Contacts of the helix formed by residues 28 - 36 (chain B) in PDB entry 4WMJ
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 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B ASP 5.0 6.1 + - - -
26B LYS 3.2 8.5 + - - +
27B ILE* 1.3 76.6 + - - +
29B ILE* 1.3 66.7 + - - +
30B LEU* 4.9 6.2 + - - +
31B GLN* 3.2 28.7 + - + +
32B LEU* 3.0 25.1 + - - +
472B LYS 5.4 1.6 - - - +
474B ASN* 3.3 25.7 + - - +
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Residues in contact with ILE 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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27B ILE 4.2 0.2 - - - -
28B ASN* 1.3 71.4 - - - +
30B LEU* 1.3 64.9 + - - +
32B LEU* 3.0 12.4 + - - +
33B PHE* 3.0 38.7 + - + -
39B ARG* 4.9 1.3 - - - +
60B SER 4.2 3.1 - - - +
61B LYS* 3.6 28.5 - - - +
62B ASN 3.6 21.5 - - - +
63B ARG* 3.9 9.6 - - + +
440B MET* 3.4 25.4 - - + -
474B ASN* 2.8 43.9 + - - +
475B ARG 4.1 3.4 - - - +
476B PRO* 3.9 12.3 - - + -
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Residues in contact with LEU 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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542A ASP* 5.2 5.2 - - + -
28B ASN* 3.3 6.6 + - - +
29B ILE* 1.3 77.3 - - - +
31B GLN* 1.3 58.9 + - - +
33B PHE* 3.0 11.0 + - + +
34B GLN* 2.9 53.1 + - - +
440B MET* 3.5 40.9 + - + +
441B LYS* 4.1 31.2 - - + +
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Residues in contact with GLN 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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26B LYS 3.9 13.9 + - - -
28B ASN* 3.2 30.7 + - + +
30B LEU* 1.3 77.0 - - - +
32B LEU* 1.3 66.3 + - + +
34B GLN* 2.9 18.0 + - + +
35B GLN* 2.9 45.0 + - - +
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Residues in contact with LEU 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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27B ILE* 3.9 25.4 - - + -
28B ASN 3.0 19.9 + - - +
29B ILE* 3.0 15.5 + - - +
31B GLN* 1.3 76.9 - - + +
33B PHE* 1.3 62.8 + - - +
35B GLN* 3.3 25.1 + - + +
36B ASP* 3.1 27.7 + - - +
39B ARG* 3.7 23.2 - - - +
62B ASN 4.5 1.6 - - - +
64B ILE 3.6 20.6 - - - +
65B ASP* 4.0 23.6 - - + +
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Residues in contact with PHE 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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542A ASP* 4.3 11.2 - - + -
543A ALA* 3.9 21.5 - - + +
544A SER* 3.5 29.4 - - - -
29B ILE* 3.0 48.2 + - + -
30B LEU* 3.0 9.6 + - + +
32B LEU* 1.3 74.2 - - - +
34B GLN* 1.4 65.6 + - - +
35B GLN 3.2 0.9 + - - -
36B ASP 3.3 17.4 + - - +
37B ALA* 4.8 2.1 - - - -
39B ARG* 3.8 26.9 - - + +
40B PHE 4.5 1.1 - - - -
60B SER* 3.3 38.6 - - - -
61B LYS* 4.1 7.2 - - + -
440B MET* 4.0 13.0 - - + -
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Residues in contact with GLN 34 (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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30B LEU* 2.9 50.3 + - - +
31B GLN* 2.9 19.0 + - + +
33B PHE* 1.4 76.3 - - - +
35B GLN* 1.3 62.9 + - + +
36B ASP 3.6 0.3 + - - -
37B ALA 5.4 0.3 + - - -
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Residues in contact with GLN 35 (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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31B GLN* 2.9 40.3 + - - +
32B LEU* 3.6 32.5 - - + +
33B PHE 3.0 0.2 - - - -
34B GLN* 1.3 81.2 - - + +
36B ASP* 1.3 58.8 + - + +
37B ALA 4.2 0.8 + - - -
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Residues in contact with ASP 36 (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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32B LEU 3.1 13.8 + - - +
33B PHE* 3.3 13.5 + - - +
34B GLN 3.5 0.6 - - - -
35B GLN* 1.3 83.3 - - + +
37B ALA* 1.3 63.2 + - - +
38B ASP* 3.1 19.9 + - - +
39B ARG* 3.1 41.4 + - + +
42B LYS* 3.2 27.5 + - - +
43B TYR* 4.8 1.7 - - - -
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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