Contacts of the helix formed by residues 1732 - 1742 (chain D) in PDB entry 6AH0
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 MET1732 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1728D LEU 3.8 8.5 - - - -
1729D ASP 4.8 3.4 - - - -
1730D HIS 3.4 5.9 + - - -
1731D CYS* 1.3 74.3 - - - +
1733D HIS* 1.3 66.4 + - - +
1734D ASP 3.4 3.8 - - - +
1735D HIS* 3.5 5.3 + - - -
1736D PHE* 3.2 18.0 + - - -
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Residues in contact with HIS1733 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1732D MET* 1.3 72.4 - - - +
1734D ASP* 1.3 65.9 + - - +
1736D PHE* 3.2 1.8 + - - +
1737D ASN* 2.9 22.7 + - - -
1792D THR* 5.5 12.0 - - - +
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Residues in contact with ASP1734 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1732D MET 3.4 3.0 - - - +
1733D HIS* 1.3 73.6 - - - +
1735D HIS* 1.3 57.3 + - - +
1737D ASN* 3.3 1.2 + - - -
1738D ALA* 2.9 25.5 + - - -
1825D ASN* 6.3 1.1 - - - +
1826D TYR* 5.5 9.9 - - - +
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Residues in contact with HIS1735 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1731D CYS 5.8 0.2 + - - -
1732D MET 3.5 6.6 + - - -
1733D HIS 3.2 0.6 - - - -
1734D ASP* 1.3 73.1 - - - +
1736D PHE* 1.3 64.1 + - - +
1738D ALA* 4.4 1.3 - - - +
1739D GLU* 2.9 22.7 + - - -
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Residues in contact with PHE1736 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1732D MET 3.2 14.2 + - - -
1733D HIS* 3.2 2.2 + - - +
1735D HIS* 1.3 75.2 - - - +
1737D ASN* 1.3 57.6 + - - +
1739D GLU* 3.8 0.8 - - - +
1740D ILE* 2.8 28.8 + - - -
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Residues in contact with ASN1737 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1733D HIS 2.9 13.9 + - - -
1734D ASP 3.6 3.6 - - - -
1736D PHE* 1.3 79.2 - - - +
1738D ALA* 1.3 61.7 + - - +
1740D ILE* 3.6 1.3 - - - +
1741D VAL* 2.9 19.9 + - - -
1801D CYS 6.2 0.2 - - - -
1816D GLY* 5.5 8.9 - - - +
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Residues in contact with ALA1738 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437D ARG 5.7 0.3 - - - +
1734D ASP 2.9 15.4 + - - -
1735D HIS* 3.8 2.5 - - - +
1737D ASN* 1.3 75.5 - - - +
1739D GLU* 1.3 60.3 + - - +
1741D VAL* 3.4 3.4 + - - +
1742D THR* 3.2 16.1 + - - -
1820D ALA* 4.9 17.4 - - - +
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Residues in contact with GLU1739 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1735D HIS 2.9 16.7 + - - -
1736D PHE* 3.8 0.9 - - - +
1738D ALA* 1.3 74.5 - - - +
1740D ILE* 1.3 63.2 + - - +
1742D THR* 3.2 3.7 + - - +
1743D LYS 3.2 3.3 + - - -
1744D THR* 2.9 28.8 + - - +
1745D ILE 3.9 7.0 - - - +
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Residues in contact with ILE1740 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1736D PHE 2.8 16.8 + - - -
1737D ASN* 3.6 1.6 - - - +
1739D GLU* 1.3 76.5 - - - +
1741D VAL* 1.3 56.4 + - - +
1743D LYS* 2.9 19.2 + - - -
1745D ILE* 3.6 23.1 - - - +
1811D ALA* 5.7 1.9 - - - -
1812D PRO* 4.9 12.0 - - - -
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Residues in contact with VAL1741 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1737D ASN 2.9 14.2 + - - -
1738D ALA* 3.7 5.8 - - - +
1739D GLU 3.2 0.2 - - - -
1740D ILE* 1.3 76.7 - - - +
1742D THR* 1.3 58.2 + - - +
1743D LYS 3.1 1.1 + - - -
1812D PRO* 5.3 10.6 - - - +
1817D MET* 6.4 1.6 - - - +
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Residues in contact with THR1742 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437D ARG 5.6 5.4 - - - -
1438D ARG* 6.4 1.1 - - - +
1738D ALA 3.2 9.5 + - - -
1739D GLU* 3.2 7.9 + - - +
1741D VAL* 1.3 72.7 - - - +
1743D LYS* 1.3 63.8 + - - +
1744D THR* 3.1 3.6 + - - +
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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
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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