Contacts of the helix formed by residues 1626 - 1639 (chain C) in PDB entry 3DQV
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 PRO1626 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1542C LYS 6.2 0.2 - - - +
1543C VAL* 4.9 8.7 - - + -
1544C PHE* 4.0 26.2 - - + +
1620C LYS* 5.6 0.2 - - + -
1624C GLU 3.6 7.2 - - - +
1625C LEU* 1.3 89.5 - - + +
1627C ASP* 1.3 69.1 + - - +
1628C ALA* 3.3 4.8 + - + +
1629C GLU* 3.4 25.1 + - + +
1630C LEU* 3.1 15.4 + - - +
1694C LEU* 5.8 1.3 - - + -
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Residues in contact with ASP1627 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1616C PHE* 3.8 9.1 - - - -
1620C LYS* 3.4 35.8 + - + +
1625C LEU 3.6 1.3 + - - -
1626C PRO* 1.3 72.8 - - - +
1628C ALA* 1.3 65.8 + - - +
1630C LEU* 3.2 6.8 + - - +
1631C ARG* 2.8 54.4 + - - +
1662C GLU* 5.0 0.5 - - - +
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Residues in contact with ALA1628 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1626C PRO* 3.3 3.2 + - + +
1627C ASP* 1.3 81.1 + - - +
1629C GLU* 1.3 69.4 + - + +
1631C ARG* 2.9 20.5 + - - +
1632C ARG* 3.0 13.0 + - - +
1695C THR* 5.5 10.5 - - + -
1696C THR* 5.5 5.6 - - - +
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Residues in contact with GLU1629 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1543C VAL* 5.0 0.2 - - + -
1598C PHE* 3.1 28.3 - - + -
1625C LEU* 4.7 2.7 - - + -
1626C PRO* 3.4 28.7 + - + +
1628C ALA* 1.3 80.1 - - + +
1630C LEU* 1.3 54.3 + - - +
1632C ARG* 2.8 34.0 + - - +
1633C THR* 2.7 39.5 + - - -
1694C LEU* 2.9 31.7 - - + +
1695C THR* 3.0 30.5 + - - -
1696C THR 5.1 0.3 + - - -
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Residues in contact with LEU1630 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1602C VAL* 4.2 9.9 - - + -
1616C PHE* 3.2 46.7 - - + +
1619C LEU* 4.3 14.4 - - + +
1620C LYS* 3.9 26.0 - - + +
1623C THR* 5.1 0.4 - - - +
1625C LEU* 3.7 31.1 - - + +
1626C PRO 3.1 13.4 + - - +
1627C ASP 3.3 8.3 - - - +
1629C GLU* 1.3 75.6 - - - +
1631C ARG* 1.3 55.8 - - - +
1633C THR* 3.6 0.6 - - - -
1634C LEU* 2.7 52.5 + - + +
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Residues in contact with ARG1631 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1616C PHE* 3.7 23.7 - - + -
1627C ASP* 2.8 41.7 + - - +
1628C ALA* 2.9 12.9 + - - +
1630C LEU* 1.3 76.2 - - - +
1632C ARG* 1.3 64.6 + - - +
1634C LEU* 4.0 1.5 - - - +
1635C TRP* 3.0 24.6 + - - +
1657C PRO* 2.7 51.3 + - + +
1658C LYS* 3.5 15.3 + - - +
1660C PHE* 3.0 43.6 + - + +
1661C THR* 5.3 1.6 - - - +
1662C GLU* 5.5 1.8 + - - -
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Residues in contact with ARG1632 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1576C LEU* 4.1 5.3 - - - +
1598C PHE* 4.9 2.0 - - - -
1628C ALA 3.0 9.6 + - - +
1629C GLU* 2.8 45.5 + - - +
1631C ARG* 1.3 74.7 - - - +
1633C THR* 1.3 67.3 + - - +
1635C TRP* 3.0 8.9 + - - +
1636C SER* 2.7 34.3 + - - -
1657C PRO* 4.8 4.9 - - - +
1691C ARG* 3.3 60.3 + - - +
1692C LEU* 3.9 22.8 + - - +
1694C LEU* 3.1 18.2 - - - +
1695C THR* 3.1 30.2 + - - +
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Residues in contact with THR1633 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1598C PHE* 3.6 30.9 - - - +
1599C GLN* 3.8 26.4 - - + +
1602C VAL* 3.7 25.4 - - + -
1625C LEU* 4.5 2.0 - - - -
1629C GLU 2.7 22.1 + - - -
1630C LEU* 3.7 5.6 - - - -
1632C ARG* 1.3 78.5 + - - +
1634C LEU* 1.3 61.0 + - - +
1636C SER* 2.8 24.5 + - - -
1637C LEU* 3.2 8.3 + - + +
1691C ARG* 4.9 2.5 + - - +
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Residues in contact with LEU1634 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1602C VAL* 3.5 31.6 - - + -
1616C PHE* 3.5 30.7 - - + -
1619C LEU* 4.0 15.9 - - + -
1630C LEU* 2.7 31.6 + - + +
1631C ARG 4.0 2.9 - - - +
1633C THR* 1.3 69.3 - - - +
1635C TRP* 1.3 58.0 + - - +
1637C LEU* 2.5 28.1 + - - +
1638C VAL* 2.9 15.6 + - - +
1648C LEU* 4.3 7.0 - - + -
1660C PHE* 4.1 4.9 - - + -
1666C PHE* 3.4 44.6 - - + -
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Residues in contact with TRP1635 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1631C ARG 3.0 8.3 + - - +
1632C ARG* 3.3 8.7 - - - +
1634C LEU* 1.3 76.5 - - - +
1636C SER* 1.3 59.4 + - - +
1638C VAL* 3.5 15.0 - - + +
1639C ALA* 2.8 59.7 + - + +
1650C TYR* 4.2 10.8 - + - -
1654C VAL* 3.8 31.4 - - + -
1655C ASN* 3.5 27.4 - - - -
1656C SER 4.1 3.8 - - - -
1657C PRO* 3.2 43.3 - - + +
1660C PHE* 4.2 7.7 - + + -
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Residues in contact with SER1636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1599C GLN* 2.9 29.5 + - - -
1632C ARG 2.7 12.3 + - - -
1633C THR* 2.8 19.1 + - - -
1634C LEU 3.0 0.2 - - - -
1635C TRP* 1.3 79.5 - - - +
1637C LEU* 1.3 61.1 + - - +
1638C VAL 3.6 0.2 - - - -
1639C ALA 5.2 0.2 - - - -
1640C PHE* 3.7 32.7 - - - +
1688C LEU* 4.6 2.7 - - - +
1691C ARG* 4.2 15.9 - - - -
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Residues in contact with LEU1637 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1599C GLN* 4.2 21.8 - - + +
1602C VAL* 4.4 13.5 - - + -
1603C LEU* 3.8 36.3 - - + -
1633C THR 3.2 11.1 + - - +
1634C LEU 2.5 19.0 + - - +
1636C SER* 1.3 81.5 - - - +
1638C VAL* 1.3 57.6 + - - -
1639C ALA 3.6 0.4 - - - -
1640C PHE* 5.6 0.2 - - - -
1646C GLN* 3.5 9.4 - - - +
1647C VAL* 3.8 18.6 + - + +
1648C LEU* 3.2 40.9 + - + -
1688C LEU* 4.2 24.9 - - + -
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Residues in contact with VAL1638 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1634C LEU 2.9 15.4 + - - +
1635C TRP* 3.5 26.5 - - + -
1637C LEU* 1.3 78.5 - - - +
1639C ALA* 1.3 63.4 + - + +
1646C GLN* 2.9 25.9 - - - +
1648C LEU* 2.9 35.4 - - + +
1650C TYR* 3.8 41.7 - - + -
1660C PHE* 4.3 6.1 - - + -
1666C PHE* 4.0 9.2 - - + -
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Residues in contact with ALA1639 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1635C TRP* 2.8 59.2 + - + +
1636C SER* 5.2 0.2 - - - -
1638C VAL* 1.3 81.3 - - + +
1640C PHE* 1.3 66.0 + - - +
1641C PRO* 3.0 8.5 - - - +
1646C GLN* 3.6 4.5 - - - +
1650C TYR* 6.4 0.4 - - + -
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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