Contacts of the helix formed by residues 45 - 53 (chain B) in PDB entry 2AJA
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 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B LEU* 1.3 76.5 - - - +
46B TYR* 1.3 61.1 + - - +
47B LYS* 4.1 7.3 + - - +
48B GLU* 3.0 34.1 + - - +
49B ALA* 2.8 26.5 + - - +
73B HIS* 3.8 1.3 - - - -
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Residues in contact with TYR 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B SER* 1.3 71.1 - - - +
47B LYS* 1.3 69.3 + - + +
49B ALA* 3.6 0.4 - - - +
50B ILE* 2.9 57.1 + - + +
69B LEU* 5.2 2.0 - - + -
73B HIS* 3.5 49.0 + + + +
76B ARG* 5.9 3.1 - - + +
78B ALA* 4.4 16.6 - - + -
80B GLN* 3.6 19.4 + - + -
81B LEU* 3.4 34.8 - - + -
84B ASP* 2.7 38.2 + - - +
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Residues in contact with LYS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B SER* 3.1 8.4 + - - +
46B TYR* 1.3 91.8 - - + +
48B GLU* 1.3 62.6 + - + +
50B ILE* 3.8 4.3 + - + +
51B HIS* 3.3 21.3 + - - +
80B GLN* 6.1 4.0 - - - +
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 3.6 32.3 - - + +
45B SER* 3.0 27.6 + - - +
47B LYS* 1.3 76.7 - - + +
49B ALA* 1.3 68.0 + - - +
51B HIS* 3.1 7.3 + - - +
52B ILE* 3.0 28.3 + - + +
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 3.5 38.7 - - - +
44B LEU* 4.0 12.0 - - + +
45B SER 2.8 19.9 + - - +
46B TYR* 3.6 4.0 - - - +
48B GLU* 1.3 72.7 - - - +
50B ILE* 1.3 59.7 + - - +
52B ILE* 3.5 1.1 + - - -
53B PHE* 2.9 30.7 + - - +
69B LEU* 4.0 12.1 - - + -
73B HIS* 3.9 6.7 - - - +
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Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B TYR* 2.9 61.4 + - + +
47B LYS* 4.2 4.5 - - - +
49B ALA* 1.3 75.5 - - - +
51B HIS* 1.3 60.2 + - - +
53B PHE* 3.4 25.4 - - + +
69B LEU* 4.8 9.9 - - + -
81B LEU* 4.8 5.8 - - + -
84B ASP* 3.8 32.3 - - + +
85B ALA* 4.8 0.9 - - - +
88B LYS* 2.9 39.7 - - + -
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Residues in contact with HIS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LYS 3.3 13.6 + - - +
48B GLU* 3.1 13.4 + - - +
50B ILE* 1.3 81.6 - - - +
52B ILE* 1.3 73.2 + - + +
53B PHE 3.1 2.0 + - - +
88B LYS* 3.1 23.5 + - - +
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Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ASN* 4.6 14.9 - - - +
40B SER* 3.8 21.8 - - - +
41B LEU* 4.5 8.1 - - + -
44B LEU* 3.8 13.9 - - + -
48B GLU* 3.4 15.3 - - + +
49B ALA 4.0 4.7 - - - +
51B HIS* 1.3 89.3 - - + +
53B PHE* 1.3 64.4 + - - +
54B LEU* 3.5 7.0 + - - +
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Residues in contact with PHE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 3.9 21.5 - - + -
49B ALA 2.9 19.8 + - - +
50B ILE* 3.4 17.0 - - + +
51B HIS 3.1 2.0 - - - -
52B ILE* 1.3 75.7 - - - +
54B LEU* 1.3 61.9 + - - +
55B PRO* 3.7 8.0 - - + +
65B GLN* 3.2 39.9 - - + -
66B LEU* 6.0 0.4 - - + -
69B LEU* 4.0 23.8 - - + -
85B ALA* 4.7 7.6 - - + -
88B LYS* 3.5 51.6 + - + +
90B ILE* 3.8 33.2 - - + -
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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