Contacts of the helix formed by residues 1679 - 1689 (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 ASN1679 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1677B GLY 3.9 7.0 + - - +
1678B ASN* 1.3 73.4 + - - +
1680B ARG* 1.3 64.3 + - - +
1681B VAL 3.4 0.9 - - - -
1682B ALA* 3.3 16.3 + - + +
1683B HIS* 3.3 21.7 + - - +
1721B GLU* 6.1 1.4 - - - +
1722B SER* 3.3 27.3 + - - +
1797B ALA* 6.0 1.3 - - + -
1798B ARG* 3.4 23.6 - - + +
1799B LEU 2.9 25.4 + - - +
1800B SER* 3.6 17.2 - - - +
1801B PRO* 4.2 6.7 - - - +
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Residues in contact with ARG1680 (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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88A PRO* 5.4 17.0 - - + +
619B ASP* 3.9 32.1 + - - +
1678B ASN* 3.5 9.2 + - - +
1679B ASN* 1.3 80.7 - - - +
1681B VAL* 1.3 60.7 + - - +
1682B ALA 3.4 0.3 + - - -
1683B HIS* 3.8 9.7 + - - +
1684B ALA* 4.0 7.6 + - - +
1797B ALA* 5.0 14.3 - - - +
1798B ARG* 5.1 18.1 + - - +
2174B GLN* 5.4 13.3 + - - +
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Residues in contact with VAL1681 (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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618B GLN* 4.3 4.0 - - + +
619B ASP* 5.6 5.2 - - - +
622B THR* 3.2 35.9 - - + +
626B LEU* 5.6 2.0 - - + -
1673B VAL* 3.3 42.4 - - + +
1674B CYS* 3.7 9.2 - - + -
1678B ASN* 3.6 26.1 + - - +
1680B ARG* 1.3 77.3 - - - +
1682B ALA* 1.3 62.9 + - - +
1683B HIS 3.3 0.2 - - - -
1684B ALA* 3.3 5.7 + - + -
1685B LEU* 2.9 30.0 + - + +
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Residues in contact with ALA1682 (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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1674B CYS* 4.4 8.5 - - + -
1678B ASN 4.0 4.3 - - - +
1679B ASN* 3.3 26.4 + - + +
1680B ARG 3.2 1.0 - - - -
1681B VAL* 1.3 83.0 - - - +
1683B HIS* 1.3 58.8 + - - +
1685B LEU* 3.3 1.1 + - - -
1686B CYS* 2.9 24.5 + - - +
1717B SER 5.4 3.4 - - - +
1718B ILE* 3.1 29.4 - - + +
1801B PRO* 4.3 16.6 - - + -
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Residues in contact with HIS1683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 6.3 1.1 - - - +
90A VAL* 4.8 1.5 - - - +
1679B ASN* 3.3 14.4 + - + -
1680B ARG 4.3 5.8 - - - +
1681B VAL 3.3 0.4 - - - -
1682B ALA* 1.3 76.0 - - - +
1684B ALA* 1.3 58.0 + - - +
1686B CYS* 3.3 6.0 + - - +
1687B SER* 2.9 29.1 + - - -
1779B SER* 4.1 4.0 + - - -
1780B ALA 3.2 26.3 + - - -
1781B PRO* 5.1 7.9 - - + -
1782B CYS 5.4 4.3 - - - -
1783B PHE* 6.3 4.7 - - + -
1798B ARG* 3.4 50.4 - - + +
1800B SER* 4.4 2.5 - - - -
1801B PRO* 3.7 33.8 - - + +
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Residues in contact with ALA1684 (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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88A PRO 3.3 26.2 - - - +
90A VAL* 3.9 16.2 - - + -
622B THR* 4.1 14.8 - - + -
626B LEU* 4.3 6.1 - - + -
1680B ARG 4.0 4.3 + - - +
1681B VAL* 3.3 13.5 + - - +
1682B ALA 3.3 0.6 - - - -
1683B HIS* 1.3 78.1 - - - +
1685B LEU* 1.3 59.8 + - - +
1687B SER* 2.9 20.1 + - - -
1688B HIS* 3.1 14.2 + - - -
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Residues in contact with LEU1685 (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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626B LEU* 4.8 4.6 - - + +
1670B TYR* 5.2 14.6 - - + +
1673B VAL* 5.4 4.5 - - + -
1674B CYS* 5.0 9.0 - - + -
1681B VAL* 2.9 20.5 + - + +
1682B ALA* 3.7 5.6 - - - +
1684B ALA* 1.3 75.5 - - - +
1686B CYS* 1.3 63.5 + - - +
1688B HIS* 3.4 17.3 + - - +
1689B VAL* 3.4 14.9 + - - +
1714B LEU* 5.7 6.7 - - + -
1718B ILE* 4.6 8.1 - - + -
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Residues in contact with CYS1686 (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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1682B ALA 2.9 16.8 + - - +
1683B HIS* 3.3 7.6 + - - +
1685B LEU* 1.3 73.9 - - - +
1687B SER* 1.3 65.4 + - - +
1689B VAL 2.8 30.1 - - - +
1690B ASP* 3.9 4.0 + - - -
1691B GLN* 4.9 12.8 - - - -
1718B ILE* 3.9 22.4 - - + +
1719B HIS* 5.3 10.3 - - - -
1781B PRO* 4.9 16.4 - - - +
1801B PRO* 5.5 8.5 - - + -
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Residues in contact with SER1687 (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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35A LYS 3.8 10.0 - - - +
36A PHE* 3.5 27.4 + - - +
37A ASP* 5.0 1.4 - - - -
90A VAL* 3.4 26.3 - - - +
629B ARG* 4.9 2.1 + - - -
1683B HIS 2.9 16.3 + - - -
1684B ALA 2.9 16.0 + - - -
1686B CYS* 1.3 78.7 - - - +
1688B HIS* 1.3 68.4 + - - +
1689B VAL 5.0 0.2 - - - -
1690B ASP* 5.1 1.4 + - - +
1783B PHE* 6.2 4.3 - - - -
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Residues in contact with HIS1688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS 4.8 6.7 - - - +
89A GLY 3.3 19.8 + - - -
626B LEU* 3.6 35.9 - - + +
629B ARG* 3.3 41.3 + - + -
634B GLN* 5.3 10.1 - - + +
635B THR 4.6 10.4 - - - +
1670B TYR* 5.7 6.7 + + + -
1684B ALA 3.1 25.4 - - - -
1685B LEU* 3.4 8.6 + - - +
1686B CYS 3.2 0.4 - - - -
1687B SER* 1.3 86.6 + - - +
1689B VAL* 1.3 67.3 + - + +
1690B ASP* 3.5 4.0 + - - +
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Residues in contact with VAL1689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B THR* 4.4 18.6 - - + +
1667B LEU* 6.3 2.7 - - + -
1670B TYR* 5.5 13.0 - - + -
1685B LEU 3.4 9.3 + - - +
1686B CYS* 2.8 23.2 - - - +
1688B HIS* 1.3 81.0 - - + +
1690B ASP* 1.3 72.2 + - - +
1691B GLN 3.9 0.3 + - - -
1693B GLN* 4.3 13.7 - - + -
1694B LEU* 4.9 8.7 - - + +
1711B TYR* 5.7 13.2 - - + -
1714B LEU* 6.1 9.9 - - + -
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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
------------------------------------------------------------
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