Contacts of the helix formed by residues 46 - 53 (chain A) in PDB entry 2IHD
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 SER 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A THR* 1.3 64.0 + - - +
48A GLU* 3.2 11.7 - - - +
49A GLU* 3.6 23.4 + - - +
50A ALA* 2.9 28.1 + - - +
171A LEU 4.7 0.2 - - - +
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Residues in contact with THR 47 (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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46A SER* 1.3 77.5 + - - +
48A GLU* 1.3 67.5 + - - +
50A ALA* 3.3 3.5 + - - +
51A THR* 3.0 26.9 + - - -
171A LEU 3.8 21.5 - - - +
172A LEU* 3.9 27.3 - - + -
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Residues in contact with GLU 48 (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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46A SER 3.8 7.4 - - - +
47A THR* 1.3 82.7 + - - +
49A GLU* 1.3 62.4 + - - +
51A THR* 3.2 9.3 + - - -
52A ARG* 3.0 39.0 + - + +
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Residues in contact with GLU 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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46A SER* 3.3 23.1 + - - +
47A THR 3.3 0.8 - - - -
48A GLU* 1.3 79.8 - - - +
50A ALA* 1.3 63.3 + - - +
52A ARG* 3.0 20.1 + - - +
53A TRP* 3.2 45.7 + - - +
63A HIS* 3.6 34.2 + - + +
65A TYR* 4.0 24.3 + - - +
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Residues in contact with ALA 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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46A SER 2.9 17.4 + - - +
47A THR 3.6 4.5 - - - +
49A GLU* 1.3 74.3 - - - +
51A THR* 1.3 57.8 + - - +
53A TRP* 3.2 24.3 + - + +
168A TYR* 2.6 32.7 + - + -
171A LEU* 3.7 41.5 - - + +
172A LEU 4.3 4.7 - - - +
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Residues in contact with THR 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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47A THR 3.0 15.2 + - - -
48A GLU* 3.4 11.5 - - - -
50A ALA* 1.3 77.2 - - - +
52A ARG* 1.3 85.3 + - - +
54A ALA* 3.1 21.4 + - + +
55A ASP* 4.1 4.2 + - - +
168A TYR* 3.6 6.5 - - - -
172A LEU* 4.2 13.2 + - - +
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Residues in contact with ARG 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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48A GLU* 3.0 31.7 + - + +
49A GLU* 3.0 17.5 + - - +
51A THR* 1.3 102.6 - - - +
53A TRP* 1.3 55.2 + - - +
55A ASP* 2.9 56.7 + - - +
59A VAL* 3.2 17.9 - - + +
63A HIS* 4.4 16.6 - - + +
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Residues in contact with TRP 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 GLU* 3.2 33.4 + - - -
50A ALA* 3.4 18.2 - - + +
51A THR 3.2 0.2 - - - -
52A ARG* 1.3 77.0 - - - +
54A ALA* 1.3 50.2 + - - +
56A SER 3.3 9.4 - - - +
59A VAL* 4.5 0.2 - - - -
60A LEU* 3.8 23.5 - - + +
63A HIS* 3.6 25.3 - + + +
65A TYR* 3.5 26.5 - - + -
66A GLY* 3.3 27.1 - - - -
69A ALA* 3.6 17.9 - - + -
159A TYR* 2.7 29.6 + - - -
162A PHE* 4.2 11.4 - + + -
163A LEU* 4.7 1.3 - - - -
168A TYR* 3.7 22.2 - + + -
171A LEU* 3.5 31.6 - - + -
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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