Contacts of the helix formed by residues 48 - 56 (chain D) in PDB entry 2IHC
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 HIS 48 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C SER* 3.4 20.8 - - - -
24D LEU* 3.4 30.3 - - + -
27D GLN* 2.9 25.8 + - + +
28D ARG 4.2 0.4 - - - -
33D LEU 3.4 24.8 + - - -
34D CYS* 3.8 17.8 - - - -
35D ASP* 3.2 6.5 - - - +
36D VAL* 4.1 1.6 - - - -
47D ALA* 1.3 73.1 - - - +
49D ARG* 1.3 66.2 + - - +
50D SER* 3.8 15.7 - - - +
51D VAL* 3.2 10.4 + - + +
52D LEU* 3.2 22.9 + - - +
92D TYR* 2.5 37.4 + + - +
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Residues in contact with ARG 49 (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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33C LEU* 4.6 11.0 - - + -
35D ASP* 2.7 29.5 + - - +
36D VAL* 3.9 17.9 - - + +
48D HIS* 1.3 71.7 - - - +
50D SER* 1.3 57.0 + - - +
52D LEU* 3.5 4.5 + - - +
53D ALA* 2.9 32.4 + - - +
63D ILE* 4.6 14.9 - - + +
71D LEU* 4.6 14.4 - - + -
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Residues in contact with SER 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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24C LEU* 3.7 11.9 - - - +
27C GLN* 3.2 35.5 + - - +
33C LEU* 4.4 10.8 + - - +
48C HIS* 3.6 24.6 - - - -
50C SER* 4.9 5.2 + - - -
35D ASP* 5.5 0.2 - - - -
48D HIS* 3.8 12.3 - - - +
49D ARG* 1.3 78.1 - - - +
51D VAL* 1.3 59.9 + - - +
54D ALA* 3.1 24.9 + - - +
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Residues in contact with VAL 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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20C VAL* 4.8 11.2 - - + -
24C LEU* 5.0 4.5 - - + -
50C SER* 5.9 0.2 - - - +
21D LEU* 5.4 1.3 - - + -
24D LEU* 3.5 32.3 - - + -
48D HIS* 3.2 20.9 + - + +
50D SER* 1.3 81.8 + - - +
52D LEU* 1.3 61.2 + - + +
54D ALA* 3.3 6.0 + - - +
55D CYS* 3.0 47.3 + - - -
91D ALA* 4.3 9.0 - - + +
92D TYR* 3.6 37.5 - - + +
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Residues in contact with LEU 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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36D VAL* 3.6 20.0 - - + -
38D ILE* 3.8 19.5 - - + -
47D ALA* 3.3 31.6 - - + -
48D HIS 3.2 11.1 + - - +
49D ARG* 3.9 4.9 - - - +
51D VAL* 1.3 79.4 - - + +
53D ALA* 1.3 55.4 + - - +
55D CYS* 3.4 3.5 + - + -
56D SER* 3.1 25.8 + - - -
59D PHE* 3.4 41.6 - - + +
84D PHE* 5.7 0.7 - - + -
88D ILE* 4.6 13.5 - - + -
91D ALA* 5.2 7.2 - - + -
92D TYR* 4.5 12.3 - - + -
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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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27C GLN* 3.9 2.2 - - - +
33C LEU* 3.6 26.2 - - + -
49D ARG 2.9 19.0 + - - +
50D SER 3.9 1.8 - - - +
52D LEU* 1.3 72.6 - - - +
54D ALA* 1.3 65.0 + - - +
56D SER 3.3 13.2 + - - +
59D PHE* 4.1 3.9 - - - +
60D HIS* 3.7 43.2 + - - +
63D ILE* 4.8 3.4 - - + -
116D HIS* 4.7 2.1 + - - -
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Residues in contact with ALA 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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20C VAL* 4.5 20.9 - - + +
23C SER* 3.9 32.2 + - - +
24C LEU* 5.2 2.2 - - + -
27C GLN* 4.0 4.2 - - - +
50D SER 3.1 19.9 + - - +
51D VAL* 3.3 10.1 + - - +
53D ALA* 1.3 77.4 - - - +
55D CYS* 1.3 59.0 + - - +
116D HIS* 3.1 17.7 + - - +
117D ASN* 5.9 0.3 + - - -
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Residues in contact with CYS 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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16C HIS* 3.6 31.0 - - + -
20C VAL* 3.9 13.7 - - - -
51D VAL* 3.0 27.7 + - - +
52D LEU* 4.1 4.7 - - + +
53D ALA 3.3 0.2 - - - -
54D ALA* 1.3 72.5 - - - +
56D SER* 1.3 60.6 + - - +
90D PHE* 6.3 0.2 - - + -
91D ALA* 3.7 28.5 - - + -
115D VAL* 3.3 12.3 - - + +
116D HIS* 3.0 35.4 + - - +
117D ASN* 6.1 0.7 - - - +
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Residues in contact with SER 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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52D LEU 3.1 11.9 + - - +
53D ALA 3.3 9.7 - - - +
54D ALA 3.5 1.6 - - - -
55D CYS* 1.3 82.1 - - - +
57D SER* 1.3 57.1 + - - +
58D TYR 3.4 4.9 + - - -
59D PHE* 3.5 21.4 + - - -
60D HIS* 3.0 22.2 + - - +
113D LEU* 2.3 39.9 + - - +
114D SER 3.5 5.8 - - - -
115D VAL* 4.5 4.3 - - - -
116D HIS* 3.5 4.2 - - - -
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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