Contacts of the helix formed by residues 1658 - 1673 (chain A) in PDB entry 3PXA
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 THR1658 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1656A ASP 5.6 0.2 - - - +
1657A LEU* 1.3 74.9 - - - +
1659A PRO* 1.3 63.7 - - + +
1660A GLU* 3.5 15.3 + - - +
1661A GLU* 2.9 42.3 + - - +
1662A PHE* 2.6 35.7 + - - +
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Residues in contact with PRO1659 (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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1657A LEU 4.6 1.1 - - - +
1658A THR* 1.3 87.8 - - - +
1660A GLU* 1.3 67.1 + - - +
1662A PHE* 3.2 8.0 + - + +
1663A MET* 2.7 52.8 + - + +
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Residues in contact with GLU1660 (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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1658A THR* 3.5 13.4 + - - +
1659A PRO* 1.3 96.6 - - - +
1661A GLU* 1.3 58.0 + - + +
1663A MET* 2.8 35.6 + - - +
1664A LEU* 3.1 9.7 + - - +
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Residues in contact with GLU1661 (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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1656A ASP 4.2 0.7 - - - +
1657A LEU* 3.5 15.9 - - + +
1658A THR* 2.9 42.7 + - - +
1660A GLU* 1.3 82.4 - - + +
1662A PHE* 1.3 60.6 + - - +
1664A LEU* 3.1 7.3 + - - +
1665A VAL* 3.1 17.8 + - - +
1690A LYS* 2.8 39.4 + - - +
1716A TYR* 3.3 42.7 - - + +
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Residues in contact with PHE1662 (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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1654A VAL* 3.6 33.7 - - + -
1657A LEU* 4.1 12.4 - - + +
1658A THR 2.6 19.0 + - - +
1659A PRO* 3.5 9.9 - - + +
1661A GLU* 1.3 68.9 - - - +
1663A MET* 1.3 80.7 - - + +
1665A VAL* 3.1 3.9 + - - +
1666A TYR* 2.9 30.2 + + + +
1676A LEU* 3.9 31.9 - - + -
1677A THR 5.4 3.6 - - - -
1678A ASN* 4.9 17.3 - - - -
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Residues in contact with MET1663 (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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1659A PRO* 2.7 47.1 + - + +
1660A GLU* 2.8 15.4 + - - +
1662A PHE* 1.3 88.1 - - + +
1664A LEU* 1.3 56.6 + - + +
1666A TYR* 3.1 11.4 + - - +
1667A LYS* 2.9 28.5 + - - +
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Residues in contact with LEU1664 (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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1660A GLU 3.1 8.2 + - - +
1661A GLU* 3.3 9.9 - - - +
1663A MET* 1.3 80.3 - - + +
1665A VAL* 1.3 61.8 + - - +
1667A LYS* 3.3 18.6 + - + +
1668A PHE* 2.9 23.4 + - - +
1716A TYR* 3.1 23.8 - - + +
1719A VAL* 4.1 3.6 - - + -
1720A THR* 3.8 19.1 - - + -
1723A ILE* 3.6 26.7 - - + +
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Residues in contact with VAL1665 (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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1652A MET* 3.5 27.4 - - + -
1654A VAL* 3.9 20.4 - - + -
1657A LEU* 3.6 22.9 - - + -
1661A GLU 3.1 15.0 + - - +
1662A PHE 3.1 6.2 + - - +
1664A LEU* 1.3 75.1 - - - +
1666A TYR* 1.3 50.9 + - - +
1668A PHE* 3.2 4.1 - - + +
1669A ALA* 2.7 33.3 + - - +
1676A LEU* 4.5 7.0 - - + -
1688A VAL* 4.6 4.9 - - + -
1716A TYR* 3.8 12.3 - - + -
1719A VAL* 3.9 25.6 - - + -
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Residues in contact with TYR1666 (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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1662A PHE* 2.9 23.6 + + + +
1663A MET* 3.3 15.0 - - - +
1665A VAL* 1.3 73.7 - - - +
1667A LYS* 1.3 60.9 + - - +
1669A ALA* 3.1 4.1 + - + +
1670A ARG* 2.8 43.0 + - + +
1676A LEU* 3.9 27.9 - - + +
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Residues in contact with LYS1667 (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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1663A MET 2.9 12.7 + - - +
1664A LEU* 3.3 26.4 + - + +
1666A TYR* 1.3 80.5 - - - +
1668A PHE* 1.3 62.7 + - - +
1670A ARG* 3.4 5.4 + - - +
1671A LYS* 3.0 24.8 + - + +
1723A ILE* 4.7 19.0 - - + +
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Residues in contact with PHE1668 (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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1652A MET* 4.4 7.9 - - + -
1664A LEU 2.9 12.8 + - - +
1665A VAL 3.2 9.9 - - - +
1667A LYS* 1.3 75.0 - - - +
1669A ALA* 1.3 67.1 + - - +
1671A LYS* 3.3 6.8 + - - +
1672A HIS* 3.2 46.2 + + - +
1674A ILE* 3.9 18.4 - - + -
1718A TRP* 4.0 28.9 - + - -
1719A VAL* 4.0 30.1 - - + -
1722A SER* 3.2 35.0 - - - -
1723A ILE* 4.1 15.0 - - + +
1728A MET* 3.7 24.0 - - + -
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Residues in contact with ALA1669 (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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1652A MET* 4.3 5.6 - - + -
1665A VAL 2.7 19.6 + - - +
1666A TYR* 3.1 11.2 + - + +
1668A PHE* 1.3 74.6 - - - +
1670A ARG* 1.3 53.6 + - - +
1673A HIS* 2.8 31.9 + - - -
1674A ILE* 3.0 42.0 + - + +
1676A LEU* 4.3 17.9 - - + -
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Residues in contact with ARG1670 (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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1666A TYR* 2.8 34.2 + - + +
1667A LYS* 3.6 8.3 - - - +
1669A ALA* 1.3 73.8 - - - +
1671A LYS* 1.3 66.2 + - - +
1673A HIS* 3.5 18.2 + - - +
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Residues in contact with LYS1671 (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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1667A LYS* 3.0 18.3 + - + +
1668A PHE* 3.3 6.0 + - - +
1670A ARG* 1.3 79.9 - - - +
1672A HIS* 1.3 92.1 + - + +
1673A HIS* 3.6 13.7 + - - -
1726A ARG* 4.3 33.6 + - - +
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Residues in contact with HIS1672 (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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1668A PHE* 3.2 50.9 + + - -
1671A LYS* 1.3 104.7 + - + +
1673A HIS* 1.3 72.5 + - - +
1674A ILE* 3.4 15.3 + - + +
1722A SER 4.9 2.0 + - - -
1726A ARG 5.0 0.6 - - - -
1727A LYS* 4.1 10.4 + - - -
1728A MET* 3.6 50.4 + - + +
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Residues in contact with HIS1673 (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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1650A MET* 5.1 1.7 - - - +
1669A ALA 2.8 10.3 + - - -
1670A ARG* 3.5 14.9 + - - +
1671A LYS 3.4 10.3 + - - -
1672A HIS* 1.3 82.4 + - - +
1674A ILE* 1.3 61.0 + - - +
1675A THR* 4.0 1.9 + - - -
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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