Contacts of the helix formed by residues 1721 - 1729 (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 GLU1721 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1674H CYS 4.8 4.7 - - - +
1675H ALA* 5.1 8.7 - - - -
1676H LEU 5.6 1.8 - - - +
1677H GLY 5.7 0.7 - - - +
1679H ASN* 6.1 1.1 - - - +
1716H ILE* 3.1 3.7 + - - -
1717H SER* 3.2 34.7 + - - +
1718H ILE 5.1 0.8 - - - -
1719H HIS 3.7 1.4 - - - -
1720H LEU* 1.3 79.8 - - - +
1722H SER* 1.3 67.9 + - - +
1724H CYS* 4.1 1.7 - - - +
1725H ARG* 3.8 25.3 + - - +
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Residues in contact with SER1722 (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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1677H GLY* 3.3 28.0 - - - -
1678H ASN 4.4 0.5 + - - -
1679H ASN* 3.3 27.3 + - - +
1721H GLU* 1.3 77.6 - - - +
1723H ALA* 1.3 62.0 + - - +
1724H CYS 3.3 0.7 - - - -
1725H ARG* 3.4 10.5 + - - +
1726H SER* 2.9 33.9 + - - -
1799H LEU 5.2 2.5 - - - -
1800H SER* 5.5 4.0 - - - -
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Residues in contact with ALA1723 (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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1719H HIS 4.9 5.2 - - - +
1720H LEU* 4.8 12.8 - - + -
1721H GLU 3.5 1.2 - - - +
1722H SER* 1.3 78.6 - - - +
1724H CYS* 1.3 58.2 + - - +
1726H SER* 3.8 5.6 - - - -
1727H ARG* 2.9 32.1 + - - +
1776H HIS* 5.4 14.6 - - + +
1778H PHE* 5.2 12.6 - - + -
1800H SER* 5.7 7.1 - - - +
1852H MET* 3.9 11.9 - - - +
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Residues in contact with CYS1724 (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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1720H LEU* 3.3 25.6 + - + +
1721H GLU 4.1 2.9 - - - +
1722H SER 3.3 0.6 - - - -
1723H ALA* 1.3 79.5 - - - +
1725H ARG* 1.3 57.1 + - - +
1727H ARG* 3.8 1.2 - - - +
1728H ARG* 2.9 58.8 + - - +
1848H THR* 4.2 19.1 - - - -
1851H VAL* 4.4 3.8 - - - -
1852H MET* 3.6 23.7 - - + -
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Residues in contact with ARG1725 (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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1676H LEU* 3.4 35.5 - - - +
1677H GLY* 3.4 26.5 - - - +
1721H GLU 3.8 18.4 + - - +
1722H SER* 3.4 8.4 + - - +
1723H ALA 3.3 0.6 - - - -
1724H CYS* 1.3 78.5 - - - +
1726H SER* 1.3 59.3 + - - +
1728H ARG* 3.8 5.5 - - - +
1729H SER* 2.9 33.9 + - - -
2165H SER* 5.5 10.1 - - - +
2168H ILE* 3.7 34.2 - - + +
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Residues in contact with SER1726 (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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1722H SER* 2.9 20.7 + - - -
1723H ALA* 3.8 7.0 - - - -
1725H ARG* 1.3 77.6 - - - +
1727H ARG* 1.3 60.5 + - - +
1729H SER* 3.9 4.6 + - - -
1730H MET* 3.4 36.4 - - - +
1774H PRO* 5.1 3.2 - - - +
2161H GLY* 4.8 11.9 + - - -
2165H SER* 4.9 9.4 - - - -
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Residues in contact with ARG1727 (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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1723H ALA 2.9 18.8 + - - +
1726H SER* 1.3 76.2 - - - +
1728H ARG* 1.3 62.6 + - - +
1729H SER 3.3 0.4 - - - -
1730H MET* 3.5 11.3 + - - +
1731H LEU* 3.3 23.3 + - + +
1774H PRO* 6.0 4.0 - - - -
1776H HIS* 5.9 4.3 - - + -
1851H VAL 5.4 2.5 - - - +
1852H MET* 3.6 26.7 - - + -
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Residues in contact with ARG1728 (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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1724H CYS* 2.9 38.1 + - - +
1725H ARG* 4.0 4.7 - - - +
1727H ARG* 1.3 72.5 - - - +
1729H SER* 1.3 63.9 + - - +
1730H MET 3.2 3.2 + - - -
1731H LEU* 3.6 33.2 + - + +
1732H SER 5.1 0.7 + - - -
1847H SER* 5.7 2.8 + - - -
1848H THR* 6.2 0.2 - - - +
1851H VAL* 4.1 29.4 - - + +
1852H MET* 5.1 0.9 - - + -
1942H ASN* 4.0 28.7 + - - +
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Residues in contact with SER1729 (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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1725H ARG* 2.9 20.7 + - - -
1726H SER* 4.2 7.9 - - - -
1727H ARG 3.3 0.6 - - - -
1728H ARG* 1.3 77.3 - - - +
1730H MET* 1.3 58.8 + - - +
1731H LEU 3.6 0.4 - - - -
1732H SER* 4.9 7.3 + - - -
2161H GLY* 5.9 1.8 - - - -
2164H ARG* 2.7 58.2 + - - +
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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