Contacts of the helix formed by residues 1835 - 1845 (chain E) in PDB entry 1T2V
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 ARG1835 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1772E PHE* 4.2 18.7 - - + +
1773E THR* 4.1 2.0 + - - +
1774E ASN* 3.8 21.4 - - - +
1775E MET* 4.1 23.3 + - - +
1780E LEU* 4.0 35.4 - - + +
1809E VAL* 3.8 10.1 - - + -
1810E VAL 2.9 16.1 + - - +
1811E GLN* 2.8 43.8 + - + +
1834E THR* 1.3 75.2 + - - +
1836E GLU* 1.3 66.4 + - + +
1838E VAL* 3.1 15.8 + - - +
1839E LEU* 3.3 25.4 + - - +
10J PHE* 4.7 9.1 - - - -
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Residues in contact with GLU1836 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1673B HIS* 5.1 11.0 + - + -
1699E ARG* 3.2 13.0 + - - -
1741E VAL* 5.3 0.7 - - - +
1834E THR* 3.0 18.2 + - + +
1835E ARG* 1.3 79.1 + - + +
1837E TRP* 1.3 58.7 - - - +
1839E LEU* 3.7 21.6 - - - +
1840E ASP* 2.8 58.2 + - - +
1853E TYR* 3.7 10.5 - - + -
10J PHE* 4.1 0.7 - - - +
11J PRO* 4.0 20.4 - - - +
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Residues in contact with TRP1837 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1761E PHE* 3.4 35.0 - + - -
1764E LEU* 3.6 20.2 - - + -
1766E ILE* 4.0 16.2 - - + -
1807E ILE* 3.9 14.8 - - + -
1809E VAL* 4.6 0.9 - - + -
1833E VAL* 4.0 17.7 - - + -
1834E THR 3.0 13.6 + - - +
1836E GLU* 1.3 74.9 - - - +
1838E VAL* 1.3 86.1 + - + +
1840E ASP* 4.4 0.2 - - - +
1841E SER* 3.1 29.2 + - - -
1847E CYS* 3.9 14.4 - - - -
1848E GLN* 2.8 39.6 + - + +
1850E LEU* 3.5 25.5 - - + +
1853E TYR* 3.3 36.3 - + + -
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Residues in contact with VAL1838 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1761E PHE* 4.4 4.9 - - + -
1780E LEU* 3.7 25.6 - - + -
1783E MET* 4.1 13.0 - - - -
1784E VAL* 3.7 30.5 - - + -
1809E VAL* 3.8 28.7 - - + -
1835E ARG 3.1 7.7 + - - +
1837E TRP* 1.3 101.1 - - + +
1839E LEU* 1.3 59.3 + - - +
1841E SER* 3.5 1.4 - - - -
1842E VAL* 2.9 38.2 + - + +
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Residues in contact with LEU1839 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1699E ARG* 3.5 12.8 - - - +
1704E PHE* 3.2 39.8 - - + -
1775E MET* 3.7 27.4 - - + -
1780E LEU* 4.1 8.5 - - + -
1783E MET* 4.1 14.8 - - - -
1835E ARG* 3.3 24.7 + - - +
1836E GLU* 3.7 24.9 - - - +
1837E TRP 3.4 0.2 - - - -
1838E VAL* 1.3 79.6 - - - +
1840E ASP* 1.3 57.8 + - - +
1842E VAL* 3.2 1.3 + - - -
1843E ALA* 2.8 27.0 + - - +
10J PHE* 4.2 17.0 - - + -
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Residues in contact with ASP1840 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1673B HIS* 5.1 10.7 + - - +
1699E ARG* 3.0 22.4 + - - +
1741E VAL* 5.0 2.8 - - - +
1742E ASN* 3.1 22.1 + - - +
1836E GLU* 2.8 30.9 + - - +
1837E TRP 4.4 0.2 - - - +
1839E LEU* 1.3 72.2 - - - +
1841E SER* 1.3 63.7 + - - +
1843E ALA* 3.9 0.2 - - - +
1844E LEU* 3.0 34.4 + - + +
1848E GLN* 4.4 3.1 - - + -
1853E TYR* 2.8 36.0 + - + +
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Residues in contact with SER1841 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1760E ILE* 3.6 6.4 - - - +
1761E PHE* 3.9 18.8 - - - -
1837E TRP* 3.1 26.5 + - - -
1838E VAL 3.5 3.1 - - - -
1840E ASP* 1.3 78.8 - - - +
1842E VAL* 1.3 51.5 + - - +
1845E TYR* 2.8 29.3 + - - -
1846E GLN 3.1 21.2 + - - -
1847E CYS* 3.7 1.0 - - - -
1848E GLN* 2.8 34.3 + - - +
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Residues in contact with VAL1842 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1704E PHE* 3.5 44.2 - - + +
1707E ILE* 3.3 16.0 - - + +
1708E ALA* 4.4 8.3 - - + +
1760E ILE* 4.2 5.2 - - + -
1761E PHE* 4.3 12.6 - - + -
1783E MET* 4.0 19.7 - - + -
1787E CYS* 3.9 22.2 - - - -
1838E VAL* 2.9 22.3 + - + +
1839E LEU 3.2 3.3 + - - +
1841E SER* 1.3 73.7 - - - +
1843E ALA* 1.3 67.5 + - - +
1845E TYR* 3.0 11.5 + - - +
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Residues in contact with ALA1843 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1699E ARG* 4.0 0.9 - - - +
1703E TYR* 4.3 2.5 - - + -
1704E PHE* 3.9 14.6 - - + -
1707E ILE* 3.5 20.8 - - - +
1739E ASP* 3.6 13.2 - - - +
1742E ASN* 3.4 29.2 - - - +
1746E HIS* 3.3 18.6 + - - -
1748E GLY* 3.6 3.3 - - - -
1839E LEU 2.8 18.8 + - - +
1840E ASP 3.9 1.1 - - - +
1842E VAL* 1.3 75.3 - - - +
1844E LEU* 1.3 59.2 + - - +
1845E TYR 3.4 0.2 + - - -
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Residues in contact with LEU1844 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1649B ARG* 3.6 37.0 - - + +
1675B THR* 4.3 5.4 - - - +
1742E ASN* 4.0 26.7 - - + +
1746E HIS* 3.8 31.2 - - + -
1748E GLY* 3.8 1.6 - - - -
1751E ARG* 2.9 27.4 + - - +
1840E ASP* 3.0 23.3 + - + +
1841E SER 4.1 1.6 - - - +
1843E ALA* 1.3 75.4 - - - +
1845E TYR* 1.3 66.5 + - - +
1846E GLN* 3.4 11.9 + - + +
1848E GLN* 3.5 27.4 - - + +
1853E TYR* 5.7 0.2 - - - +
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Residues in contact with TYR1845 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1707E ILE* 4.2 13.9 - - + -
1708E ALA* 5.0 3.4 + - - -
1748E GLY 3.7 17.7 - - - +
1751E ARG* 3.3 11.0 - - + +
1752E ALA* 3.5 31.0 - - + +
1755E SER* 3.3 34.8 + - - -
1756E GLN* 4.2 5.3 + - - -
1758E ARG 4.3 3.8 - - - -
1759E LYS* 3.4 33.1 - - - +
1760E ILE* 3.5 40.2 + - + +
1786E LEU 5.4 0.2 + - - -
1787E CYS* 4.1 16.8 - - - -
1841E SER 2.8 11.6 + - - -
1842E VAL* 3.0 10.4 + - - +
1843E ALA 3.2 0.2 - - - -
1844E LEU* 1.3 78.9 - - - +
1846E GLN* 1.3 61.0 + - - +
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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