Contacts of the helix formed by residues 40 - 53 (chain V) 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 ALA 40 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25O ASP* 3.6 26.0 - - + +
29O MET* 6.2 1.1 - - - -
35V TYR* 3.1 3.9 + - + +
36V LYS* 2.8 33.9 + - + +
39V VAL* 1.3 79.6 - - - +
41V GLU* 1.3 64.6 + - - +
43V ARG* 2.9 9.0 + - - +
44V LYS* 3.0 36.7 + - + +
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Residues in contact with GLU 41 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36V LYS* 2.7 39.8 + - + +
37V PHE* 3.6 39.3 - - + +
40V ALA* 1.3 72.2 - - - +
42V LYS* 1.3 62.7 + - - +
44V LYS* 3.2 26.2 + - - +
45V LYS* 3.1 23.8 + - - +
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Residues in contact with LYS 42 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132Q GLN* 3.3 29.4 - - - +
37V PHE 3.7 7.9 + - - +
38V ALA 3.8 19.9 + - - +
39V VAL* 3.2 37.4 + - - +
40V ALA 3.2 0.4 - - - -
41V GLU* 1.3 78.5 - - - +
43V ARG* 1.3 67.7 + - - +
45V LYS* 3.3 17.5 + - - +
46V ALA* 2.9 26.3 + - + +
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Residues in contact with ARG 43 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O GLY* 6.0 3.0 - - - -
9O PHE 6.0 2.6 + - - +
21O LEU* 4.2 27.8 + - - +
22O HIS* 3.7 21.1 - - + +
25O ASP* 2.6 45.7 + - - +
132Q GLN* 3.2 38.5 + - - +
35V TYR* 4.2 1.2 + - - -
39V VAL* 3.0 30.0 + - - +
40V ALA 2.9 4.0 + - - +
42V LYS* 1.3 84.3 - - - +
44V LYS* 1.3 65.2 + - - +
45V LYS 3.0 1.8 - - - -
46V ALA* 4.1 0.2 - - - -
47V TYR* 3.2 29.3 + - + -
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Residues in contact with LYS 44 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22O HIS* 3.0 61.2 + - + +
25O ASP* 3.2 24.0 + - - +
36V LYS* 5.4 3.6 - - - +
40V ALA* 3.0 31.1 + - - +
41V GLU* 3.2 31.8 + - - +
43V ARG* 1.3 77.0 - - - +
45V LYS* 1.3 61.6 + - - +
47V TYR* 3.8 2.4 + - - +
48V ALA* 3.3 21.8 + - - +
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Residues in contact with LYS 45 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41V GLU 3.1 10.8 + - - +
42V LYS* 3.4 19.6 - - - +
44V LYS* 1.3 75.3 - - - +
46V ALA* 1.3 66.3 + - - +
47V TYR 3.1 1.8 - - - -
48V ALA* 2.9 6.4 + - + +
49V ASP* 2.8 50.8 + - - +
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Residues in contact with ALA 46 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Q ILE* 3.5 11.1 - - + +
132Q GLN* 3.6 34.8 - - + +
42V LYS* 2.9 17.3 + - + +
43V ARG 3.3 5.6 + - - +
45V LYS* 1.3 78.0 - - - +
47V TYR* 1.3 61.9 + - + +
49V ASP* 4.1 4.8 - - - +
50V PHE* 3.2 24.3 + - - +
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Residues in contact with TYR 47 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11O ASP* 3.6 13.7 + - - +
12O ALA* 3.0 38.6 + - + -
18O GLU* 3.7 33.0 - - + +
21O LEU* 3.2 22.4 - - + +
22O HIS* 4.8 9.2 - + - +
131Q ILE* 3.3 43.3 - - + -
132Q GLN* 3.8 20.0 + - - -
43V ARG* 3.2 21.9 + - + +
44V LYS 4.2 3.6 - - - +
45V LYS 3.1 0.6 - - - -
46V ALA* 1.3 77.4 - - + +
48V ALA* 1.3 65.7 + - - +
50V PHE* 4.5 0.7 - - - -
51V TYR* 3.2 31.6 + + - +
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Residues in contact with ALA 48 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44V LYS 3.3 16.5 + - - +
45V LYS* 2.9 8.5 + - + +
47V TYR* 1.3 78.4 - - - +
49V ASP* 1.3 66.2 + - - +
51V TYR* 4.0 1.4 - - - +
52V ARG* 3.3 39.6 + - - +
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Residues in contact with ASP 49 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45V LYS* 2.8 41.4 + - - +
46V ALA* 4.1 5.1 - - - +
48V ALA* 1.3 77.0 - - - +
50V PHE* 1.3 66.5 + - - +
52V ARG* 3.3 34.7 + - - +
53V ASN* 4.0 3.3 + - - +
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Residues in contact with PHE 50 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188O ARG* 4.1 14.1 - - - -
130Q PRO* 3.2 50.5 - - + -
131Q ILE* 3.8 22.4 - - + +
46V ALA 3.2 19.5 + - - +
47V TYR 3.9 3.1 - - - +
48V ALA 3.4 0.2 - - - -
49V ASP* 1.3 78.9 - - - +
51V TYR* 1.3 72.3 + + + +
52V ARG 3.2 3.8 + - - -
53V ASN 3.9 5.7 + - - +
54V TYR* 3.4 49.8 + + - +
59V ASP* 5.5 1.3 - - - -
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Residues in contact with TYR 51 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O ALA 3.5 6.2 + - - -
13O THR 4.4 1.0 + - - -
18O GLU* 4.1 21.3 + - - -
187O SER* 3.8 28.3 + - - -
188O ARG* 2.8 50.2 + - + -
131Q ILE* 3.4 20.9 - - + -
47V TYR* 3.2 29.0 + + - +
48V ALA* 4.0 2.0 - - - +
50V PHE* 1.3 84.7 - + - +
52V ARG* 1.3 63.1 + - - +
53V ASN 3.6 0.2 - - - -
54V TYR* 3.9 25.5 + + - +
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Residues in contact with ARG 52 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48V ALA* 3.3 32.0 + - - +
49V ASP* 3.5 30.4 + - - +
50V PHE 3.1 1.4 - - - -
51V TYR* 1.3 80.6 - - - +
53V ASN* 1.3 81.0 + - - +
54V TYR 3.5 2.0 + - - +
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Residues in contact with ASN 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49V ASP 4.0 2.9 + - - +
50V PHE 3.9 5.8 + - - +
52V ARG* 1.3 96.5 + - - +
54V TYR* 1.3 58.3 + - - +
55V ASP 4.3 0.2 + - - -
58V LYS* 5.4 2.6 + - - -
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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