Contacts of the helix formed by residues 1721 - 1729 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1674D CYS 4.8 4.5 - - - +
1675D ALA* 5.1 9.4 - - + -
1676D LEU 5.6 1.3 - - - +
1677D GLY 5.7 0.9 - - - +
1679D ASN* 6.1 1.1 - - - +
1716D ILE* 3.1 3.3 + - - -
1717D SER* 3.2 34.1 - - - +
1718D ILE 5.1 0.9 - - - -
1719D HIS 3.7 1.8 - - - +
1720D LEU* 1.3 80.8 - - - +
1722D SER* 1.3 67.9 + - - +
1724D CYS* 4.1 1.7 - - - +
1725D ARG* 3.8 25.4 + - - +
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Residues in contact with SER1722 (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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1677D GLY* 3.3 28.5 + - - -
1678D ASN 4.4 0.3 + - - -
1679D ASN* 3.3 27.8 + - - +
1721D GLU* 1.3 76.7 - - - +
1723D ALA* 1.3 62.7 + - - +
1724D CYS 3.3 0.4 - - - -
1725D ARG* 3.4 10.8 + - - +
1726D SER* 2.9 32.7 + - - -
1799D LEU 5.2 2.5 - - - -
1800D SER* 5.5 3.6 - - - -
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Residues in contact with ALA1723 (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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1719D HIS 4.9 4.9 - - - +
1720D LEU* 4.8 12.6 - - + -
1721D GLU 3.5 1.4 - - - +
1722D SER* 1.3 79.9 - - - +
1724D CYS* 1.3 56.7 + - - +
1726D SER* 3.3 6.4 + - - -
1727D ARG* 2.9 32.6 + - - +
1776D HIS* 5.4 15.0 - - + +
1778D PHE* 5.2 12.3 - - + -
1800D SER* 5.7 7.5 - - - +
1852D MET* 4.1 11.9 - - - -
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Residues in contact with CYS1724 (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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1720D LEU* 3.3 25.2 + - + +
1721D GLU 4.1 2.9 - - - +
1722D SER 3.3 0.6 - - - -
1723D ALA* 1.3 78.6 - - - +
1725D ARG* 1.3 56.6 + - - +
1727D ARG* 3.8 1.0 - - - +
1728D ARG* 2.9 58.6 + - - +
1848D THR* 4.2 19.3 - - - -
1851D VAL* 4.4 4.0 - - - -
1852D MET* 3.6 23.5 - - + -
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Residues in contact with ARG1725 (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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1676D LEU* 3.4 35.3 - - - +
1677D GLY* 3.4 25.9 - - - +
1721D GLU 3.8 17.1 + - - +
1722D SER* 3.4 8.4 + - - +
1723D ALA 3.3 0.2 - - - -
1724D CYS* 1.3 78.6 - - - +
1726D SER* 1.3 58.7 + - - +
1728D ARG* 3.7 5.0 - - - +
1729D SER* 2.9 34.0 + - - -
2165D SER* 5.5 10.5 - - - +
2168D ILE* 3.7 34.8 - - + +
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Residues in contact with SER1726 (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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1722D SER* 2.9 20.0 + - - -
1723D ALA* 3.8 6.7 - - - -
1725D ARG* 1.3 77.9 - - - +
1727D ARG* 1.3 61.3 + - - +
1729D SER* 3.9 5.2 + - - -
1730D MET* 3.4 36.4 - - - +
1774D PRO* 5.1 4.0 - - - +
2161D GLY* 4.8 12.5 + - - -
2165D SER* 4.9 9.2 - - - -
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Residues in contact with ARG1727 (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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1723D ALA 2.9 16.4 + - - +
1726D SER* 1.3 77.9 - - - +
1728D ARG* 1.3 62.8 + - - +
1729D SER 3.3 0.7 - - - -
1730D MET* 3.5 11.3 + - - +
1731D LEU* 3.3 23.4 + - + +
1774D PRO* 6.0 3.8 - - - -
1776D HIS* 5.9 4.7 - - + -
1851D VAL 5.4 2.9 - - - +
1852D MET* 3.6 26.2 - - + -
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Residues in contact with ARG1728 (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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1724D CYS* 2.9 38.7 + - - +
1725D ARG* 4.0 4.3 - - - +
1727D ARG* 1.3 72.5 - - - +
1729D SER* 1.3 62.8 + - - +
1730D MET 3.2 3.2 + - - -
1731D LEU* 3.6 33.4 + - + +
1732D SER 5.1 0.5 + - - -
1847D SER* 5.7 2.4 + - - -
1848D THR* 6.2 0.6 - - - +
1851D VAL* 4.1 29.6 - - + +
1852D MET* 5.1 1.3 - - + -
1942D ASN* 4.0 29.0 + - - +
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Residues in contact with SER1729 (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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1725D ARG* 2.9 21.6 + - - -
1726D SER* 4.2 7.4 - - - -
1727D ARG 3.3 0.6 - - - -
1728D ARG* 1.3 76.2 - - - +
1730D MET* 1.3 61.2 + - - +
1731D LEU 3.6 0.2 - - - -
1732D SER* 4.9 6.7 + - - -
2161D GLY* 5.9 2.2 - - - -
2164D ARG* 2.7 57.8 + - - +
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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