Contacts of the helix formed by residues 40 - 51 (chain A) in PDB entry 1PR9
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LYS* 4.5 3.3 + - - +
38A SER* 4.4 1.9 + - - -
39A ARG* 1.3 89.5 + - - +
41A GLN* 1.3 66.5 + - - +
42A ALA* 3.9 14.4 - - + +
43A ASP* 3.1 34.3 + - - +
44A LEU* 3.4 9.1 + - - +
58A CYS* 4.1 2.0 - - - -
245A NAP 2.5 26.7 + - - -
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Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A THR* 1.3 70.1 - - - +
42A ALA* 1.3 61.2 + - - +
44A LEU* 2.9 16.7 + - - +
45A ASP* 2.8 53.5 + - - +
56A PRO* 5.3 6.3 - - - +
58A CYS* 3.3 35.2 - - - +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A THR* 3.3 10.3 - - + +
41A GLN* 1.3 80.4 - - - +
43A ASP* 1.3 64.4 + - - +
45A ASP* 3.7 12.8 - - - +
46A SER* 3.3 23.6 + - - -
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Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY* 3.7 30.6 - - - +
17A LYS* 2.5 41.9 + - - +
21A ARG* 3.2 21.3 + - - +
38A SER* 4.8 0.8 + - - +
40A THR* 3.1 25.1 + - - +
41A GLN 3.0 0.6 - - - -
42A ALA* 1.3 81.1 - - - +
44A LEU* 1.3 62.9 + - + +
46A SER* 3.3 4.6 + - - -
47A LEU* 3.2 11.4 + - - +
245A NAP 3.6 3.1 + - - -
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 4.9 1.3 - - + -
16A GLY 4.9 1.6 - - - +
36A ALA* 3.7 32.5 - - + +
38A SER* 3.9 26.0 - - - +
40A THR 3.4 10.3 + - - +
41A GLN* 2.9 12.6 + - - +
43A ASP* 1.3 79.1 - - - +
45A ASP* 1.3 66.1 + - - +
47A LEU* 3.6 11.5 - - + +
48A VAL* 2.9 30.5 + - - +
54A ILE* 5.5 0.4 - - + -
56A PRO* 3.9 18.6 - - + -
57A VAL 3.6 24.2 - - - +
58A CYS* 3.8 22.4 - - + -
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Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLN* 2.8 45.8 + - - +
42A ALA* 3.7 12.7 - - - +
43A ASP 3.4 0.2 - - - -
44A LEU* 1.3 74.8 - - - +
46A SER* 1.3 60.5 + - - +
48A VAL* 2.8 29.8 - - - +
49A ARG* 3.1 11.8 + - - +
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Residues in contact with SER 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 3.2 18.4 + - - -
42A ALA 3.3 11.0 + - - -
43A ASP* 3.3 9.0 + - - -
45A ASP* 1.3 80.2 - - - +
47A LEU* 1.3 59.5 + - - +
49A ARG* 3.3 30.7 + - - +
50A GLU* 2.8 34.3 + - - +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA 3.4 26.0 - - - +
16A GLY* 5.1 0.2 - - - -
21A ARG* 3.5 18.4 - - + +
24A VAL* 4.0 19.1 - - + -
25A GLN* 4.0 7.0 - - + +
36A ALA* 4.2 10.5 - - + -
43A ASP 3.2 14.5 + - - +
44A LEU* 3.2 11.4 + - + +
46A SER* 1.3 79.3 + - - +
48A VAL* 1.3 59.8 + - - +
50A GLU* 3.3 17.2 + - - +
51A CYS* 2.8 45.3 + - - +
54A ILE* 3.7 21.7 - - + +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU 2.9 18.3 + - - +
45A ASP* 2.8 30.5 - - - +
47A LEU* 1.3 77.6 - - - +
49A ARG* 1.3 64.0 + - + +
51A CYS 4.1 6.5 - - - +
52A PRO* 3.3 26.8 - - + +
53A GLY 5.9 0.9 - - - +
54A ILE* 3.7 21.8 - - + +
56A PRO* 3.7 31.4 - - + -
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Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASP 3.1 12.0 + - - +
46A SER* 3.6 34.8 + - - +
47A LEU 3.2 0.2 - - - -
48A VAL* 1.3 81.5 - - + +
50A GLU* 1.3 61.3 + - + +
52A PRO* 4.3 8.9 - - - +
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 2.5 34.2 + - - -
25A GLN* 2.9 32.9 + - - +
28A HIS* 5.0 1.4 + - - -
46A SER* 2.8 20.3 + - - +
47A LEU* 3.3 7.5 - - - +
49A ARG* 1.3 80.6 - - + +
51A CYS* 1.3 62.0 + - - +
52A PRO* 3.4 8.6 - - - +
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Residues in contact with CYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 4.7 1.8 - - - -
25A GLN* 3.9 42.6 - - - -
28A HIS* 3.6 26.7 - - + -
47A LEU* 2.8 24.6 + - + +
48A VAL 3.4 5.5 - - - +
50A GLU* 1.3 84.0 - - - +
52A PRO* 1.3 69.7 - - - +
53A GLY 3.4 0.2 + - - -
54A ILE* 3.4 27.6 + - + +
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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