Contacts of the helix formed by residues 49 - 60 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C LYS* 6.1 2.5 - - + -
47C GLY 3.5 9.8 - - - +
48C VAL* 1.3 90.3 - - + +
50C PRO* 1.3 73.8 - - + +
51C GLU* 3.6 17.5 - - + +
52C GLU* 3.1 19.4 + - + +
53C ALA* 3.0 18.9 + - - +
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Residues in contact with PRO 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C PRO* 4.6 4.3 - - + -
48C VAL 3.6 3.6 - - - +
49C PRO* 1.3 83.1 - - + +
51C GLU* 1.3 74.7 + - - +
53C ALA* 3.8 7.4 - - + +
54C GLY* 2.9 25.1 + - - -
87C ILE* 3.7 18.6 - - + +
95C ASN* 5.7 1.1 - - - +
97C TYR* 3.8 53.6 - - + +
99C CYS* 4.4 3.8 - - - -
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Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LYS* 4.0 16.8 - - + +
25C TYR* 3.7 45.2 + - + +
49C PRO* 3.6 17.4 - - + +
50C PRO* 1.3 91.4 - - - +
52C GLU* 1.3 58.6 + - - +
54C GLY 4.0 0.3 - - - -
55C ALA* 3.0 29.3 + - - +
87C ILE* 3.7 14.1 - - + +
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Residues in contact with GLU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ASP* 3.4 16.6 - - - +
20C TYR* 2.9 36.4 + - + -
21C LYS* 3.0 35.8 + - + +
48C VAL* 4.4 10.1 - - + -
49C PRO* 3.1 26.6 + - + +
51C GLU* 1.3 77.2 - - - +
53C ALA* 1.3 61.8 + - - +
55C ALA* 3.3 0.7 + - - +
56C ALA* 2.9 29.9 + - + +
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Residues in contact with ALA 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C VAL* 4.1 7.2 - - + -
44C PRO* 3.9 23.3 - - + -
48C VAL* 4.2 7.8 - - + +
49C PRO 3.0 16.5 + - - +
50C PRO 3.8 3.8 - - - +
52C GLU* 1.3 78.0 - - - +
54C GLY* 1.3 62.9 + - - +
56C ALA* 3.3 6.8 + - - +
57C VAL* 3.1 27.8 + - - +
129C ALA* 6.3 0.7 - - - -
130C LEU* 3.8 25.3 - - + +
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Residues in contact with GLY 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C VAL* 5.3 0.4 - - - -
50C PRO 2.9 16.7 + - - -
53C ALA* 1.3 76.7 - - - +
55C ALA* 1.3 60.3 + - - +
57C VAL* 3.4 8.1 + - - +
58C ALA* 3.1 22.7 + - - +
84C CYS* 3.8 17.8 - - - +
99C CYS* 4.0 23.9 - - - -
101C VAL* 4.5 2.4 - - - +
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Residues in contact with ALA 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C TYR* 3.6 6.1 - - - +
21C LYS* 3.4 35.7 - - - +
24C TYR* 3.5 23.3 - - + +
25C TYR* 4.1 2.0 - - + +
51C GLU 3.0 19.7 + - - +
52C GLU 3.7 2.7 - - - +
53C ALA 3.3 0.2 - - - -
54C GLY* 1.3 74.3 - - - +
56C ALA* 1.3 60.4 + - - +
58C ALA* 3.3 0.6 + - - -
59C ALA* 2.9 31.0 + - - +
84C CYS* 4.3 1.4 - - - +
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Residues in contact with ALA 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C TYR* 3.6 32.9 - - + +
52C GLU* 2.9 19.1 + - + +
53C ALA* 3.6 8.3 - - - +
54C GLY 3.3 0.2 - - - -
55C ALA* 1.3 72.3 - - - +
57C VAL* 1.3 68.2 + - + +
60C GLU* 3.0 30.5 + - - +
124C VAL* 4.5 0.8 - - - +
127C PHE* 4.9 13.9 - - + -
130C LEU* 5.9 4.0 - - + -
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Residues in contact with VAL 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C PHE* 3.7 43.3 - - + -
42C VAL* 4.9 5.4 - - + -
53C ALA 3.1 16.0 + - - +
54C GLY* 3.6 10.1 - - - +
55C ALA 3.3 0.2 - - - -
56C ALA* 1.3 80.6 - - + +
58C ALA* 1.3 55.7 + - - +
61C SER* 2.7 35.5 + - - +
99C CYS* 6.4 0.4 - - + -
101C VAL* 4.8 3.1 - - + -
124C VAL* 3.5 18.2 - - + +
130C LEU* 4.1 25.1 - - + -
133C LEU* 4.4 13.9 - - + -
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Residues in contact with ALA 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TYR* 4.2 6.3 - - + +
54C GLY 3.1 16.3 + - - +
55C ALA 3.7 4.0 - - - +
56C ALA 3.3 0.2 - - - -
57C VAL* 1.3 78.0 - - - +
59C ALA* 1.3 54.3 + - - +
61C SER* 3.3 14.0 + - - -
62C SER* 2.7 27.5 + - - -
82C GLY* 4.0 4.2 - - - +
83C ARG* 3.9 8.3 - - - -
84C CYS 3.8 24.5 - - - +
101C VAL* 3.9 21.1 - - + +
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Residues in contact with ALA 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C TYR* 3.5 21.5 - - + -
24C TYR* 3.4 44.4 - - + -
55C ALA 2.9 14.1 + - - +
56C ALA 3.9 0.4 - - - +
58C ALA* 1.3 77.3 - - - +
60C GLU* 1.3 58.9 + - - +
61C SER 3.0 5.6 + - - -
62C SER 3.1 9.9 + - - -
63C THR 3.2 1.0 + - - -
64C GLY* 3.0 25.2 + - - +
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Residues in contact with GLU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C TYR* 2.6 29.9 + - + +
56C ALA 3.0 16.2 + - - +
59C ALA* 1.3 73.2 - - - +
61C SER* 1.3 57.9 + - - +
62C SER 3.5 1.1 - - - -
64C GLY 3.7 16.2 - - - +
65C THR* 3.3 20.4 + - - -
66C TRP* 3.4 4.3 + - - +
119C SER 4.9 0.3 - - - +
123C ASN* 4.9 19.8 + - + +
124C VAL* 3.9 11.6 + - + +
127C PHE* 3.1 39.2 - - + -
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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