Contacts of the helix formed by residues 37 - 48 (chain B) in PDB entry 4K8T
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 ASP 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B ILE* 1.3 76.8 - - - +
38B ALA* 1.3 64.1 + - - +
39B GLU* 3.3 10.9 + - - +
40B ARG* 2.9 37.0 + - - +
41B ALA* 3.0 21.7 + - - +
128B TYR* 3.8 6.5 - - - -
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Residues in contact with ALA 38 (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 ASP* 1.3 75.8 - - - +
39B GLU* 1.3 61.8 + - - +
41B ALA* 3.3 3.5 + - - +
42B GLU* 3.2 28.4 + - + +
107B PHE* 6.6 0.2 - - + -
128B TYR* 3.8 14.5 - - + +
403B DMS 3.7 38.0 - - + +
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Residues in contact with GLU 39 (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 ASP* 3.3 11.2 + - - +
38B ALA* 1.3 80.0 - - - +
40B ARG* 1.3 61.6 + - - +
42B GLU* 3.4 8.8 + - + +
43B LEU* 3.1 21.1 + - + +
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Residues in contact with ARG 40 (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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26B ASN* 2.7 31.3 + - - +
27B GLN* 4.4 6.0 + - - +
28B ILE* 3.8 17.0 - - - +
36B ILE* 3.7 31.9 - - + +
37B ASP* 2.9 22.2 + - - +
39B GLU* 1.3 72.8 - - - +
41B ALA* 1.3 60.6 + - - +
43B LEU* 3.3 20.8 + - - +
44B LEU* 2.8 51.9 + - + +
126B ASN* 4.8 1.8 + - - -
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Residues in contact with ALA 41 (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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36B ILE* 3.7 13.2 - - + +
37B ASP 3.0 15.1 + - - +
38B ALA* 3.4 9.9 - - - +
39B GLU 3.2 0.2 - - - -
40B ARG* 1.3 76.7 - - - +
42B GLU* 1.3 62.2 + - - +
45B TYR* 3.0 23.0 + - - +
114B MSE 3.3 20.1 - - + +
128B TYR* 4.3 7.2 - - + -
402B DMS 3.5 22.7 - - - +
403B DMS 3.9 10.1 - - + -
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Residues in contact with GLU 42 (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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38B ALA* 3.2 14.3 + - + +
39B GLU* 3.7 10.1 - - + +
41B ALA* 1.3 75.9 - - - +
43B LEU* 1.3 64.1 + - - +
45B TYR* 3.4 4.2 + - - +
46B SER* 3.1 24.1 + - - -
402B DMS 3.7 20.1 - - + +
403B DMS 3.2 22.7 + - - +
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Residues in contact with LEU 43 (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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26B ASN* 4.6 3.6 - - - +
39B GLU* 3.1 14.7 + - + +
40B ARG* 3.6 30.7 - - - +
41B ALA 3.3 0.2 - - - -
42B GLU* 1.3 77.0 - - - +
44B LEU* 1.3 66.6 + - + +
46B SER* 2.5 31.6 + - - +
47B ARG* 3.4 45.0 + - - +
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Residues in contact with LEU 44 (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 PHE* 5.0 1.7 - - + -
26B ASN* 4.1 18.8 - - - +
28B ILE* 4.0 18.6 - - + -
36B ILE* 4.1 10.5 - - + -
40B ARG* 2.8 59.5 + - - +
41B ALA 4.0 2.9 - - - +
43B LEU* 1.3 75.5 - - + +
45B TYR* 1.3 57.6 + - - +
47B ARG* 3.1 6.4 + - - +
48B MSE 3.0 27.0 + - - +
114B MSE 4.0 11.9 - - + -
116B PHE* 4.5 11.6 - - + -
126B ASN* 3.8 37.2 - - + +
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Residues in contact with TYR 45 (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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86A ASP* 4.4 10.8 - - + -
87A ILE* 3.6 26.4 + - + +
90A HIS* 2.9 78.2 + + + +
91A ASP* 4.5 2.3 + - - -
14B ILE* 3.9 23.4 - - + +
41B ALA 3.0 18.0 + - - +
42B GLU* 3.8 6.1 - - - +
44B LEU* 1.3 77.0 - - - +
46B SER* 1.3 61.9 + - - +
48B MSE 3.1 12.2 + - - -
51B ALA* 5.3 0.7 - - + -
53B GLU* 4.8 2.8 + - - -
114B MSE 3.6 19.7 - - - -
402B DMS 3.7 36.8 - - + -
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Residues in contact with SER 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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90A HIS* 5.0 3.6 + - - -
94A ALA* 5.7 2.1 - - - +
42B GLU 3.1 13.9 + - - -
43B LEU* 2.5 30.0 + - - +
45B TYR* 1.3 78.4 - - - +
47B ARG* 1.3 62.9 + - - +
48B MSE 4.5 2.4 - - - +
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Residues in contact with ARG 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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22B PHE* 3.6 26.7 - - + -
25B ASP* 4.7 8.9 + - - +
26B ASN* 2.9 34.5 + - - +
43B LEU* 3.6 39.9 - - - +
44B LEU* 3.1 9.8 + - - +
45B TYR 3.1 0.6 - - - -
46B SER* 1.3 83.8 + - - +
48B MSE 1.3 60.4 + - - +
49B GLY 3.8 1.0 + - - -
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Residues in contact with MSE 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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90A HIS* 2.9 21.6 + - - +
94A ALA* 3.4 8.0 - - - +
14B ILE* 3.4 45.8 - - - +
15B ILE 4.1 0.2 - - - -
16B SER* 3.5 28.5 - - - +
22B PHE* 4.7 0.9 - - - -
44B LEU 3.0 11.8 + - - +
45B TYR* 3.1 19.2 + - - +
46B SER 4.5 1.7 - - - +
47B ARG* 1.3 79.7 - - - +
49B GLY* 1.3 70.4 + - - +
51B ALA* 4.4 3.1 - - - -
114B MSE 3.8 20.9 - - + +
115B ILE 3.7 6.1 - - - +
116B PHE* 3.5 33.4 - - + -
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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