Contacts of the helix formed by residues 1716 - 1725 (chain A) in PDB entry 4IFI
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 TYR1716 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1657A LEU* 3.7 30.1 - - + -
1661A GLU* 3.4 45.6 + - + +
1664A LEU* 3.7 18.2 - - + +
1665A VAL* 3.7 25.8 - - + -
1688A VAL* 3.5 12.0 - - + +
1689A MET 2.6 20.8 + - - +
1690A LYS* 4.4 13.5 - - + -
1691A THR 5.0 1.6 - - - +
1714A VAL 3.7 0.8 + - - -
1715A SER* 1.3 70.5 + - - +
1717A PHE* 1.3 68.5 + + + +
1718A TRP 3.1 0.2 - - - -
1719A VAL* 2.9 22.7 + - + +
1720A THR* 3.2 37.7 + - + +
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Residues in contact with PHE1717 (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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1690A LYS* 5.5 8.5 - - - -
1691A THR* 3.7 15.3 - - - -
1692A ASP 3.6 24.7 - - - -
1693A ALA* 4.4 7.4 - - + -
1695A PHE* 4.3 11.4 - + + -
1715A SER* 2.9 22.7 + - - +
1716A TYR* 1.3 87.6 - + + +
1718A TRP* 1.3 60.2 + - - +
1719A VAL 3.1 0.2 - - - -
1720A THR* 3.5 16.4 - - + -
1721A GLN* 2.8 39.6 + - + +
1734A PHE* 3.7 15.0 - - + -
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Residues in contact with TRP1718 (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* 3.5 26.7 - - + -
1652A MET* 3.8 22.7 - - - -
1668A PHE* 4.6 6.3 - + - -
1686A HIS* 3.9 15.0 - + - -
1688A VAL* 4.3 6.7 - - + -
1714A VAL* 3.6 24.5 - - + -
1715A SER 2.9 14.1 + - - +
1717A PHE* 1.3 78.8 - - - +
1719A VAL* 1.3 73.6 + - + +
1721A GLN* 4.5 0.3 - - - +
1722A SER* 2.8 36.1 + - - -
1728A MET* 3.7 22.9 - - + -
1729A LEU* 2.8 36.4 + - + +
1730A ASN 4.4 4.3 - - - -
1731A GLU* 4.2 20.8 - - + +
1734A PHE* 3.5 35.7 - + + -
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Residues in contact with VAL1719 (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* 5.3 0.7 - - - -
1664A LEU* 4.9 0.7 - - + -
1665A VAL* 4.1 27.6 - - + +
1668A PHE* 3.8 31.8 - - + -
1688A VAL* 3.8 30.3 - - + -
1716A TYR* 2.9 14.4 + - + +
1718A TRP* 1.3 94.0 - - + +
1720A THR* 1.3 60.9 + - + +
1722A SER* 3.2 4.9 + - - -
1723A ILE* 2.9 39.1 + - + +
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Residues in contact with THR1720 (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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1664A LEU* 4.8 10.5 - - + -
1716A TYR* 3.2 46.3 + - + +
1717A PHE* 3.4 26.8 + - + -
1719A VAL* 1.3 78.2 - - + +
1721A GLN* 1.3 60.4 + - - +
1723A ILE* 3.4 9.1 + - + +
1724A LYS* 2.9 28.7 + - - +
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Residues in contact with GLN1721 (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 PHE* 2.8 28.1 + - + +
1720A THR* 1.3 77.3 + - - +
1722A SER* 1.3 57.8 + - - +
1724A LYS* 3.3 12.4 + - - +
1725A GLU* 2.7 58.1 + - - +
1729A LEU* 3.6 20.5 - - + +
1734A PHE* 3.7 17.3 - - + -
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Residues in contact with SER1722 (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* 3.9 22.3 - - - -
1672A HIS* 5.7 0.9 + - - -
1718A TRP* 2.8 27.1 + - - -
1719A VAL 3.5 4.0 - - - -
1721A GLN* 1.3 73.4 - - - +
1723A ILE* 1.3 60.6 + - - +
1725A GLU 3.5 0.2 + - - -
1726A ARG* 2.8 25.3 + - - -
1727A LYS 2.8 30.3 + - - -
1728A MET* 3.6 2.8 - - - -
1729A LEU* 2.8 24.2 + - - +
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Residues in contact with ILE1723 (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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1664A LEU* 4.1 27.1 - - + +
1667A LYS* 6.3 0.4 - - + -
1668A PHE* 3.8 36.0 - - + -
1671A LYS* 6.3 2.2 - - + -
1672A HIS* 6.1 0.9 - - - -
1719A VAL* 2.9 24.5 + - + +
1720A THR* 3.6 10.8 - - - +
1722A SER* 1.3 74.4 - - - +
1724A LYS* 1.3 58.5 + - - +
1726A ARG* 2.8 26.7 + - - +
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Residues in contact with LYS1724 (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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1720A THR 2.9 20.0 + - - +
1721A GLN* 3.3 18.1 + - - +
1723A ILE* 1.3 76.8 - - - +
1725A GLU* 1.3 61.4 + - + +
1726A ARG* 3.5 1.7 + - - +
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Residues in contact with GLU1725 (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 GLN* 2.7 45.0 + - - +
1722A SER 4.5 0.9 - - - +
1724A LYS* 1.3 73.7 - - + +
1726A ARG* 1.3 71.1 + - - +
1727A LYS* 3.0 11.6 + - + +
1729A LEU* 3.5 29.6 - - + +
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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