Contacts of the helix formed by residues 22 - 33 (chain B) in PDB entry 1IJK
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 ASN 22 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B MET* 1.3 76.3 - - - +
23B TRP* 1.3 64.9 + - - +
24B ALA* 3.2 8.7 + - - +
25B ASP* 2.6 54.6 + - - +
26B ALA* 2.9 19.8 + - - +
68B TRP* 3.3 0.2 - - - -
120B CYS 3.2 14.6 - - - +
121B ALA* 3.9 13.7 + - - +
122B GLN 2.9 13.9 - - - +
123B LYS* 3.9 18.4 - - + +
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Residues in contact with TRP 23 (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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22B ASN* 1.3 73.5 - - - +
24B ALA* 1.3 69.2 + - + +
26B ALA* 3.3 3.3 + - - +
27B GLU* 2.9 32.8 + - + +
39B LEU* 3.5 13.1 - - + +
68B TRP* 3.0 37.3 - + + +
69B ILE 2.9 22.9 + - - -
70B GLY* 3.6 19.5 - - - -
71B LEU 3.8 6.9 + - - -
72B ARG* 3.2 54.7 - - + -
103B CYS* 3.3 43.1 - - + -
104B PHE 4.1 0.9 + - - -
120B CYS* 3.3 8.4 + - + +
280C THR* 4.6 15.0 - - - -
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Residues in contact with ALA 24 (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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22B ASN* 3.2 8.3 + - - +
23B TRP* 1.3 91.3 - - + +
25B ASP* 1.3 69.5 + - - +
27B GLU* 3.5 5.9 + - - +
28B ARG* 3.1 22.3 + - - +
72B ARG* 6.0 1.3 - - - +
120B CYS* 5.7 1.7 - - + +
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Residues in contact with ASP 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B MET* 3.5 29.0 - - + +
22B ASN* 2.6 43.0 + - - +
24B ALA* 1.3 74.8 - - - +
26B ALA* 1.3 61.2 + - - +
28B ARG* 3.4 8.7 + - - +
29B PHE* 2.9 30.5 + - - +
123B LYS* 4.9 3.6 + - - -
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Residues in contact with ALA 26 (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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21B MET* 4.1 8.4 - - + +
22B ASN 2.9 13.7 + - - +
23B TRP 3.5 8.3 - - - +
25B ASP* 1.3 77.2 - - - +
27B GLU* 1.3 61.8 + - - +
29B PHE* 3.3 6.6 + - - +
30B CYS* 3.0 28.6 + - - -
39B LEU* 4.0 11.0 - - + -
68B TRP* 4.1 11.4 - - + -
126B PHE* 3.8 31.1 - - + -
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 2.9 27.8 + - + +
24B ALA* 3.7 8.5 - - - +
25B ASP 3.3 0.2 - - - -
26B ALA* 1.3 76.3 - - - +
28B ARG* 1.3 62.6 + - - +
30B CYS* 3.4 2.5 + - - +
31B SER* 3.2 20.6 + - - -
37B GLY 4.6 0.3 - - - +
38B HIS* 2.7 27.2 + - - -
39B LEU* 3.2 23.2 + - + +
280C THR* 2.8 40.1 + - - +
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Residues in contact with ARG 28 (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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24B ALA 3.1 17.2 + - - +
25B ASP* 3.8 9.0 - - - +
27B GLU* 1.3 77.9 - - - +
29B PHE* 1.3 65.0 + - - +
31B SER* 2.7 28.7 + - - +
32B GLU* 3.2 26.2 + - + +
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Residues in contact with PHE 29 (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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17B PHE* 3.6 42.0 - + - -
19B GLN* 4.1 18.6 - - + -
21B MET* 4.1 23.1 - - + -
25B ASP 2.9 17.7 + - - +
26B ALA 3.5 4.3 - - - +
28B ARG* 1.3 76.5 - - - +
30B CYS* 1.3 63.9 + - - +
32B GLU* 3.2 17.5 + - - +
33B GLN* 3.0 52.3 - - + +
126B PHE* 3.4 20.2 - + + -
128B CYS* 3.9 0.4 - - - -
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Residues in contact with CYS 30 (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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6B TRP* 5.5 0.7 - - - -
26B ALA 3.0 20.2 + - - +
27B GLU 3.8 1.8 - - - +
29B PHE* 1.3 76.5 - - - +
31B SER* 1.3 61.1 + - - +
33B GLN* 3.3 16.5 + - - +
34B ALA 3.9 0.3 + - - -
37B GLY* 3.5 15.0 - - - -
38B HIS* 3.5 22.9 - - - +
39B LEU* 3.8 13.5 - - - +
126B PHE* 3.6 11.2 - - - -
128B CYS* 2.0 57.2 - - + +
130B SER* 5.3 0.2 - - - -
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Residues in contact with SER 31 (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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27B GLU* 3.2 16.7 + - - -
28B ARG* 2.7 26.4 + - - +
30B CYS* 1.3 76.7 - - - +
32B GLU* 1.3 62.7 + - - +
33B GLN 3.4 0.2 - - - -
34B ALA 2.9 18.9 - - - +
36B GLY 5.2 0.3 + - - -
37B GLY 3.0 19.9 + - - +
38B HIS* 5.1 3.4 - - - -
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Residues in contact with GLU 32 (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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28B ARG* 3.2 33.8 + - + +
29B PHE* 3.2 12.8 + - - +
30B CYS 3.2 0.6 - - - -
31B SER* 1.3 82.0 + - - +
33B GLN* 1.3 68.9 + - - +
34B ALA* 3.2 2.9 + - - -
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Residues in contact with GLN 33 (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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6B TRP* 3.8 25.6 - - + +
17B PHE* 4.1 16.0 - - + -
29B PHE* 3.0 61.7 - - + +
30B CYS* 3.3 11.4 + - - +
32B GLU* 1.3 83.5 - - - +
34B ALA* 1.3 61.7 + - - +
128B CYS* 4.4 1.6 - - - -
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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