Contacts of the helix formed by residues 1721 - 1729 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1674B CYS 4.8 4.7 - - - +
1675B ALA* 5.1 8.1 - - - -
1676B LEU 5.6 1.8 - - - +
1677B GLY 5.7 1.1 - - - +
1679B ASN* 6.1 1.1 - - - +
1716B ILE* 3.1 3.3 + - - -
1717B SER* 3.2 34.7 + - - +
1718B ILE* 5.1 0.6 - - - -
1719B HIS 3.7 1.4 - - - -
1720B LEU* 1.3 79.6 - - - +
1722B SER* 1.3 67.1 + - - +
1723B ALA 4.3 0.4 - - - +
1724B CYS* 4.1 1.7 - - - +
1725B ARG* 3.8 25.5 + - - +
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Residues in contact with SER1722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1677B GLY* 3.3 27.8 + - - -
1678B ASN 4.4 0.3 + - - -
1679B ASN* 3.3 27.2 + - - +
1721B GLU* 1.3 77.4 - - - +
1723B ALA* 1.3 61.4 + - - +
1724B CYS 3.3 0.4 - - - -
1725B ARG* 3.4 10.1 + - - +
1726B SER* 2.9 34.5 + - - -
1799B LEU 5.2 2.9 - - - -
1800B SER* 5.5 3.4 - - - -
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Residues in contact with ALA1723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1719B HIS 4.9 4.7 - - - +
1720B LEU* 4.8 12.8 - - + -
1721B GLU 3.5 1.2 - - - +
1722B SER* 1.3 79.0 - - - +
1724B CYS* 1.3 56.9 + - - +
1726B SER* 3.3 5.9 + - - -
1727B ARG* 2.9 31.9 + - - +
1776B HIS* 5.4 14.6 - - + +
1778B PHE* 5.2 12.8 - - + -
1800B SER* 5.7 7.6 - - - +
1852B MET* 3.9 12.2 - - - +
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Residues in contact with CYS1724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1720B LEU* 3.3 24.9 + - + +
1721B GLU 4.1 3.4 - - - +
1722B SER 3.3 0.8 - - - -
1723B ALA* 1.3 78.9 - - - +
1725B ARG* 1.3 56.3 + - - +
1727B ARG* 3.4 1.0 + - - +
1728B ARG* 2.9 58.4 + - - +
1848B THR* 4.2 19.1 - - - -
1851B VAL* 4.4 4.3 - - - -
1852B MET* 3.6 22.6 - - + -
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Residues in contact with ARG1725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1676B LEU* 3.4 34.9 - - - +
1677B GLY* 3.4 26.3 - - - +
1721B GLU 3.8 16.5 + - - +
1722B SER* 3.4 9.2 + - - +
1723B ALA 3.3 0.4 - - - -
1724B CYS* 1.3 79.1 - - - +
1726B SER* 1.3 58.7 + - - +
1728B ARG* 3.8 4.7 - - - +
1729B SER* 2.9 34.1 + - - -
2165B SER* 5.5 9.6 - - - +
2168B ILE* 3.7 34.8 - - + +
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Residues in contact with SER1726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1722B SER* 2.9 20.5 + - - -
1723B ALA* 3.8 7.0 - - - -
1725B ARG* 1.3 77.6 - - - +
1727B ARG* 1.3 60.2 + - - +
1729B SER* 3.9 4.6 + - - -
1730B MET* 3.4 35.8 - - - +
1774B PRO* 5.1 2.6 - - - +
2161B GLY* 4.8 12.2 + - - -
2165B SER* 4.9 9.5 - - - -
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Residues in contact with ARG1727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1723B ALA 2.9 17.3 + - - +
1726B SER* 1.3 76.9 - - - +
1728B ARG* 1.3 63.1 + - - +
1729B SER 3.3 0.7 - - - -
1730B MET* 3.5 10.6 + - - +
1731B LEU* 3.3 23.9 + - + +
1774B PRO* 6.0 4.0 - - - -
1776B HIS* 5.9 4.5 - - + -
1851B VAL* 5.4 2.7 - - + +
1852B MET* 3.6 27.1 - - + -
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Residues in contact with ARG1728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1724B CYS* 2.9 37.3 + - - +
1725B ARG* 4.0 5.4 - - - +
1727B ARG* 1.3 73.0 - - - +
1729B SER* 1.3 63.7 + - - +
1730B MET 3.2 2.5 + - - -
1731B LEU* 3.6 33.2 + - + +
1732B SER 5.1 0.7 + - - -
1847B SER* 5.7 2.4 + - - -
1848B THR* 6.2 0.4 - - - +
1851B VAL* 4.1 29.4 - - + +
1852B MET* 5.1 1.1 - - + -
1942B ASN* 4.0 28.6 + - - +
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Residues in contact with SER1729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1725B ARG* 2.9 20.9 + - - -
1726B SER* 4.2 7.6 - - - -
1727B ARG 3.3 0.6 - - - -
1728B ARG* 1.3 77.7 - - - +
1730B MET* 1.3 59.0 + - - +
1731B LEU 3.6 0.2 - - - -
1732B SER* 4.9 7.1 + - - -
2161B GLY* 5.9 2.2 - - - -
2164B 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