Contacts of the helix formed by residues 1713 - 1726 (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 ILE1713 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1711A THR 4.1 1.7 + - - -
1712A PHE* 1.3 66.7 - - - +
1714A MET* 1.3 54.2 + - - +
1715A LEU 3.0 0.7 - - - -
1716A THR* 3.1 21.9 - - - +
1717A TYR* 2.2 37.1 + - - +
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Residues in contact with MET1714 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1712A PHE* 2.4 10.7 + - + +
1713A ILE* 1.3 72.7 - - - +
1715A LEU* 1.3 49.6 + - - +
1717A TYR* 3.0 10.7 - - - +
1718A LEU* 2.1 38.8 + - - +
1748A SER* 3.9 27.7 - - - -
1751A GLU* 5.7 0.2 - - - -
1843A PRO* 6.4 0.9 - - - -
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Residues in contact with LEU1715 (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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1710A TRP* 3.3 30.6 - - + +
1711A THR 3.5 4.5 - - - +
1712A PHE 2.0 46.8 + - - +
1714A MET* 1.3 64.2 - - - +
1716A THR* 1.3 54.1 + - - +
1718A LEU* 2.5 12.2 + - - +
1719A ASN* 2.1 41.6 + - - +
1751A GLU* 5.7 3.0 - - - +
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Residues in contact with THR1716 (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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1711A THR 5.3 0.2 + - - -
1713A ILE* 2.7 31.7 + - - +
1715A LEU* 1.3 73.9 - - - +
1717A TYR* 1.3 50.2 + - - +
1719A ASN* 3.1 10.4 - - - +
1720A ASN* 2.3 37.5 + - - +
1865A HIS* 5.9 7.4 - - - -
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Residues in contact with TYR1717 (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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1713A ILE 2.2 26.4 + - - +
1714A MET* 3.0 14.4 - - - +
1716A THR* 1.3 64.9 - - - +
1718A LEU* 1.3 53.6 + - - +
1720A ASN* 2.5 12.8 + - - +
1721A THR* 2.2 39.9 + - - -
1843A PRO* 5.3 16.2 - - + -
1844A TYR* 5.8 1.6 - - - +
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Residues in contact with LEU1718 (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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1710A TRP* 5.6 2.9 - - + -
1714A MET 2.1 31.7 + - - +
1715A LEU* 2.5 16.6 + - + +
1717A TYR* 1.3 64.7 - - - +
1719A ASN* 1.3 59.8 + - - +
1721A THR* 3.0 12.5 - - - -
1722A LEU* 2.9 18.0 + - - +
1748A SER* 5.9 0.4 - - - -
1751A GLU* 4.5 19.7 - - + -
1752A ILE 5.8 0.7 - - - +
1755A MET* 6.3 2.5 - - + -
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Residues in contact with ASN1719 (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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1707A GLU* 5.0 17.0 - - + -
1710A TRP* 5.9 3.1 - - + -
1715A LEU 2.1 27.2 + - - +
1716A THR* 3.1 14.8 - - - +
1718A LEU* 1.3 63.6 - - - +
1720A ASN* 1.3 58.2 + - - +
1722A LEU* 2.4 38.2 + - - +
1723A VAL* 3.2 2.3 + - - +
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Residues in contact with ASN1720 (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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1716A THR 2.3 32.2 + - - +
1717A TYR* 2.5 11.9 + - - +
1719A ASN* 1.3 65.0 - - - +
1721A THR* 1.3 54.5 + - - +
1723A VAL* 2.7 32.5 + - - +
1724A GLU* 2.8 10.6 + - - +
1862A LEU* 5.2 14.1 - - + -
1865A HIS* 6.1 2.7 - - + -
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Residues in contact with THR1721 (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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1717A TYR 2.2 27.1 + - - -
1718A LEU* 3.0 19.3 - - - -
1720A ASN* 1.3 67.2 - - - +
1722A LEU* 1.3 48.1 - - - +
1724A GLU* 2.9 13.1 + - - +
1725A ASP* 2.4 38.4 + - - +
1743A THR* 5.5 12.3 - - - -
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Residues in contact with LEU1722 (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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1707A GLU* 6.5 1.1 - - + -
1718A LEU 2.9 7.8 + - - +
1719A ASN* 2.4 34.4 + - - +
1721A THR* 1.3 65.9 - - - +
1723A VAL* 1.3 48.7 - - - +
1725A ASP* 2.5 13.3 + - + +
1726A CYS* 2.1 40.9 + - - -
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Residues in contact with VAL1723 (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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1719A ASN 3.2 1.6 + - - +
1720A ASN* 2.7 21.0 + - - +
1722A LEU* 1.3 73.3 - - - +
1724A GLU* 1.3 55.5 + - - +
1726A CYS* 2.9 16.0 - - + +
1727A VAL* 2.7 24.3 + - - +
1858A TRP* 6.2 2.5 - - + +
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Residues in contact with GLU1724 (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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1720A ASN 2.8 7.1 + - - +
1721A THR* 2.9 22.7 - - - +
1723A VAL* 1.3 76.3 - - - +
1725A ASP* 1.3 47.6 + - - +
1727A VAL* 2.2 45.2 + - - +
1736A CYS* 6.0 7.1 - - + +
1740A ILE* 6.5 1.6 - - + -
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Residues in contact with ASP1725 (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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1721A THR 2.4 27.4 + - - +
1722A LEU* 2.5 15.1 + - - +
1724A GLU* 1.3 66.6 - - - +
1726A CYS* 1.3 55.7 + - - +
1727A VAL 2.8 19.3 - - - +
1728A LYS* 3.2 7.4 + - - +
1761A LEU* 5.6 12.1 - - + +
1762A ALA* 6.5 0.4 - - - -
1765A GLN* 5.1 15.7 - - + -
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Residues in contact with CYS1726 (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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1722A LEU 2.1 27.7 + - - +
1723A VAL* 2.9 21.8 - - + +
1725A ASP* 1.3 67.0 - - - +
1727A VAL* 1.3 58.0 + - - +
1728A LYS 3.2 4.6 + - - -
1729A VAL* 4.5 6.2 - - - +
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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