Contacts of the helix formed by residues 1656 - 1674 (chain F) in PDB entry 6X34
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 ARG1656 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1237F TRP* 5.1 12.6 - - - -
1604F SER* 5.7 0.4 + - - -
1605F TRP* 4.1 19.2 + - - +
1606F SER* 5.4 2.6 - - - +
1648F MET* 3.4 43.4 - - - +
1649F ASP 5.3 0.8 + - - +
1652F GLU 4.2 9.7 + - - -
1653F LEU* 3.2 47.0 + - + +
1654F SER 3.5 0.6 - - - -
1655F GLU* 1.3 75.1 - - + +
1657F LEU* 1.3 62.8 + - - +
1658F ASP* 3.3 2.9 - - + +
1659F LEU* 4.4 20.6 - - + +
1660F GLN* 3.6 14.4 + - - +
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Residues in contact with LEU1657 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1654F SER 5.0 4.0 - - - +
1655F GLU 3.0 10.6 + - - +
1656F ARG* 1.3 70.4 - - - +
1658F ASP* 1.3 64.0 + - - +
1660F GLN* 3.6 21.3 + - - +
1661F GLN* 3.7 13.3 + - - +
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Residues in contact with ASP1658 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1656F ARG* 3.3 1.9 - - + -
1657F LEU* 1.3 81.5 - - - +
1659F LEU* 1.3 70.9 + - + +
1660F GLN 3.5 0.7 + - - -
1661F GLN* 3.9 3.1 + - - +
1662F PHE* 3.7 17.3 + - - +
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Residues in contact with LEU1659 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595F ARG* 6.5 0.9 - - - -
633F LEU* 4.3 27.3 - - + +
1639F LEU* 6.3 0.7 - - + -
1641F ILE* 4.9 13.9 - - + -
1648F MET* 5.1 13.0 - - + -
1653F LEU* 4.5 19.5 - - + +
1656F ARG* 3.9 20.4 + - + +
1657F LEU 3.5 0.2 - - - -
1658F ASP* 1.3 86.2 - - + +
1660F GLN* 1.3 60.1 + - - +
1661F GLN 3.5 0.2 - - - -
1662F PHE* 3.9 9.9 - - + +
1663F HIS* 3.0 29.5 + - - +
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Residues in contact with GLN1660 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1653F LEU* 4.4 18.6 - - + +
1654F SER* 4.5 11.0 - - - +
1656F ARG 3.6 14.4 + - - +
1657F LEU* 3.9 16.9 - - - +
1658F ASP 3.3 1.0 - - - -
1659F LEU* 1.3 75.8 - - - +
1661F GLN* 1.3 60.6 + - - +
1663F HIS* 3.3 5.3 + - - +
1664F SER* 2.9 28.1 + - - -
1704F PRO* 4.3 15.6 - - + +
1706F PRO* 4.0 30.7 - - + +
1707F LEU* 4.5 14.9 - - + +
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Residues in contact with GLN1661 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597F HIS* 3.5 17.1 - - + +
598F LYS* 4.1 11.4 + - - +
1657F LEU 3.7 11.3 + - - +
1658F ASP 4.4 3.4 - - - +
1660F GLN* 1.3 79.1 - - - +
1662F PHE* 1.3 58.0 + - - +
1664F SER* 3.3 6.1 + - - -
1665F HIS* 2.9 61.1 + - + +
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Residues in contact with PHE1662 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590F LEU* 5.6 6.5 - - + -
595F ARG* 3.6 49.1 - - + -
596F ASN 4.5 9.4 - - - -
597F HIS* 5.0 5.3 - - + +
600F LEU* 3.7 25.8 - - + -
631F LEU 4.3 3.8 - - - -
632F LEU* 3.6 29.2 - - + -
633F LEU* 3.4 33.7 - - + -
1658F ASP 3.7 14.6 + - - +
1659F LEU* 3.6 10.0 + - + +
1660F GLN 3.3 0.4 - - - -
1661F GLN* 1.3 79.0 - - - +
1663F HIS* 1.3 52.2 + - - +
1665F HIS* 3.3 6.5 + - - +
1666F THR* 2.6 39.1 + - - -
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Residues in contact with HIS1663 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633F LEU* 4.8 23.9 - - + +
635F THR* 4.3 17.5 - - + +
1639F LEU* 6.0 4.5 - - + -
1650F ILE* 6.1 2.8 - - - +
1653F LEU* 5.5 8.1 - - + -
1659F LEU 3.0 19.6 + - - +
1660F GLN* 3.7 5.4 - - - +
1661F GLN 3.3 0.2 - - - -
1662F PHE* 1.3 75.6 - - - +
1664F SER* 1.3 61.6 + - - +
1666F THR* 3.3 8.5 + - + +
1667F LEU* 2.9 60.7 + - + +
1707F LEU* 3.8 33.1 - - + +
1711F TYR* 3.4 22.9 + - - -
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Residues in contact with SER1664 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1660F GLN* 2.9 17.8 + - - -
1661F GLN* 3.7 8.3 - - - -
1663F HIS* 1.3 76.8 - - - +
1665F HIS* 1.3 62.8 + - - +
1667F LEU* 3.3 7.7 + - - +
1668F ARG* 2.9 34.2 + - - +
1706F PRO* 3.9 30.2 + - - +
1707F LEU* 4.9 6.0 - - - +
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Residues in contact with HIS1665 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597F HIS* 2.8 38.9 + - + +
598F LYS* 5.4 1.6 - - + -
600F LEU* 3.5 24.3 - - + +
601F ASP* 5.3 4.4 + - + -
1661F GLN* 2.9 51.2 + - + +
1662F PHE* 3.8 4.9 - - - +
1664F SER* 1.3 78.2 - - - +
1666F THR* 1.3 61.2 + - - +
1668F ARG* 3.3 26.3 + - - +
1669F LEU* 2.9 29.6 + - - +
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Residues in contact with THR1666 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600F LEU* 3.5 11.3 - - + +
632F LEU* 3.6 35.4 - - + +
633F LEU* 5.0 7.2 - - + +
1662F PHE* 2.6 30.8 + - - -
1663F HIS* 3.6 12.9 - - + +
1665F HIS* 1.3 76.9 - - - +
1667F LEU* 1.3 59.8 + - + +
1669F LEU* 3.3 4.6 + - + +
1670F TYR* 2.9 56.5 + - + +
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Residues in contact with LEU1667 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1663F HIS* 2.9 59.8 + - + +
1664F SER* 3.7 7.0 - - - +
1666F THR* 1.3 79.9 - - + +
1668F ARG* 1.3 58.7 + - - +
1670F TYR* 3.3 10.3 + - + -
1671F ARG* 2.9 24.1 + - - +
1689F VAL* 6.3 2.2 - - + -
1706F PRO 5.9 0.2 - - - +
1707F LEU* 5.2 4.3 - - - +
1710F GLY* 3.9 22.2 - - - +
1711F TYR* 3.7 30.7 - - + -
1714F LEU* 3.1 37.9 - - + +
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Residues in contact with ARG1668 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604F CYS* 4.8 21.3 - - + -
1664F SER* 2.9 22.2 + - - +
1665F HIS* 3.6 24.6 + - - +
1666F THR 3.3 0.2 - - - -
1667F LEU* 1.3 77.2 - - - +
1669F LEU* 1.3 55.9 + - - +
1671F ARG* 3.2 6.9 + - + +
1672F ALA* 2.9 29.0 + - + +
1710F GLY* 5.8 0.6 - - - -
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Residues in contact with LEU1669 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600F LEU* 4.3 23.6 - - + +
603F LEU* 3.8 35.9 - - + +
604F CYS* 4.0 19.3 - - + +
607F CYS* 5.4 4.3 - - + -
621F ILE* 6.5 0.9 - - + -
625F LEU* 4.2 24.9 - - + -
632F LEU* 6.2 1.8 - - + -
1665F HIS 2.9 17.0 + - - +
1666F THR* 3.7 6.5 - - + +
1668F ARG* 1.3 77.2 - - - +
1670F TYR* 1.3 67.3 + - + +
1672F ALA* 3.8 3.3 - - + +
1673F VAL* 2.9 38.9 + - + +
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Residues in contact with TYR1670 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625F LEU* 4.0 16.8 - - + +
626F LEU* 3.7 30.4 - - + +
632F LEU* 4.2 14.8 - - + +
633F LEU 4.8 8.6 + - - -
1666F THR* 2.9 39.4 + - + +
1667F LEU* 3.7 13.5 - - + +
1669F LEU* 1.3 85.2 - - + +
1671F ARG* 1.3 62.4 + - - +
1673F VAL* 3.2 24.1 - - + +
1674F CYS* 3.9 8.0 + - - +
1685F LEU* 5.2 10.1 - - + +
1688F HIS* 5.7 7.4 + + + -
1689F VAL* 5.5 12.1 - - + -
1714F LEU* 3.7 23.4 - - + +
1717F SER* 4.9 0.3 + - - -
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Residues in contact with ARG1671 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1667F LEU 2.9 17.4 + - - +
1668F ARG* 3.6 7.2 - - - +
1670F TYR* 1.3 78.6 - - - +
1672F ALA* 1.3 60.6 + - - +
1674F CYS 3.2 20.1 - - - +
1675F ALA* 4.0 4.2 - - - +
1713F ASP* 4.3 22.2 - - + +
1714F LEU* 3.6 18.8 - - + +
1717F SER* 3.5 10.5 + - - -
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Residues in contact with ALA1672 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604F CYS* 4.1 27.6 - - + +
607F CYS* 3.4 18.3 - - + -
608F VAL* 5.4 9.3 - - + +
618F GLN* 4.5 2.4 + - - -
1668F ARG* 2.9 17.9 + - + +
1669F LEU* 4.0 4.7 - - + +
1671F ARG* 1.3 74.7 - - - +
1673F VAL* 1.3 63.7 + - - +
1674F CYS 3.2 1.5 + - - -
1675F ALA* 4.1 13.4 + - - +
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Residues in contact with VAL1673 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607F CYS* 3.6 16.1 - - - -
618F GLN* 2.9 38.1 - - + +
621F ILE* 5.1 8.7 - - + -
622F THR* 4.4 8.1 - - - +
1669F LEU* 2.9 22.7 + - + +
1670F TYR* 3.2 31.9 - - + +
1672F ALA* 1.3 77.1 - - - +
1674F CYS* 1.3 61.1 + - + +
1675F ALA 3.8 0.2 - - - -
1681F VAL* 3.3 27.0 - - + +
1685F LEU* 5.4 4.9 - - + -
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Residues in contact with CYS1674 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1670F TYR 4.3 8.1 - - - +
1671F ARG 3.2 3.0 + - - +
1672F ALA 3.2 0.2 - - - -
1673F VAL* 1.3 80.6 - - + +
1675F ALA* 1.3 60.7 + - - +
1678F ASN 4.4 7.9 - - - +
1681F VAL* 3.7 21.3 - - + +
1682F ALA* 4.4 14.1 - - + -
1685F LEU* 5.0 5.8 - - + -
1717F SER* 2.3 46.3 + - - +
1718F ILE* 5.5 2.7 - - + -
1721F GLU* 4.8 0.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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