Contacts of the helix formed by residues 49 - 60 (chain D) in PDB entry 1IR1
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 PRO 49 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D LYS* 4.6 15.7 - - - +
47D GLY 3.5 9.8 - - - +
48D VAL* 1.3 90.7 - - + +
50D PRO* 1.3 71.7 - - + +
51D GLU* 3.6 15.7 - - - +
52D GLU* 3.0 21.3 + - + +
53D ALA* 3.0 18.9 + - - +
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Residues in contact with PRO 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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44D PRO* 4.6 4.9 - - + -
48D VAL 3.6 3.3 - - - +
49D PRO* 1.3 82.3 - - + +
51D GLU* 1.3 75.6 - - - +
53D ALA* 3.8 7.0 - - + +
54D GLY* 2.8 28.6 + - - -
87D ILE* 3.7 17.0 - - + +
95D ASN* 5.6 1.3 - - - +
97D TYR* 3.9 53.2 - - + +
99D CYS* 4.4 3.4 - - - -
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Residues in contact with GLU 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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21D LYS* 3.9 19.7 + - + +
25D TYR* 3.7 45.7 + - + +
49D PRO* 3.6 14.1 - - + +
50D PRO* 1.3 95.8 - - - +
52D GLU* 1.3 56.3 + - - +
54D GLY* 4.1 0.3 - - - -
55D ALA* 3.1 27.7 + - - +
87D ILE* 3.7 14.8 - - + +
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Residues in contact with GLU 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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19D ASP* 3.5 18.0 - - - +
20D TYR* 2.8 36.0 + - + -
21D LYS* 2.9 40.6 + - + +
48D VAL* 4.5 9.0 - - + -
49D PRO* 3.0 27.9 + - + +
51D GLU* 1.3 78.4 - - - +
53D ALA* 1.3 60.5 + - - +
55D ALA* 3.6 1.6 - - - +
56D ALA* 2.8 29.4 + - + +
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Residues in contact with ALA 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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42D VAL* 4.1 6.7 - - + -
44D PRO* 3.8 26.2 - - + -
48D VAL* 4.0 12.0 - - + +
49D PRO 3.0 15.0 + - - +
50D PRO 3.8 2.9 - - - +
52D GLU* 1.3 77.2 - - - +
54D GLY* 1.3 62.2 + - - +
56D ALA* 3.3 7.0 + - - +
57D VAL* 3.1 29.0 + - - +
129D ALA* 6.3 0.7 - - - -
130D LEU* 3.9 20.2 - - + +
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Residues in contact with GLY 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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42D VAL* 5.3 0.9 - - - -
50D PRO 2.8 16.9 + - - -
51D GLU 4.2 0.2 - - - -
53D ALA* 1.3 76.2 - - - +
55D ALA* 1.3 62.3 + - - +
57D VAL* 3.4 8.0 + - - +
58D ALA* 3.1 22.2 + - - +
84D CYS* 3.8 16.8 - - - +
99D CYS* 3.9 23.9 - - - -
101D VAL* 4.6 2.4 - - - +
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Residues in contact with ALA 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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20D TYR* 3.6 6.5 - - - +
21D LYS* 3.4 34.1 - - - +
24D TYR* 3.5 22.9 - - + +
25D TYR* 4.2 1.6 - - + +
51D GLU 3.1 21.3 + - - +
52D GLU 3.6 3.1 - - - +
54D GLY* 1.3 74.7 - - - +
56D ALA* 1.3 59.8 + - - +
58D ALA* 3.2 1.2 + - - -
59D ALA* 2.8 31.4 + - - +
84D CYS* 4.3 1.3 - - - +
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Residues in contact with ALA 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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20D TYR* 3.5 34.7 - - + +
52D GLU* 2.8 17.5 + - + +
53D ALA* 3.3 7.6 + - - +
55D ALA* 1.3 76.2 - - - +
57D VAL* 1.3 64.1 + - + +
60D GLU* 3.0 30.7 + - - +
127D PHE* 4.9 14.3 - - + -
130D LEU* 6.2 2.5 - - + -
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Residues in contact with VAL 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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40D PHE* 3.8 44.6 - - + -
42D VAL* 4.9 5.2 - - + -
53D ALA 3.1 15.3 + - - +
54D GLY* 3.6 10.3 - - - +
55D ALA 3.3 0.2 - - - -
56D ALA* 1.3 79.5 - - + +
58D ALA* 1.3 54.1 + - - +
61D SER* 2.6 33.5 + - - +
99D CYS* 6.4 0.9 - - + -
101D VAL* 4.8 2.7 - - + -
124D VAL* 3.6 18.6 - - + +
130D LEU* 4.0 25.4 - - + -
133D LEU* 4.4 13.9 - - + -
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Residues in contact with ALA 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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24D TYR* 4.2 6.3 - - + +
54D GLY 3.1 14.3 + - - +
55D ALA 3.6 7.2 - - - +
57D VAL* 1.3 78.1 - - - +
59D ALA* 1.3 54.1 + - - +
61D SER* 3.3 12.7 + - - -
62D SER* 2.8 27.6 + - - -
82D GLY* 3.9 12.3 - - - +
83D ARG* 4.1 0.2 - - - -
84D CYS 3.8 17.9 - - - +
101D VAL* 3.8 27.1 - - + +
103D TYR* 4.5 0.5 - - - -
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Residues in contact with ALA 59 (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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20D TYR* 3.4 23.1 - - + -
24D TYR* 3.4 39.7 - - + -
55D ALA 2.8 17.3 + - - +
56D ALA 3.8 0.7 - - - +
58D ALA* 1.3 76.9 - - - +
60D GLU* 1.3 57.1 + - - +
61D SER 3.1 4.8 + - - -
62D SER 3.2 9.2 + - - -
63D THR 3.2 1.0 + - - -
64D GLY* 2.9 25.7 + - - +
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Residues in contact with GLU 60 (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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20D TYR* 2.7 28.3 + - + +
56D ALA 3.0 17.2 + - - +
59D ALA* 1.3 74.2 - - - +
61D SER* 1.3 57.2 + - - +
62D SER 3.5 0.7 - - - -
64D GLY 3.7 14.9 - - - +
65D THR* 3.2 21.1 + - - -
66D TRP* 3.4 4.0 + - - +
119D SER 4.9 0.3 - - - +
123D ASN* 4.9 20.5 + - + +
124D VAL* 3.8 18.7 - - + +
127D PHE* 3.2 33.9 - - + -
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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