Contacts of the helix formed by residues 48 - 56 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.4 29.4 - - + -
27A GLN* 2.8 30.1 + - + +
28A ARG* 4.1 5.8 - - + -
33A LEU 3.4 24.5 + - - -
34A CYS* 4.2 8.0 - - - -
35A ASP* 3.5 9.9 - - - +
36A VAL* 3.7 2.0 - - - -
47A ALA* 1.3 76.0 - - - +
49A ARG* 1.3 65.0 + - - +
50A SER* 4.0 13.9 - - - +
51A VAL* 3.1 12.4 + - + +
52A LEU* 3.1 22.3 + - - +
92A TYR* 2.6 33.1 + + - +
50B SER* 3.4 21.7 - - - +
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Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ASP* 2.5 56.7 + - - +
36A VAL* 3.4 11.7 - - + +
48A HIS* 1.3 70.8 - - - +
50A SER* 1.3 60.0 + - - +
52A LEU* 3.4 3.4 + - - +
53A ALA* 3.0 30.8 + - - +
63A ILE* 3.5 40.8 + - + +
66A GLN 4.3 17.8 - - - -
70A GLU* 4.2 8.9 - - - +
71A LEU* 3.4 35.8 - - - +
33B LEU* 4.1 20.3 - - + +
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Residues in contact with SER 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ASP* 5.0 2.8 + - - -
48A HIS* 4.0 12.1 - - - +
49A ARG* 1.3 77.0 + - - +
51A VAL* 1.3 62.6 + - - +
53A ALA* 3.6 0.3 + - - +
54A ALA* 3.1 23.9 + - - +
24B LEU* 3.8 9.1 - - - +
27B GLN* 3.1 35.8 + - - -
33B LEU* 4.0 13.0 - - - -
35B ASP* 5.6 0.7 + - - -
48B HIS* 3.7 23.2 - - - -
50B SER* 4.8 5.9 + - - -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 5.3 1.3 - - + -
24A LEU* 3.7 31.2 - - + -
48A HIS* 3.1 19.3 + - + +
50A SER* 1.3 78.3 + - - +
52A LEU* 1.3 66.9 + - + +
54A ALA* 3.3 5.3 + - - +
55A CYS* 3.0 44.2 + - - -
91A ALA* 4.2 7.6 - - + +
92A TYR* 3.6 36.8 - - + +
20B VAL* 4.6 12.1 - - + -
24B LEU* 4.7 6.7 - - + -
50B SER* 6.0 0.2 - - - +
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 4.1 16.2 - - + -
38A ILE* 3.5 37.7 - - + -
47A ALA* 4.1 15.3 - - + -
48A HIS 3.1 16.6 + - - +
49A ARG* 3.9 5.4 - - - +
51A VAL* 1.3 77.5 - - + +
53A ALA* 1.3 57.6 + - - +
55A CYS* 4.5 3.8 - - + +
56A SER* 3.0 30.9 + - - +
59A PHE* 3.5 38.6 - - + +
63A ILE* 5.1 2.9 - - + -
84A PHE* 5.7 0.4 - - + -
88A ILE* 4.4 17.3 - - + -
91A ALA* 5.5 6.1 - - + -
92A TYR* 4.6 8.5 - - + -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ARG 3.0 18.2 + - - +
50A SER 3.8 3.1 - - - +
52A LEU* 1.3 76.0 - - - +
54A ALA* 1.3 64.8 + - - +
56A SER 3.3 14.4 + - - +
59A PHE* 4.3 0.8 - - - +
60A HIS* 3.6 43.7 + - - +
63A ILE* 4.8 4.0 - - + -
116A HIS* 4.6 2.6 + - - -
27B GLN* 4.5 3.4 - - - +
33B LEU* 3.7 23.1 - - + -
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A SER 3.1 17.7 + - - +
51A VAL* 3.6 7.6 - - - +
53A ALA* 1.3 76.7 - - - +
55A CYS* 1.3 60.3 + - - +
116A HIS* 2.9 22.3 + - - -
117A ASN* 5.6 0.2 - - - +
20B VAL* 4.6 16.2 - - + +
23B SER* 3.6 35.7 + - - +
24B LEU* 5.2 2.0 - - + +
27B GLN* 4.2 5.1 - - - +
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Residues in contact with CYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 3.0 31.3 + - - +
52A LEU* 4.1 4.3 - - - +
54A ALA* 1.3 77.2 - - - +
56A SER* 1.3 59.9 + - - +
91A ALA* 3.8 29.4 - - + -
115A VAL* 3.3 12.9 - - + +
116A HIS* 3.0 32.0 + - - -
117A ASN* 5.9 0.7 - - - -
16B HIS* 3.6 31.0 - - + -
20B VAL* 3.9 12.1 - - - -
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Residues in contact with SER 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU 3.0 12.1 + - - +
53A ALA 3.3 10.4 - - - +
54A ALA 3.5 2.0 + - - -
55A CYS* 1.3 80.8 - - - +
57A SER* 1.3 57.2 + - - +
58A TYR* 3.6 1.0 - - - +
59A PHE* 3.2 32.7 + - - -
60A HIS 2.9 23.2 + - - -
113A LEU* 2.3 29.1 + - - +
114A SER 3.4 5.6 - - - -
115A VAL* 4.3 10.1 - - - -
116A HIS* 4.0 2.0 + - - -
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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