Contacts of the helix formed by residues 40 - 48 (chain B) in PDB entry 6WVM
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 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TYR* 3.0 17.2 + - - -
39B ASP* 1.3 84.2 - - - +
41B ASP* 1.3 68.3 + - - +
42B LEU* 3.4 22.1 + - - +
43B GLN* 3.0 27.1 + - - +
44B LEU* 3.8 1.4 + - - +
369B ARG* 6.0 0.2 - - - -
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Residues in contact with ASP 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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39B ASP 5.5 0.5 - - - +
40B SER* 1.3 73.8 + - - +
42B LEU* 1.3 59.6 + - + +
44B LEU* 3.0 10.8 + - - +
47B GLU* 2.9 29.5 + - - +
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Residues in contact with LEU 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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77A GLU* 4.3 16.2 - - - +
28B HIS* 5.0 0.7 + - - -
40B SER* 3.2 12.7 - - - +
41B ASP* 1.3 79.6 - - + +
43B GLN* 1.3 60.4 + - + +
44B LEU 3.4 0.3 + - - -
47B GLU* 3.6 23.8 + - + +
48B ARG 4.2 1.2 + - - -
243B ARG 4.1 6.9 - - - +
244B PHE* 3.6 26.8 - - + -
245B PRO* 4.1 26.0 - - + -
358B ILE* 3.5 32.5 - - + -
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Residues in contact with GLN 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 ASP 4.1 0.4 + - - -
27B GLU 2.8 25.7 + - - +
28B HIS* 2.9 47.9 + - - +
29B GLY* 3.6 14.5 - - - +
36B TYR* 3.3 3.3 + - + +
38B GLY* 3.2 8.8 - - - -
39B ASP 2.9 26.2 + - - -
40B SER* 3.0 23.6 + - - +
41B ASP 3.2 0.4 - - - -
42B LEU* 1.3 78.6 - - + +
44B LEU* 1.3 58.4 + - - +
49B ILE* 3.9 6.4 + - - +
244B PHE* 4.3 9.0 - - + -
369B ARG* 3.1 28.4 - - - +
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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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36B TYR* 3.5 47.6 - - + -
40B SER 4.5 4.0 - - - +
41B ASP* 3.0 13.5 + - - +
43B GLN* 1.3 76.6 - - - +
47B GLU* 1.3 64.4 + - - +
48B ARG 3.2 4.3 + - - -
49B ILE* 3.2 31.0 - - + +
50B ASN* 5.1 0.2 - - - +
61B TYR* 3.9 23.8 - - - +
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Residues in contact with GLU 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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76A ASP* 3.9 13.1 - - + +
80A THR* 5.2 9.3 + - - +
41B ASP* 2.9 15.8 + - - +
42B LEU* 3.8 21.5 - - + +
43B GLN 3.6 0.6 - - - -
44B LEU* 1.3 75.6 - - - +
48B ARG* 1.3 109.3 + - + +
50B ASN* 3.6 8.1 - - - +
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Residues in contact with ARG 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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72A PRO* 4.0 16.4 - - - +
73A THR* 4.0 16.7 + - + +
76A ASP* 2.8 35.9 + - - +
1B MET* 5.2 15.1 - - - +
2B ARG* 4.4 10.4 - - - +
28B HIS* 4.3 9.5 + - + -
42B LEU 4.2 3.4 + - - -
43B GLN 4.6 0.2 + - - -
44B LEU 3.3 0.4 - - - -
47B GLU* 1.3 115.8 + - + +
49B ILE* 1.3 59.3 + - - +
50B ASN* 3.1 14.7 + - - +
51B VAL* 2.9 31.9 + - + +
52B TYR 4.6 0.2 + - - -
242B LEU 3.6 17.9 + - - +
243B ARG* 3.3 36.6 - - + +
244B PHE* 5.5 0.9 - - - -
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Residues in contact with ILE 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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28B HIS* 4.3 11.4 - - + +
30B ILE* 3.6 34.1 - - + -
36B TYR* 4.8 0.2 - - + -
43B GLN 3.9 14.4 + - - +
44B LEU* 3.2 33.7 + - + +
48B ARG* 1.3 76.1 - - - +
50B ASN* 1.3 64.7 + - + +
51B VAL 3.2 0.7 + - - -
52B TYR 3.4 0.9 + - - -
53B TYR* 3.1 30.0 + - + +
55B GLU* 4.6 9.2 - - + +
61B TYR* 3.5 55.2 - - + +
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Residues in contact with ASN 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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1B MET* 3.5 26.7 + - - +
3B GLU* 2.8 30.1 + - - +
44B LEU 5.1 0.2 - - - +
47B GLU 3.6 7.8 - - - +
48B ARG* 3.5 19.8 + - - +
49B ILE* 1.3 84.5 + - + +
51B VAL* 1.3 51.6 + - - +
52B TYR 3.2 0.4 - - - -
53B TYR 3.3 15.0 - - - +
55B GLU* 5.5 7.6 - - + +
64B ARG* 2.8 31.1 + - - +
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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