 3.9 26.5 + - + +
47D ALA* 3.6 11.9 - - + -
48D THR* 3.0 33.0 + - - +
50D GLN* 1.3 84.2 - - - +
52D LEU* 1.3 62.3 + - - +
54D THR* 3.3 9.6 + - - -
55D MET* 3.1 27.3 + - - +
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D PHE* 3.6 32.7 - - + -
44D SER* 4.0 10.3 - - - -
47D ALA* 3.9 21.1 - - + +
48D THR 3.0 21.4 + - - +
49D PRO* 3.8 7.6 - - + +
50D GLN 3.2 0.2 - - - -
51D ASP* 1.3 75.7 - - - +
53D ASN* 1.3 59.3 + - - +
55D MET* 3.2 9.0 + - - +
56D LEU* 3.0 32.0 + - - +
127D GLY 3.6 23.6 - - - +
130D TYR* 3.8 23.6 - - + -
131D LYS* 4.2 10.5 - - + +
134D ILE* 4.0 13.2 - - + -
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Residues in contact with ASN 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D PRO 2.9 19.1 + - - +
50D GLN* 3.3 7.3 + - - +
52D LEU* 1.3 74.9 - - - +
54D THR* 1.3 59.8 + - - +
56D LEU* 3.2 7.9 + - - +
57D ASN* 2.8 47.8 + - - +
105D ALA 3.0 21.3 + - - -
106D GLY 3.8 16.6 + - - -
107D THR* 4.8 5.4 - - - +
130D TYR* 2.8 26.2 + - - -
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Residues in contact with THR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C PRO* 4.9 4.5 - - + +
42C ALA* 3.6 31.1 - - + +
15D ILE* 4.3 11.2 - - + +
20D LEU* 3.8 17.0 - - + -
50D GLN* 3.1 20.0 + - - +
51D ASP* 3.5 11.3 - - - -
52D LEU 3.3 0.2 - - - -
53D ASN* 1.3 76.4 - - - +
55D MET* 1.3 62.4 + - - +
57D ASN* 4.0 5.1 - - - +
58D THR* 2.7 35.0 + - + +
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Residues in contact with MET 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ILE* 3.9 19.5 - - + -
19D THR* 5.4 2.5 - - + -
20D LEU* 4.6 2.7 - - + -
23D TRP* 2.7 60.3 + - + +
40D PHE* 3.9 27.1 - - + -
43D LEU* 4.1 25.1 - - + +
44D SER* 4.0 22.2 - - - -
47D ALA* 5.3 2.7 - - - -
51D ASP* 3.1 17.4 + - - +
52D LEU* 3.5 13.7 - - - +
53D ASN 3.2 0.4 - - - -
54D THR* 1.3 76.4 - - - +
56D LEU* 1.3 61.7 + - + +
58D THR* 3.3 10.3 + - - -
59D VAL* 3.7 4.7 - - - +
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Residues in contact with LEU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ARG* 5.4 0.9 + - - -
23D TRP* 5.0 8.3 - - + -
40D PHE* 5.0 9.4 - - + -
52D LEU 3.0 14.3 + - - +
53D ASN* 3.8 8.5 - - - +
55D MET* 1.3 78.7 - - - +
57D ASN* 1.3 64.2 + - - +
58D THR 3.3 1.2 + - - -
59D VAL* 3.4 11.7 + - - +
66D MET* 3.5 27.9 - - + +
69D LEU* 4.0 25.1 - - + -
73D ILE* 4.2 11.0 - - + -
130D TYR* 4.1 14.4 - - - +
134D ILE* 3.9 39.0 - - + -
138D LEU* 6.1 1.3 - - + -
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Residues in contact with ASN 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLU* 3.5 7.6 - - - +
38C PRO* 3.6 22.2 - - + +
173C ARG* 2.6 37.8 + - - +
53D ASN* 2.8 37.1 + - - +
54D THR* 4.3 2.8 - - - +
56D LEU* 1.3 75.8 - - - +
58D THR* 1.3 60.1 + - - +
59D VAL 3.3 0.7 - - - -
70D LYS* 5.3 6.6 + - - -
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Residues in contact with THR 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LYS* 3.0 25.3 + - - -
35C GLU* 3.7 6.2 - - - +
38C PRO* 4.1 4.7 - - + -
39C MET* 3.3 54.3 - - + +
20D LEU* 3.6 13.3 - - + +
23D TRP* 4.2 0.3 - - - -
24D VAL* 3.7 12.2 - - - +
54D THR* 2.7 31.9 + - + +
55D MET 3.3 8.3 + - - -
56D LEU 3.2 0.4 - - - -
57D ASN* 1.3 77.8 - - - +
59D VAL* 1.3 62.8 + - - +
60D GLY 3.4 0.2 + - - -
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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