Contacts of the helix formed by residues 43 - 53 (chain V) in PDB entry 3HOU
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 ARG 43 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004N GLU* 3.3 44.7 + - - +
1005N GLY 5.6 0.2 - - - -
1006N ILE* 4.2 16.6 - - + +
1037N LEU* 5.9 0.2 - - - -
1064N TYR* 4.8 1.8 - - - -
175O ALA* 3.4 28.9 - - - +
177O GLU* 4.1 12.3 + - - +
231O ASN* 5.7 1.6 - - - +
233O GLU* 2.6 35.9 + - - +
10V CYS* 3.7 12.4 - - - -
12V LYS* 3.9 10.9 - - - +
42V LYS* 1.3 98.6 - - - +
44V TYR* 1.3 68.0 + - + +
45V CYS* 3.4 20.6 - - - +
46V CYS* 3.0 27.7 + - - +
47V ARG* 3.1 9.0 + - - -
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Residues in contact with TYR 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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824N ILE* 4.0 22.7 - - + -
1006N ILE* 3.4 25.0 - - + +
1033N LYS* 3.5 14.7 - - + -
1036N ALA* 3.6 25.8 - - + -
1037N LEU* 4.1 12.1 - - + +
1064N TYR* 3.3 33.9 - + - -
1070N GLU* 2.4 37.3 + - - -
1087N PHE* 3.8 4.9 - + - -
1088N GLY* 4.2 6.3 - - - -
1089N PRO* 3.9 26.5 - - + -
42V LYS 4.0 0.8 + - - -
43V ARG* 1.3 72.3 - - + +
45V CYS* 1.3 56.1 + - - +
47V ARG* 3.5 14.1 - - - +
48V ARG* 2.7 37.3 + - + +
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Residues in contact with CYS 45 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824N ILE* 4.3 3.8 - - + -
1006N ILE* 3.6 19.3 - - + -
7V CYS* 3.3 12.7 - - - -
9V SER* 3.4 21.5 - - - +
10V CYS* 3.2 18.2 - - - -
43V ARG* 3.0 14.6 + - - +
44V TYR* 1.3 81.8 - - - +
46V CYS* 1.3 65.3 + - - +
48V ARG* 3.5 15.8 - - - +
49V MET* 3.3 16.6 - - - +
9998V ZN 2.4 35.4 - - - -
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Residues in contact with CYS 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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7V CYS* 4.2 6.5 - - + -
10V CYS* 3.4 4.5 - - - -
12V LYS* 4.2 12.1 - - + -
14V VAL* 5.0 4.5 - - + +
41V LEU* 4.2 32.1 - - + +
42V LYS 4.9 2.2 - - - -
43V ARG* 3.0 42.0 + - - +
45V CYS* 1.3 81.1 - - - +
47V ARG* 1.3 65.0 + - - +
49V MET* 3.2 16.5 + - - +
50V ILE* 3.6 4.7 + - - +
9998V ZN 2.6 31.0 - - - -
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Residues in contact with ARG 47 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036N ALA 3.4 20.3 + - - +
1037N LEU* 3.3 33.5 + - - +
1039N GLY 4.8 0.4 - - - +
33V GLY* 3.0 17.2 + - - -
36V LEU* 3.1 45.7 - - + +
37V SER* 2.6 33.1 + - - +
41V LEU* 3.5 22.5 + - + +
42V LYS 3.3 20.6 + - - -
43V ARG 3.1 6.9 + - - +
44V TYR* 3.6 15.9 - - - +
46V CYS* 1.3 77.8 - - - +
48V ARG* 1.3 63.6 + - - +
49V MET 3.0 0.9 + - - -
50V ILE* 3.2 3.1 + - - +
51V LEU* 3.0 27.3 + - - +
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Residues in contact with ARG 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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800N GLN* 3.8 14.7 + - - +
803N LEU* 4.7 13.5 - - + -
822N ASN* 3.1 28.1 + - - -
824N ILE* 2.8 37.2 - - + +
1009N ASP* 3.0 14.3 + - - -
1036N ALA* 4.6 15.2 - - + +
1089N PRO* 5.3 0.9 - - + -
8V PHE* 4.0 8.3 - - - +
9V SER* 2.7 27.4 + - - +
44V TYR* 2.7 23.4 + - + +
45V CYS* 3.5 6.7 - - - +
47V ARG* 1.3 74.1 - - - +
49V MET* 1.3 89.2 + - - +
51V LEU* 4.4 4.0 - - - -
52V THR* 2.9 33.9 + - - +
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Residues in contact with MET 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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800N GLN* 3.9 16.3 + - - +
4V PRO* 4.5 21.7 - - + +
7V CYS* 3.4 17.3 - - + +
8V PHE* 3.2 55.6 - - + +
14V VAL* 5.0 11.4 - - + -
45V CYS 3.3 18.8 - - - +
46V CYS 3.2 13.2 - - - +
47V ARG 3.0 0.6 - - - -
48V ARG* 1.3 107.2 - - - +
50V ILE* 1.3 61.3 + - - +
53V HIS* 3.3 22.2 + - - +
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Residues in contact with ILE 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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3V VAL* 3.9 19.3 - - + -
14V VAL* 3.3 37.2 - - + +
17V LYS* 4.7 5.4 - - + -
18V TRP* 4.0 26.5 - - + +
21V TYR* 3.9 28.0 - - + -
36V LEU* 3.5 20.4 - - + -
41V LEU* 3.6 23.3 - - + -
46V CYS 3.6 1.5 + - - +
47V ARG 3.2 5.6 + - - +
49V MET* 1.3 75.0 - - - +
51V LEU* 1.3 69.7 + - - +
52V THR 3.0 3.3 + - - -
53V HIS* 3.2 17.0 + - + +
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Residues in contact with LEU 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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801N LYS* 3.7 18.1 + - - +
803N LEU* 4.7 8.7 - - + -
1035N ALA 3.5 14.1 - - - +
1036N ALA* 3.9 15.3 - - - +
1039N GLY* 3.4 42.2 - - - +
1040N ASN 5.9 0.4 - - - -
1041N GLU* 5.9 2.2 - - - +
21V TYR* 4.4 9.6 + - - +
32V GLU* 4.3 18.2 - - + -
36V LEU* 3.9 10.3 - - + +
47V ARG 3.0 17.8 + - - +
48V ARG* 4.4 1.8 - - - -
50V ILE* 1.3 82.0 - - - +
52V THR* 1.3 62.3 + - - +
53V HIS 4.9 0.7 - - - +
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Residues in contact with THR 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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800N GLN* 3.0 26.3 - - + -
801N LYS* 2.6 50.8 + - + +
803N LEU* 3.6 24.4 - - - +
822N ASN* 3.2 6.2 + - - +
48V ARG* 2.9 22.3 + - - -
50V ILE 3.0 0.4 - - - -
51V LEU* 1.3 79.7 - - - +
53V HIS* 1.3 67.3 + - - +
54V VAL* 3.3 5.0 + - - +
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Residues in contact with HIS 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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798N TYR* 6.3 2.5 - - + -
799N PRO 4.6 11.0 - - - -
800N GLN* 5.1 2.9 - - - +
801N LYS* 5.1 3.1 - - - -
1V MET* 3.7 3.8 - - + -
2V ILE 3.1 15.1 + - - -
3V VAL* 3.0 40.6 - - + +
4V PRO* 4.2 13.0 - - + -
18V TRP* 4.2 21.0 - + + -
49V MET 3.3 17.5 + - - +
50V ILE* 3.2 13.4 + - - +
51V LEU 4.9 1.4 - - - +
52V THR* 1.3 78.4 - - - +
54V VAL* 1.3 89.1 + - - +
55V ASP* 3.0 44.5 + - - -
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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