Contacts of the helix formed by residues 1656 - 1674 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1237B TRP* 5.1 13.6 - - - -
1604B SER* 5.7 0.4 + - - -
1605B TRP* 4.1 19.4 + - - +
1606B SER* 5.4 2.6 - - - +
1648B MET* 3.4 42.5 - - - +
1649B ASP 5.3 1.4 + - - +
1652B GLU 4.2 8.7 + - - -
1653B LEU* 3.2 47.6 + - + +
1654B SER 3.5 0.6 - - - -
1655B GLU* 1.3 74.8 - - + +
1657B LEU* 1.3 63.7 + - - +
1658B ASP* 3.3 3.4 - - + +
1659B LEU* 3.9 20.1 + - + +
1660B GLN* 3.6 14.2 + - - +
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Residues in contact with LEU1657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1654B SER 5.0 3.8 - - - +
1655B GLU 3.0 10.2 + - - +
1656B ARG* 1.3 71.4 - - - +
1658B ASP* 1.3 64.4 + - - +
1660B GLN* 3.6 20.3 + - - +
1661B GLN* 3.7 13.5 + - - +
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Residues in contact with ASP1658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1656B ARG* 3.3 2.1 - - + +
1657B LEU* 1.3 79.8 - - - +
1659B LEU* 1.3 70.8 + - + +
1660B GLN 3.5 0.3 + - - -
1661B GLN* 3.9 3.9 + - - +
1662B PHE* 3.7 17.3 + - - +
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Residues in contact with LEU1659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B ARG* 6.5 0.9 - - - -
633B LEU* 4.3 26.3 - - + +
1639B LEU* 6.3 0.7 - - + -
1641B ILE* 4.9 14.1 - - + -
1648B MET* 5.1 12.3 - - + -
1653B LEU* 4.5 20.2 - - + +
1656B ARG* 3.9 21.0 + - + +
1657B LEU 3.5 0.2 - - - -
1658B ASP* 1.3 86.6 - - + +
1660B GLN* 1.3 59.9 + - - +
1662B PHE* 3.9 10.3 - - + +
1663B HIS* 3.0 30.0 + - - +
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Residues in contact with GLN1660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1653B LEU* 4.4 19.2 - - + +
1654B SER* 4.5 10.9 - - - +
1656B ARG 3.6 14.4 + - - +
1657B LEU* 3.9 17.1 - - - +
1658B ASP 3.3 0.8 - - - -
1659B LEU* 1.3 74.7 - - - +
1661B GLN* 1.3 61.5 + - - +
1663B HIS* 3.3 5.9 + - - +
1664B SER* 2.9 28.5 + - - -
1704B PRO* 4.3 15.9 - - + +
1706B PRO* 4.0 30.5 - - + +
1707B LEU* 4.5 14.9 - - + +
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Residues in contact with GLN1661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597B HIS* 3.5 17.2 - - + +
598B LYS* 4.1 10.3 + - - +
1657B LEU 3.7 11.8 + - - +
1658B ASP* 3.9 4.0 + - - +
1659B LEU 3.5 0.2 - - - -
1660B GLN* 1.3 78.9 - - - +
1662B PHE* 1.3 57.2 + - - +
1664B SER* 3.3 5.8 + - - -
1665B HIS* 2.9 61.0 + - + +
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Residues in contact with PHE1662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590B LEU* 5.6 5.8 - - + -
595B ARG* 3.6 52.5 - - + -
596B ASN 4.5 8.3 - - - -
597B HIS* 5.0 4.9 - - + +
600B LEU* 3.7 26.9 - - + +
631B LEU 4.3 4.5 - - - -
632B LEU* 3.6 28.5 - - + -
633B LEU* 3.4 33.4 - - + -
1658B ASP 3.7 14.9 + - - +
1659B LEU* 3.6 9.3 + - + +
1660B GLN 3.3 0.6 - - - -
1661B GLN* 1.3 79.6 - - - +
1663B HIS* 1.3 51.9 + - - +
1665B HIS* 3.3 6.3 + - - +
1666B THR* 2.6 39.1 + - - -
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Residues in contact with HIS1663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633B LEU* 4.8 24.5 - - + +
635B THR* 4.3 17.2 - - + +
1639B LEU* 6.0 4.7 - - + -
1650B ILE* 6.1 2.6 - - - +
1653B LEU* 5.5 8.1 - - + -
1659B LEU 3.0 20.3 + - - +
1660B GLN* 3.7 5.8 - - - +
1662B PHE* 1.3 76.0 - - - +
1664B SER* 1.3 61.4 + - - +
1666B THR* 3.3 8.9 + - + -
1667B LEU* 2.9 59.9 + - + +
1707B LEU* 3.8 33.2 - - + +
1711B TYR* 3.4 22.9 + + - -
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Residues in contact with SER1664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1660B GLN* 2.9 17.8 + - - -
1661B GLN* 3.7 8.1 - - - -
1663B HIS* 1.3 77.2 - - - +
1665B HIS* 1.3 62.1 + - - +
1667B LEU* 3.3 7.5 + - - +
1668B ARG* 2.9 34.9 + - - +
1706B PRO* 3.9 30.5 + - - +
1707B LEU* 4.9 5.6 - - - +
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Residues in contact with HIS1665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597B HIS* 2.8 38.0 + - + +
598B LYS* 5.4 1.6 - - + -
600B LEU* 3.5 23.9 - - + +
601B ASP* 5.3 5.1 + - + -
1661B GLN* 2.9 50.6 + - + +
1662B PHE* 3.8 4.9 - - - +
1664B SER* 1.3 78.8 - - - +
1666B THR* 1.3 61.1 + - - +
1668B ARG* 3.3 26.7 + - - +
1669B LEU* 2.9 29.8 + - - +
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Residues in contact with THR1666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600B LEU* 3.5 10.7 - - + +
632B LEU* 3.6 34.1 - - + +
633B LEU* 5.0 7.2 - - + +
1662B PHE* 2.6 31.1 + - - -
1663B HIS* 3.3 12.3 + - + +
1665B HIS* 1.3 77.2 - - - +
1667B LEU* 1.3 60.9 + - + +
1669B LEU* 3.3 4.4 + - + +
1670B TYR* 2.9 56.4 + - + +
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Residues in contact with LEU1667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1663B HIS* 2.9 60.2 + - + +
1664B SER* 3.7 7.0 - - - +
1666B THR* 1.3 79.9 - - + +
1668B ARG* 1.3 57.9 + - - +
1670B TYR* 3.3 10.6 + - + +
1671B ARG* 2.9 25.1 + - - +
1689B VAL* 6.3 2.5 - - + -
1707B LEU* 5.2 4.7 - - + +
1710B GLY* 3.9 21.8 - - - +
1711B TYR* 3.7 31.6 - - + -
1714B LEU* 3.1 36.9 - - + +
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Residues in contact with ARG1668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604B CYS* 4.8 20.2 - - + -
1664B SER* 2.9 22.4 + - - +
1665B HIS* 3.6 24.2 + - - +
1667B LEU* 1.3 77.2 - - - +
1669B LEU* 1.3 56.7 + - - +
1671B ARG* 3.2 6.5 + - - +
1672B ALA* 2.9 29.0 + - + +
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Residues in contact with LEU1669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600B LEU* 4.3 24.0 - - + +
603B LEU* 3.8 35.4 - - + +
604B CYS* 4.0 18.2 - - - +
607B CYS* 5.4 3.8 - - + -
621B ILE* 6.5 0.4 - - + -
625B LEU* 4.2 24.7 - - + -
632B LEU* 6.2 2.2 - - + -
1665B HIS 2.9 16.5 + - - +
1666B THR* 3.7 7.0 - - + +
1668B ARG* 1.3 78.7 - - - +
1670B TYR* 1.3 66.0 + - + +
1672B ALA* 4.4 2.9 - - + +
1673B VAL* 2.9 38.4 + - + +
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Residues in contact with TYR1670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625B LEU* 4.0 17.2 - - + +
626B LEU* 3.7 31.2 - - + +
632B LEU* 4.2 14.1 - - + +
633B LEU 4.8 8.8 + - - -
1666B THR* 2.9 40.9 + - + +
1667B LEU* 3.7 13.2 - - + +
1669B LEU* 1.3 85.1 - - + +
1671B ARG* 1.3 61.6 + - - +
1673B VAL* 3.2 23.7 - - + +
1674B CYS* 3.9 8.0 + - - +
1685B LEU* 5.2 9.7 - - + +
1688B HIS* 5.7 7.4 + + + -
1689B VAL* 5.5 12.8 - - + -
1714B LEU* 3.7 22.8 - - + +
1717B SER* 4.9 0.3 + - - -
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Residues in contact with ARG1671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1667B LEU 2.9 16.6 + - - +
1668B ARG* 3.6 7.4 - - - +
1669B LEU 3.2 0.2 - - - -
1670B TYR* 1.3 78.8 - - - +
1672B ALA* 1.3 60.4 + - - +
1674B CYS 3.2 20.4 - - - +
1675B ALA* 4.0 4.3 - - - +
1713B ASP* 4.3 22.4 - - + +
1714B LEU* 3.6 19.5 - - + +
1717B SER* 3.5 9.2 + - - -
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Residues in contact with ALA1672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604B CYS* 4.1 27.4 - - + +
607B CYS* 3.4 17.6 - - + -
608B VAL* 5.4 9.4 - - + +
618B GLN* 4.5 2.3 + - - -
1668B ARG* 2.9 17.9 + - + +
1669B LEU* 3.3 5.1 + - + +
1671B ARG* 1.3 76.2 - - - +
1673B VAL* 1.3 64.9 + - - +
1674B CYS 3.2 1.4 + - - -
1675B ALA* 4.1 14.3 + - - +
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Residues in contact with VAL1673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B CYS* 3.6 16.1 - - - -
618B GLN* 2.9 38.1 + - + +
621B ILE* 5.1 8.7 - - + -
622B THR* 4.4 7.9 - - - +
1669B LEU* 2.9 23.5 + - + +
1670B TYR* 3.2 30.7 - - + +
1672B ALA* 1.3 77.1 - - - +
1674B CYS* 1.3 62.0 + - + +
1675B ALA 3.8 0.6 + - - -
1681B VAL* 3.3 26.4 - - + +
1685B LEU* 5.4 5.8 - - + -
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Residues in contact with CYS1674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1670B TYR 4.3 8.5 - - - +
1671B ARG 3.2 3.5 + - - +
1672B ALA 3.2 0.4 - - - -
1673B VAL* 1.3 81.3 - - + +
1675B ALA* 1.3 61.1 + - - +
1678B ASN 4.4 7.2 - - - +
1681B VAL* 3.7 21.3 - - + +
1682B ALA* 4.4 13.7 - - + -
1685B LEU* 5.0 5.6 - - + -
1717B SER* 2.3 45.7 + - - +
1718B ILE* 5.5 2.5 - - + -
1721B GLU* 5.6 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
------------------------------------------------------------
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