Contacts of the helix formed by residues 45 - 57 (chain R) in PDB entry 1OCR
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 45 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43R PRO 3.7 1.8 - - - +
44R GLU* 1.3 98.1 - - + +
46R LYS* 1.3 57.3 + - - +
48R ILE* 2.9 13.5 + - + +
49R ASP* 2.8 29.0 + - - +
84R TYR* 4.0 28.0 - - + +
85R VAL* 4.4 17.3 - - + -
88R GLU* 3.8 26.9 - - + +
89R LEU* 3.5 12.4 - - + +
9V MET* 4.5 6.3 - - + -
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Residues in contact with LYS 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R GLU* 5.0 5.1 + - - +
12R ASP* 3.9 33.6 + - - +
13R ALA* 4.8 6.5 - - - +
16R VAL* 4.1 23.4 - - + +
44R GLU* 4.1 17.9 - - + +
45R PRO* 1.3 79.6 - - - +
47R ILE* 1.3 61.6 + - + +
49R ASP* 3.6 8.8 - - - +
50R ALA* 3.3 20.1 + - - +
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Residues in contact with ILE 47 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R PHE* 4.8 6.3 - - + -
12R ASP* 3.9 26.9 - - - +
15R TRP* 3.9 30.3 - - + -
16R VAL* 4.1 18.6 - - + -
19R PHE* 4.2 10.3 - - + -
36R LEU* 3.7 26.5 - - + -
43R PRO* 4.3 10.5 - - + -
44R GLU* 2.9 27.3 + - + +
46R LYS* 1.3 74.4 - - + +
48R ILE* 1.3 69.6 + - + +
50R ALA* 3.2 5.9 + - - +
51R ALA* 3.0 21.1 + - + +
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Residues in contact with ILE 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R MET* 5.3 9.2 - - + -
43R PRO* 3.6 33.9 - - + +
44R GLU 3.6 11.9 - - - +
45R PRO* 2.9 8.0 + - + +
47R ILE* 1.3 80.3 - - + +
49R ASP* 1.3 55.8 + - - +
51R ALA* 3.3 5.3 + - - +
52R LEU* 2.8 44.6 + - + +
67R ILE* 4.2 18.4 - - + -
68R LEU* 4.4 3.6 - - + -
71R VAL* 3.7 29.2 - - + -
85R VAL* 4.5 4.7 - - + -
89R LEU* 3.6 25.8 - - + -
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Residues in contact with ASP 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R PRO 2.8 15.7 + - - +
46R LYS* 3.6 11.0 - - - +
48R ILE* 1.3 75.5 - - - +
50R ALA* 1.3 64.8 + - - +
52R LEU* 3.0 9.7 + - - +
53R ARG* 3.0 48.2 + - - +
88R GLU 5.5 1.0 - - - +
89R LEU* 3.7 15.7 - - + +
92R THR* 2.4 31.2 + - - -
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Residues in contact with ALA 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R VAL* 4.1 15.0 - - + +
19R PHE* 3.8 19.2 - - + +
20R ASN* 3.6 25.4 - - - +
46R LYS 3.3 10.1 + - - +
47R ILE* 3.2 9.0 + - - +
49R ASP* 1.3 81.4 + - - +
51R ALA* 1.3 62.6 + - - +
53R ARG* 3.0 8.5 + - - +
54R ALA* 2.9 21.7 + - - +
57R ARG* 4.6 0.7 + - - -
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Residues in contact with ALA 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R PHE* 3.7 39.2 - - + +
29R LEU* 4.2 1.7 - - + +
33R MET* 4.4 6.7 - - - -
47R ILE 3.0 13.5 + - - +
48R ILE* 3.8 9.0 - - - +
50R ALA* 1.3 74.3 - - - +
52R LEU* 1.3 63.7 + - - +
54R ALA* 3.1 4.6 + - - +
55R CYS* 3.0 26.1 + - - -
67R ILE* 4.0 19.7 - - + -
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Residues in contact with LEU 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Q TRP* 5.0 0.5 - - - -
48R ILE* 2.8 26.6 + - + +
49R ASP* 3.0 9.6 + - - +
51R ALA* 1.3 76.1 - - - +
53R ARG* 1.3 61.8 + - - +
55R CYS* 3.1 20.9 - - - +
56R ARG* 3.2 6.6 + - - +
64R ALA* 3.8 39.5 - - + +
67R ILE* 4.4 13.0 - - + -
68R LEU* 4.3 6.5 - - + -
89R LEU* 4.1 23.3 - - + -
92R THR* 4.6 10.5 - - + -
93R LEU* 3.9 27.1 - - + -
96R LEU* 4.4 4.4 - - - +
98R ILE* 4.3 15.1 - - + +
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Residues in contact with ARG 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20R ASN* 5.5 4.5 - - - +
49R ASP* 3.0 36.3 + - - +
50R ALA* 3.6 8.7 - - - +
52R LEU* 1.3 72.9 - - - +
54R ALA* 1.3 66.8 + - - +
55R CYS 3.0 1.3 - - - -
56R ARG* 3.0 19.2 + - + +
57R ARG* 3.0 25.3 + - + +
92R THR* 2.7 40.7 + - + +
95R GLU* 2.9 41.2 + - - -
96R LEU* 4.1 15.3 - - + +
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Residues in contact with ALA 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R PHE* 3.4 24.0 - - + +
24R ILE* 3.8 17.5 - - + -
29R LEU* 4.2 13.7 - - + -
50R ALA 2.9 7.6 + - - +
51R ALA* 3.5 10.3 - - - +
53R ARG* 1.3 76.1 - - - +
55R CYS* 1.3 62.4 + - - +
57R ARG* 3.3 18.1 + - - +
58R LEU* 3.1 28.7 + - - +
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Residues in contact with CYS 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48Q TRP* 3.9 2.7 - - + -
29R LEU* 4.4 9.4 - - - -
51R ALA 3.0 15.7 + - - -
52R LEU* 3.1 13.9 - - - +
54R ALA* 1.3 77.8 - - - +
56R ARG* 1.3 55.0 + - - +
58R LEU* 3.2 8.0 + - - +
59R ASN 2.9 8.3 + - - -
60R ASP* 2.9 39.7 + - - +
63R SER* 3.8 15.3 - - - -
64R ALA* 3.7 32.1 - - + -
67R ILE* 3.9 17.3 - - - -
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Residues in contact with ARG 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Q GLU 2.9 22.2 + - - -
45Q LYS 3.7 3.8 + - - -
46Q ALA 2.7 24.4 + - - -
47Q SER* 3.9 3.0 - - - +
48Q TRP* 3.2 52.8 - - + +
52R LEU 3.2 5.1 + - - +
53R ARG* 3.0 14.9 + - - +
55R CYS* 1.3 76.8 - - - +
57R ARG* 1.3 63.7 + - + +
59R ASN* 2.8 47.9 + - - +
96R LEU* 4.3 28.6 + - + +
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Residues in contact with ARG 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R PHE 2.9 24.0 + - - -
20R ASN* 3.6 19.8 + - - +
21R LYS 2.9 22.6 + - - -
22R PRO* 3.6 24.6 + - - +
24R ILE* 3.3 22.1 - - + +
50R ALA 4.6 0.6 + - - -
53R ARG* 3.0 15.4 + - - +
54R ALA* 3.3 23.3 + - - +
56R ARG* 1.3 77.8 - - + +
58R LEU* 1.3 63.5 + - + +
59R ASN* 3.2 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