Contacts of the helix formed by residues 151 - 156 (chain 4) in PDB entry 2WSC
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 GLU 151 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1484 GLU* 2.9 45.2 - - + +
1494 ALA* 2.9 32.6 + - + +
1504 LYS* 1.3 73.6 - - - +
1524 LYS* 1.3 75.9 + - + +
1534 GLU 3.1 4.3 - - - +
1544 ILE* 2.3 44.9 - - + +
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Residues in contact with LYS 152 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1484 GLU* 5.9 2.0 - - - +
1494 ALA 4.2 0.2 + - - -
1514 GLU* 1.3 90.8 - - + +
1534 GLU* 1.3 56.8 + - - +
1544 ILE* 3.3 4.4 + - + -
1554 ALA* 3.5 26.9 - - + +
1564 ASN* 3.8 25.3 + - - +
12014 CLA 3.6 69.0 + - + +
40074 CLA 5.6 8.3 - - - +
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Residues in contact with GLU 153 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494 ARG* 3.6 26.1 + - - +
524 MET* 3.6 24.6 - - + +
1494 ALA 4.3 3.6 + - - +
1504 LYS* 3.7 27.6 - - + +
1514 GLU 3.1 7.1 - - - +
1524 LYS* 1.3 80.0 - - - +
1544 ILE* 1.3 58.5 + - - +
1564 ASN* 4.6 9.4 + - + +
1574 GLY* 4.8 4.0 + - - -
12004 CLA 4.5 30.2 + - - +
12014 CLA 5.3 19.5 - - + +
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Residues in contact with ILE 154 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1224 LYS* 5.9 3.1 - - - +
1504 LYS* 3.1 26.7 - - + +
1514 GLU* 2.3 36.5 + - - +
1524 LYS* 5.7 0.2 - - + -
1534 GLU* 1.3 76.8 - - - +
1554 ALA* 1.3 69.4 + - + +
1564 ASN 3.1 0.7 - - - -
1574 GLY* 2.3 34.9 + - - -
1584 ARG* 6.0 2.0 - - - +
12024 CLA 2.8 65.7 - - + -
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Residues in contact with ALA 155 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1524 LYS* 3.5 32.8 - - + +
1544 ILE* 1.3 85.7 - - + +
1564 ASN* 1.3 56.5 + - - +
1574 GLY 2.8 10.7 + - - -
1584 ARG* 2.8 22.7 + - - +
1594 LEU* 2.9 16.9 + - + +
12014 CLA 6.0 0.4 - - + -
12024 CLA 4.2 5.8 - - - -
40074 CLA 6.1 5.6 - - + -
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Residues in contact with ASN 156 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524 MET* 2.9 27.0 - - + +
1524 LYS 3.8 16.6 + - - +
1534 GLU* 4.6 5.7 + - - +
1544 ILE 3.1 0.6 - - - -
1554 ALA* 1.3 80.0 - - - +
1574 GLY* 1.3 56.5 + - - +
1594 LEU* 4.4 6.7 - - - +
1604 MET* 2.8 30.5 - - - +
12014 CLA 2.3 90.4 + - + +
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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