Contacts of the helix formed by residues 1578 - 1583 (chain A) in PDB entry 5NP1
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 GLN1578 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1539A LEU* 6.3 4.5 - - + -
1575A ARG 4.6 1.0 + - - -
1576A ILE 2.9 3.4 + - - -
1577A THR* 1.3 71.8 - - - +
1579A GLN* 1.3 50.9 + - - +
1580A LYS 2.7 6.0 + - - -
1581A ILE* 2.2 34.0 + - + +
1582A LYS* 3.0 5.4 + - - -
1627A GLN* 5.4 6.5 - - + -
1629A VAL* 3.4 24.5 - - + -
1630A ASP* 3.6 11.9 - - + -
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Residues in contact with GLN1579 (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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1576A ILE* 2.6 33.8 + - + +
1578A GLN* 1.3 68.4 - - - +
1580A LYS* 1.3 51.5 + - - +
1582A LYS* 3.0 19.4 - - + +
1583A TYR* 2.4 37.1 + - - +
1595A ASN* 3.7 16.4 - - + +
1598A LEU* 5.5 3.4 - - + -
1599A SER* 4.7 8.7 - - - +
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Residues in contact with LYS1580 (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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1577A THR 3.1 15.7 + - - +
1578A GLN 2.8 0.2 - - - -
1579A GLN* 1.3 75.9 - - - +
1581A ILE* 1.3 58.4 + - - +
1583A TYR* 2.7 30.8 + - - +
1584A SER* 3.3 6.1 + - - -
1599A SER* 4.7 8.5 - - - -
1630A ASP* 3.5 20.6 - - + +
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Residues in contact with ILE1581 (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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1578A GLN* 2.2 25.5 + - + +
1580A LYS* 1.3 72.5 - - - +
1582A LYS* 1.3 58.4 + - - +
1583A TYR 3.2 0.7 + - - -
1584A SER* 3.2 19.2 + - - -
1585A ARG 4.5 2.1 + - - -
1629A VAL* 3.4 38.8 - - + +
1630A ASP* 4.4 1.8 - - - +
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Residues in contact with LYS1582 (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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1542A LEU* 5.6 10.3 - - + -
1578A GLN 3.0 4.2 + - - -
1579A GLN* 2.9 24.1 + - + +
1581A ILE* 1.3 77.2 - - - +
1583A TYR* 1.3 55.6 + - - +
1584A SER 3.3 1.3 + - - -
1585A ARG 5.2 0.2 - - - -
1586A GLY* 4.5 3.5 + - - -
1591A LEU 4.5 0.2 - - - -
1592A GLU* 3.1 20.4 + - - +
1595A ASN* 3.1 14.2 - - + +
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Residues in contact with TYR1583 (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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1579A GLN 2.4 22.4 + - - +
1580A LYS* 2.7 19.6 + - - +
1582A LYS* 1.3 69.1 - - - +
1584A SER* 1.3 55.3 + - - +
1592A GLU* 3.0 28.1 - - - +
1593A GLU* 4.2 0.5 + - - -
1596A HIS* 3.3 33.8 - - + +
1599A SER* 4.9 1.6 - - - -
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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