Contacts of the helix formed by residues 1679 - 1689 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1677H GLY* 3.9 7.0 + - - +
1678H ASN* 1.3 74.0 + - - +
1680H ARG* 1.3 64.4 + - - +
1681H VAL 3.4 0.7 - - - -
1682H ALA* 3.3 16.5 + - + +
1683H HIS* 3.3 20.7 + - - +
1721H GLU* 6.1 0.8 - - - +
1722H SER* 3.3 26.6 + - - +
1797H ALA* 6.0 1.1 - - + -
1798H ARG* 3.4 23.2 - - + +
1799H LEU 2.9 24.0 + - - +
1800H SER* 3.6 17.6 - - - +
1801H PRO* 4.2 7.1 - - - +
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Residues in contact with ARG1680 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G PRO* 5.4 17.0 - - + +
619H ASP* 3.9 31.9 + - - +
1678H ASN* 3.5 8.6 + - - +
1679H ASN* 1.3 80.0 - - - +
1681H VAL* 1.3 61.3 + - - +
1682H ALA 3.4 0.5 + - - -
1683H HIS* 3.8 9.7 + - - +
1684H ALA* 4.0 8.3 + - - +
1797H ALA* 5.0 15.0 - - - +
1798H ARG* 5.1 18.7 + - - +
2174H GLN* 5.4 13.7 - - - +
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Residues in contact with VAL1681 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618H GLN* 4.3 4.5 - - + +
619H ASP* 5.6 5.3 + - - +
622H THR* 3.2 36.3 - - + +
626H LEU* 5.6 2.5 - - + -
1673H VAL* 3.3 41.5 - - + +
1674H CYS* 3.7 9.4 - - + -
1678H ASN* 3.6 26.5 + - - +
1680H ARG* 1.3 76.1 - - - +
1682H ALA* 1.3 62.0 + - - +
1683H HIS 3.3 0.2 - - - -
1684H ALA* 3.3 6.2 + - + -
1685H LEU* 2.9 30.7 + - + +
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Residues in contact with ALA1682 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1674H CYS* 4.4 8.3 - - + -
1678H ASN 4.0 4.0 - - - +
1679H ASN* 3.3 26.4 + - - +
1680H ARG 3.2 1.2 - - - -
1681H VAL* 1.3 82.7 - - - +
1683H HIS* 1.3 57.2 + - - +
1685H LEU* 3.3 1.1 + - - +
1686H CYS* 2.9 25.2 + - - +
1717H SER 5.4 3.4 - - - +
1718H ILE* 3.1 28.3 - - + +
1801H PRO* 4.3 17.0 - - + -
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Residues in contact with HIS1683 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G HIS* 6.3 1.1 - - - +
90G VAL* 4.8 1.5 - - - +
1679H ASN* 3.3 13.6 + - + -
1680H ARG 3.8 6.0 + - - +
1681H VAL 3.3 0.2 - - - -
1682H ALA* 1.3 76.1 - - - +
1684H ALA* 1.3 58.2 + - - +
1686H CYS* 3.3 6.6 + - - +
1687H SER* 2.9 29.3 + - - -
1779H SER* 4.1 3.6 + - - -
1780H ALA 3.2 26.3 + - - -
1781H PRO* 5.1 7.4 - - + -
1782H CYS 5.4 4.7 - - - -
1783H PHE* 6.3 4.7 - - + -
1798H ARG* 3.4 49.0 - - + +
1800H SER* 4.4 2.2 - - - -
1801H PRO* 3.7 34.8 - - + +
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Residues in contact with ALA1684 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G PRO* 3.3 26.7 - - + +
90G VAL* 3.9 16.3 - - + +
622H THR* 4.1 15.0 - - + -
626H LEU* 4.3 6.7 - - + -
1680H ARG 4.0 4.5 + - - +
1681H VAL* 3.3 12.9 + - - +
1682H ALA 3.3 0.4 - - - -
1683H HIS* 1.3 78.9 - - - +
1685H LEU* 1.3 60.2 + - - +
1687H SER* 2.9 19.6 + - - -
1688H HIS* 3.1 13.8 - - - -
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Residues in contact with LEU1685 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626H LEU* 4.8 4.4 - - + +
1670H TYR* 5.2 13.9 - - + +
1673H VAL* 5.4 4.0 - - + -
1674H CYS* 5.0 9.4 - - + -
1681H VAL* 2.9 20.7 + - + +
1682H ALA* 3.7 4.7 - - - +
1684H ALA* 1.3 76.0 - - - +
1686H CYS* 1.3 63.2 + - - +
1688H HIS* 3.4 17.9 + - - +
1689H VAL* 3.4 14.6 + - - +
1714H LEU* 5.7 7.0 - - + -
1718H ILE* 4.6 8.5 - - + -
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Residues in contact with CYS1686 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1682H ALA 2.9 17.6 + - - +
1683H HIS* 3.3 7.4 + - - +
1685H LEU* 1.3 74.3 - - - +
1687H SER* 1.3 64.3 + - - +
1689H VAL 2.8 30.0 - - - +
1690H ASP* 3.9 3.9 + - - -
1691H GLN* 4.9 12.6 - - - -
1718H ILE* 3.9 21.9 - - + +
1719H HIS* 5.3 9.9 - - - -
1781H PRO* 4.9 16.8 - - - +
1801H PRO* 5.5 8.7 - - + -
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Residues in contact with SER1687 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G LYS 3.8 9.5 - - - +
36G PHE* 3.5 28.1 + - - +
37G ASP* 5.0 1.9 - - - +
90G VAL* 3.4 27.4 - - - +
629H ARG* 4.9 2.0 + - - -
1683H HIS 2.9 15.9 + - - -
1684H ALA 2.9 15.2 + - - -
1685H LEU 3.2 0.2 - - - -
1686H CYS* 1.3 79.2 - - - +
1688H HIS* 1.3 68.2 + - - +
1690H ASP* 5.1 1.6 + - - +
1783H PHE* 6.2 3.4 - - - -
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Residues in contact with HIS1688 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G LYS 4.8 6.9 - - - +
89G GLY 3.3 19.3 + - - -
626H LEU* 3.6 37.4 - - + +
629H ARG* 3.3 40.5 + - + +
634H GLN* 5.3 10.7 - - + +
635H THR* 4.6 11.0 + - - +
1670H TYR* 5.7 6.5 + + + -
1684H ALA 3.1 25.4 - - - -
1685H LEU* 3.4 7.7 + - - +
1686H CYS 3.2 0.8 - - - -
1687H SER* 1.3 86.8 + - - +
1689H VAL* 1.3 68.3 + - + +
1690H ASP* 3.5 3.8 + - - +
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Residues in contact with VAL1689 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635H THR* 4.4 18.2 - - + +
1667H LEU* 6.3 2.5 - - + -
1670H TYR* 5.5 12.6 - - + -
1685H LEU 3.4 9.5 + - - +
1686H CYS* 2.8 23.5 - - - +
1688H HIS* 1.3 81.2 - - + +
1690H ASP* 1.3 71.8 + - - +
1693H GLN* 4.3 13.7 - - + -
1694H LEU* 4.9 8.5 - - + +
1711H TYR* 5.7 13.7 - - + -
1714H LEU* 6.1 10.1 - - + -
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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