Contacts of the helix formed by residues 1577 - 1582 (chain A) in PDB entry 5FZT
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 SER1577 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1463A GLU* 4.0 11.3 + - - -
1573A SER 4.2 6.7 + - - -
1574A ALA* 2.9 13.3 + - - -
1576A ALA* 1.3 76.6 - - - +
1578A ASN* 1.3 67.3 + - - +
1579A PRO* 3.3 6.4 - - - +
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Residues in contact with ASN1578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1574A ALA* 3.2 14.0 - - - +
1575A PHE* 2.9 26.8 + - - +
1576A ALA 3.5 1.6 - - - +
1577A SER* 1.3 78.1 - - - +
1579A PRO* 1.3 72.3 - - - +
1580A GLU* 2.8 31.8 + - - +
1581A PHE* 3.2 27.3 + - + +
1582A SER* 4.0 4.0 + - - -
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Residues in contact with PRO1579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1458A GLN* 4.7 0.7 + - - -
1577A SER 3.3 6.0 - - - +
1578A ASN* 1.3 84.7 - - + +
1580A GLU* 1.3 72.2 + - - +
1581A PHE 3.0 0.2 - - - -
1582A SER* 2.7 30.5 + - - +
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Residues in contact with GLU1580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1458A GLN* 2.8 20.6 + - - +
1518A ASN* 5.4 1.0 + - - -
1578A ASN* 2.8 39.9 + - - +
1579A PRO* 1.3 79.5 - - - +
1581A PHE* 1.3 83.5 + - + +
1582A SER 3.5 0.4 - - - -
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Residues in contact with PHE1581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1458A GLN* 3.7 5.2 - - - +
1459A GLN 3.9 2.7 - - - +
1460A GLY* 3.2 5.0 - - - -
1461A LEU* 3.2 47.4 + - + +
1518A ASN* 3.6 38.8 - - + -
1520A THR* 4.3 15.7 - - + -
1521A ALA* 4.0 13.5 - - + -
1575A PHE* 3.3 38.4 - + - +
1576A ALA 5.8 0.2 - - - +
1578A ASN* 3.2 24.6 + - + +
1579A PRO 3.0 1.4 + - - -
1580A GLU* 1.3 107.7 - - + +
1582A SER* 1.3 59.0 + - - +
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Residues in contact with SER1582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1458A GLN* 2.7 27.0 + - - +
1460A GLY* 3.7 2.2 - - - -
1461A LEU 6.0 0.4 - - - -
1578A ASN 4.0 1.3 + - - -
1579A PRO* 2.7 29.6 + - - +
1580A GLU 3.5 0.2 - - - -
1581A PHE* 1.3 78.7 - - - +
1583A SER* 1.3 70.9 + - - +
1584A VAL* 3.4 7.6 + - - +
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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