Contacts of the helix formed by residues 1639 - 1652 (chain P) in PDB entry 5IJO
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 LEU1639 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1634P SER* 5.3 1.3 - - - -
1635P MET* 2.7 40.7 + - + +
1637P GLN* 3.0 6.0 - - - +
1638P HIS* 1.3 87.2 - - - +
1640P GLN* 1.3 62.1 + - - +
1641P ALA* 3.1 6.5 - - + +
1642P ALA* 3.1 18.9 + - - +
1643P GLY 3.7 2.4 + - - -
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Residues in contact with GLN1640 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1638P HIS 3.7 0.4 + - - -
1639P LEU* 1.3 71.0 - - - +
1641P ALA* 1.3 65.5 + - - +
1642P ALA 3.2 0.2 - - - -
1643P GLY* 3.2 4.6 + - - +
1644P GLN* 3.1 21.2 + - - +
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Residues in contact with ALA1641 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1630P ILE 4.8 1.6 - - - +
1631P LEU* 3.9 22.6 - - - +
1634P SER* 3.8 28.9 - - - -
1635P MET 4.6 5.2 - - - +
1636P ALA* 5.2 0.2 - - - -
1639P LEU* 3.1 2.0 - - + +
1640P GLN* 1.3 80.8 - - - +
1642P ALA* 1.3 62.0 + - - +
1644P GLN* 3.2 8.0 + - - +
1645P VAL* 3.0 23.0 + - - +
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Residues in contact with ALA1642 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1631P LEU* 6.1 0.7 - - - -
1635P MET 4.8 1.4 + - - -
1636P ALA* 4.5 6.0 - - - +
1637P GLN* 2.7 41.5 - - - +
1639P LEU 3.1 4.4 + - - +
1641P ALA* 1.3 77.5 - - - +
1643P GLY* 1.3 62.5 + - - +
1645P VAL* 3.3 6.4 + - - +
1646P LEU* 3.0 22.7 + - - +
1684P ALA* 4.3 9.1 - - - +
1685P LEU* 4.5 17.9 + - + +
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Residues in contact with GLY1643 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1639P LEU 3.7 4.0 + - - -
1640P GLN* 3.2 8.0 + - - -
1642P ALA* 1.3 79.4 - - - +
1644P GLN* 1.3 60.5 + - - +
1646P LEU* 3.3 7.3 + - - +
1647P GLN* 3.1 21.5 + - - +
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Residues in contact with GLN1644 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1640P GLN 3.1 12.8 + - - +
1641P ALA* 3.2 10.3 + - - +
1643P GLY* 1.3 77.1 - - - +
1645P VAL* 1.3 62.2 + - - +
1647P GLN* 3.2 9.4 + - - +
1648P PHE* 3.1 19.2 + - - +
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Residues in contact with VAL1645 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1627P CYS 5.8 0.7 - - - +
1631P LEU* 4.2 22.7 - - + -
1641P ALA 3.0 12.6 + - - +
1642P ALA* 3.8 6.7 - - - +
1644P GLN* 1.3 74.5 - - - +
1646P LEU* 1.3 65.7 + - - +
1648P PHE* 2.9 20.5 + - + +
1649P LEU* 3.0 13.0 + - - +
1680P ILE* 5.3 7.9 - - + +
1684P ALA* 4.5 13.0 - - + -
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Residues in contact with LEU1646 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1642P ALA 3.0 13.7 + - - +
1643P GLY* 3.7 9.4 - - - +
1644P GLN 3.3 0.2 - - - -
1645P VAL* 1.3 76.9 - - - +
1647P GLN* 1.3 65.1 + - - +
1649P LEU* 3.1 8.0 + - - +
1650P ILE* 2.9 24.9 + - - +
1684P ALA* 4.7 10.9 - - + +
1685P LEU* 5.4 6.1 - - + +
1687P GLY* 6.2 4.0 - - - -
1690P SER* 5.6 10.3 - - - -
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Residues in contact with GLN1647 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1643P GLY 3.1 12.8 + - - +
1644P GLN* 3.5 10.8 - - - +
1645P VAL 3.2 0.2 - - - -
1646P LEU* 1.3 76.0 - - - +
1648P PHE* 1.3 64.1 + - - +
1650P ILE* 4.2 4.4 - - - +
1651P SER* 2.9 29.4 + - - -
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Residues in contact with PHE1648 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1579P ILE* 6.2 4.3 - - + -
1627P CYS* 5.9 6.5 - - + -
1644P GLN 3.1 11.5 + - - +
1645P VAL* 2.9 18.3 + - + +
1647P GLN* 1.3 77.7 - - - +
1649P LEU* 1.3 60.2 + - - +
1651P SER* 4.0 2.8 - - - -
1652P HIS* 3.0 26.3 + - - +
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Residues in contact with LEU1649 (chain P).
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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1645P VAL 3.0 11.8 + - - +
1646P LEU* 3.7 9.4 - - - +
1648P PHE* 1.3 73.9 - - - +
1650P ILE* 1.3 61.3 + - - +
1652P HIS* 3.1 4.9 - - - +
1653P SER* 2.8 30.2 + - - -
1656P ILE* 5.8 1.4 - - - +
1680P ILE* 6.1 5.4 - - + -
1681P SER* 6.3 3.6 - - - -
1687P GLY* 5.9 7.6 - - - -
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Residues in contact with ILE1650 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1646P LEU 2.9 15.6 + - - +
1647P GLN* 4.2 4.0 - - - +
1649P LEU* 1.3 76.4 - - - +
1651P SER* 1.3 64.5 + - - +
1653P SER* 3.0 22.5 + - - -
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Residues in contact with SER1651 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1589P ASP* 5.8 3.3 - - - +
1647P GLN* 2.9 18.4 + - - -
1648P PHE* 4.1 3.4 - - - -
1650P ILE* 1.3 77.6 - - - +
1652P HIS* 1.3 58.0 + - - +
1653P SER 3.5 2.6 + - - +
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Residues in contact with HIS1652 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1588P TYR* 4.2 31.6 - - + +
1589P ASP* 5.3 4.0 - - - +
1648P PHE 3.0 18.2 + - - +
1649P LEU* 3.1 5.2 - - - +
1651P SER* 1.3 76.8 - - - +
1653P SER* 1.3 65.7 + - - +
1655P THR* 3.5 18.8 + - - -
1656P ILE* 3.9 5.4 + - - +
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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