Contacts of the helix formed by residues 1574 - 1578 (chain B) in PDB entry 4J5L
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 GLU1574 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1812A LYS* 6.0 0.2 - - - +
1572B SER* 3.1 21.1 + - - +
1573B GLY* 1.3 81.1 - - - +
1575B GLU* 1.3 66.3 + - - +
1576B GLY* 3.3 2.9 - - - +
1577B PHE* 3.2 23.2 + - + +
1578B MET* 3.2 17.8 - - - +
1594B ASP* 3.9 11.8 - - - +
1596B ALA* 4.9 0.9 - - - +
1599B ARG* 3.3 34.9 + - - -
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Residues in contact with GLU1575 (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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1573B GLY 3.9 1.2 + - - -
1574B GLU* 1.3 72.0 - - + +
1576B GLY* 1.3 70.4 + - - +
1578B MET* 3.2 26.3 + - + +
1579B LYS* 3.7 35.4 + - - +
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Residues in contact with GLY1576 (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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1574B GLU* 3.3 3.2 + - - +
1575B GLU* 1.3 89.2 + - - +
1577B PHE* 1.3 67.7 + - - +
1578B MET 3.4 0.4 + - - -
1579B LYS* 4.4 11.5 + - - +
1831B PHE* 5.0 3.3 - - - -
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Residues in contact with PHE1577 (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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1569B LYS* 3.1 66.4 - - + +
1570B GLN* 3.9 7.3 - - - -
1572B SER* 3.7 10.5 - - - -
1574B GLU* 3.2 25.4 + - + +
1575B GLU 3.2 1.0 - - - -
1576B GLY* 1.3 82.3 - - - +
1578B MET* 1.3 61.8 + - + +
1579B LYS 3.6 1.7 + - - -
1580B HIS* 5.0 0.9 + - - +
1581B ASN* 3.9 6.1 - - - +
1599B ARG* 4.0 13.2 - - - -
1831B PHE* 3.4 44.5 - + + -
1833B PRO* 5.1 0.2 - - - +
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Residues in contact with MET1578 (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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1570B GLN 3.7 15.5 - - - +
1573B GLY* 3.7 19.7 - - - +
1574B GLU 3.2 28.5 - - - +
1575B GLU* 3.2 15.2 + - + +
1577B PHE* 1.3 82.2 - - + +
1579B LYS* 1.3 58.2 + - - +
1580B HIS 3.1 11.2 + - - -
1581B ASN* 3.4 21.2 + - - +
1586B ASN* 3.8 22.4 + - - +
1589B CYS* 3.5 27.4 - - - -
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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