Contacts of the helix formed by residues 1721 - 1729 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1674F CYS 4.8 4.9 - - - +
1675F ALA* 5.1 8.3 - - + -
1676F LEU 5.6 2.0 - - - +
1677F GLY 5.7 0.9 - - - +
1679F ASN* 6.1 0.9 - - - +
1716F ILE* 3.1 3.9 + - - -
1717F SER* 3.2 35.0 - - - +
1718F ILE 5.5 0.4 - - - -
1719F HIS 3.7 1.8 - - - +
1720F LEU* 1.3 81.0 - - - +
1722F SER* 1.3 67.2 + - - +
1723F ALA 4.3 0.4 - - - +
1724F CYS* 4.1 1.9 - - - +
1725F ARG* 3.8 24.8 + - - +
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Residues in contact with SER1722 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1677F GLY* 3.3 28.1 + - - -
1678F ASN 4.4 0.5 + - - -
1679F ASN* 3.3 27.4 + - - +
1721F GLU* 1.3 77.3 - - - +
1723F ALA* 1.3 61.3 + - - +
1724F CYS 3.3 0.4 - - - -
1725F ARG* 3.4 10.5 + - - +
1726F SER* 2.9 34.1 + - - -
1799F LEU 5.2 2.7 - - - -
1800F SER* 5.5 3.6 - - - -
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Residues in contact with ALA1723 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1719F HIS 4.9 4.7 - - - +
1720F LEU* 4.8 13.9 - - + -
1721F GLU 3.5 1.2 - - - +
1722F SER* 1.3 79.7 - - - +
1724F CYS* 1.3 57.6 + - - +
1726F SER* 3.3 6.1 + - - -
1727F ARG* 2.9 32.7 + - - +
1776F HIS* 5.4 14.8 - - + +
1778F PHE* 5.2 12.8 - - + -
1800F SER* 5.7 6.7 - - - +
1852F MET* 3.9 12.1 - - - +
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Residues in contact with CYS1724 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1720F LEU* 3.3 25.8 + - + +
1721F GLU 4.1 3.1 - - - +
1722F SER 3.3 0.4 - - - -
1723F ALA* 1.3 80.1 - - - +
1725F ARG* 1.3 56.8 + - - +
1727F ARG* 3.8 1.0 - - - +
1728F ARG* 2.9 57.6 + - - +
1848F THR* 4.2 18.8 - - - -
1851F VAL* 4.4 4.5 - - - -
1852F MET* 3.6 23.4 - - + -
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Residues in contact with ARG1725 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1676F LEU* 3.4 35.1 - - - +
1677F GLY* 3.4 25.9 - - - +
1721F GLU 3.8 16.9 + - - +
1722F SER* 3.4 9.1 + - - +
1723F ALA 3.3 0.2 - - - -
1724F CYS* 1.3 78.6 - - - +
1726F SER* 1.3 58.3 + - - +
1728F ARG* 3.3 5.2 + - - +
1729F SER* 2.9 34.3 + - - -
2165F SER* 5.5 10.5 - - - +
2168F ILE* 3.7 34.8 - - + +
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Residues in contact with SER1726 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1722F SER* 2.9 20.4 + - - -
1723F ALA* 3.8 6.7 - - - -
1725F ARG* 1.3 78.5 - - - +
1727F ARG* 1.3 59.6 + - - +
1729F SER* 3.9 4.9 + - - -
1730F MET* 3.4 37.0 - - - +
1774F PRO* 5.1 4.1 - - - +
2161F GLY* 4.8 12.3 + - - -
2165F SER* 4.9 9.0 - - - -
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Residues in contact with ARG1727 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1723F ALA 2.9 18.1 + - - +
1726F SER* 1.3 77.6 - - - +
1728F ARG* 1.3 62.2 + - - +
1729F SER 3.3 0.2 - - - -
1730F MET* 3.5 10.9 + - - +
1731F LEU* 3.3 23.5 + - + +
1774F PRO* 6.0 4.3 - - - -
1776F HIS* 5.9 4.9 - - + -
1851F VAL* 5.4 2.9 - - + +
1852F MET* 3.6 26.2 - - + -
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Residues in contact with ARG1728 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1724F CYS* 2.9 37.5 + - - +
1725F ARG* 3.3 4.7 + - - +
1727F ARG* 1.3 73.6 - - - +
1729F SER* 1.3 63.0 + - - +
1730F MET 3.2 3.0 + - - -
1731F LEU* 3.6 31.8 + - + +
1732F SER 5.1 0.7 + - - -
1847F SER* 5.7 2.6 + - - -
1848F THR* 6.2 0.2 - - - +
1851F VAL* 4.1 31.0 - - + +
1852F MET* 5.1 1.1 - - + -
1942F ASN* 4.0 28.4 + - - +
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Residues in contact with SER1729 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1725F ARG* 2.9 22.4 + - - -
1726F SER* 4.2 7.6 - - - -
1727F ARG 3.3 0.8 - - - -
1728F ARG* 1.3 77.3 - - - +
1730F MET* 1.3 60.2 + - - +
1731F LEU 3.6 0.2 - - - -
1732F SER* 4.9 7.1 + - - -
2161F GLY* 5.9 1.8 - - - -
2164F ARG* 2.7 58.8 + - - +
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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