Contacts of the helix formed by residues 173 - 188 (chain 3) in PDB entry 5IY8
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 GLN 173 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1303 GLU* 2.9 51.4 + - - +
1313 THR 2.9 26.7 + - - +
1323 LEU* 5.2 1.9 - - + +
1333 LEU* 3.8 12.0 - - + +
1683 GLU 3.8 0.2 - - - +
1693 ASP* 2.9 23.7 - - - +
1703 SER* 2.6 32.3 + - - +
1713 ALA 3.0 0.2 - - - -
1723 LEU* 1.3 75.9 - - + +
1743 TYR* 1.3 59.8 + - - +
1763 ASN* 2.7 42.8 + - - +
1773 PHE* 2.9 8.0 + - - +
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Residues in contact with TYR 174 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550 LEU* 3.4 39.6 + - + +
560 GLY* 4.2 4.0 + - - -
1693 ASP* 5.2 0.2 - - - +
1703 SER 3.5 4.7 + - - +
1713 ALA* 2.9 20.6 + - - +
1733 GLN* 1.3 76.9 - - - +
1753 MET* 1.3 69.4 + - + +
1773 PHE* 4.0 0.6 - - - +
1783 MET* 3.0 58.4 + - + +
2023 LEU* 3.4 25.4 - - + -
2053 GLN* 5.0 0.2 - - - -
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Residues in contact with MET 175 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1713 ALA 4.6 0.4 + - - -
1723 LEU 4.2 5.7 + - - +
1733 GLN 3.4 0.6 - - - -
1743 TYR* 1.3 86.8 - - + +
1763 ASN* 1.3 69.4 + - + +
1783 MET* 3.9 2.7 - - - +
1793 ASN* 2.9 25.5 + - + +
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Residues in contact with ASN 176 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1333 LEU* 4.3 1.4 - - - +
1343 ALA* 2.7 26.6 - - + +
1723 LEU* 3.2 16.4 + - - +
1733 GLN* 2.7 44.6 + - - +
1753 MET* 1.3 84.8 - - + +
1773 PHE* 1.3 77.6 + - - +
1793 ASN* 3.2 14.6 + - - +
1803 VAL* 3.3 17.7 + - - +
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Residues in contact with PHE 177 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1333 LEU* 2.9 37.7 - - + -
1343 ALA* 3.9 5.6 - - - +
1373 LEU* 3.0 35.9 - - + -
1693 ASP* 4.9 3.6 - - - +
1733 GLN 2.9 13.8 + - - +
1743 TYR* 4.1 2.5 - - - +
1763 ASN* 1.3 85.9 + - - +
1783 MET* 1.3 58.7 + - - +
1803 VAL* 3.0 5.9 + - - +
1813 ILE* 2.9 65.9 + - + +
1913 ILE* 5.7 0.7 - - + -
2023 LEU* 3.6 33.9 - - + -
2033 LEU* 3.0 32.1 - - + -
2063 ALA* 3.8 5.6 - - + -
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Residues in contact with MET 178 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550 LEU* 3.3 7.0 - - + -
1743 TYR* 3.0 54.1 + - + +
1753 MET* 3.9 2.9 - - - +
1773 PHE* 1.3 73.3 - - - +
1793 ASN* 1.3 66.4 + - - +
1813 ILE* 3.3 20.9 - - + -
1823 PHE* 2.8 54.7 + - + -
2023 LEU* 2.9 33.2 - - + -
2053 GLN* 3.3 26.0 - - + +
2093 ILE* 4.5 4.3 - - - -
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Residues in contact with ASN 179 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1753 MET* 2.9 18.0 + - + +
1763 ASN* 3.4 12.1 - - - +
1773 PHE 3.1 0.4 - - - -
1783 MET* 1.3 77.0 - - - +
1803 VAL* 1.3 65.7 + - + +
1823 PHE* 3.4 4.6 + - - +
1833 ALA* 3.1 22.9 + - - +
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Residues in contact with VAL 180 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1343 ALA* 3.4 26.2 - - + +
1373 LEU* 2.9 35.7 - - + -
1383 ALA* 4.0 11.7 - - + +
1413 LEU* 3.6 21.5 - - + -
1763 ASN 3.6 13.0 - - - +
1773 PHE 3.0 6.9 + - - +
1793 ASN* 1.3 78.4 - - + +
1813 ILE* 1.3 63.2 - - - +
1833 ALA* 3.2 6.1 + - - +
1843 ALA* 3.1 19.9 + - + +
1913 ILE* 5.6 0.4 - - + -
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Residues in contact with ILE 181 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1373 LEU* 4.6 1.8 - - + -
1773 PHE* 2.9 62.3 + - + +
1783 MET* 3.3 30.7 - - - +
1803 VAL* 1.3 75.6 - - - +
1823 PHE* 1.3 59.9 + - + +
1843 ALA* 3.0 5.9 + - - +
1853 GLN* 2.9 23.2 + - - +
1913 ILE* 4.3 8.7 - - + -
2023 LEU 4.0 3.8 - - - +
2063 ALA* 3.8 30.1 - - + +
2093 ILE* 4.2 18.6 - - + -
2103 THR* 3.9 12.5 + - - +
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Residues in contact with PHE 182 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540 ARG* 2.2 70.4 - - + +
550 LEU 2.9 31.9 - - - -
1783 MET* 2.8 54.6 + - + +
1793 ASN* 4.0 4.0 - - - +
1813 ILE* 1.3 75.0 - - + +
1833 ALA* 1.3 65.2 + - - +
1853 GLN* 3.2 5.7 + - + +
1863 LYS* 3.0 39.0 + - + +
2093 ILE* 3.7 9.2 - - + -
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Residues in contact with ALA 183 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1413 LEU* 3.8 13.9 - - + -
1793 ASN* 3.1 17.6 + - - +
1803 VAL* 3.5 12.3 - - - +
1813 ILE 3.2 0.4 - - - -
1823 PHE* 1.3 78.1 - - - +
1843 ALA* 1.3 56.0 + - - +
1863 LYS* 3.2 12.0 + - - +
1873 GLN* 2.9 30.2 + - - +
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Residues in contact with ALA 184 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1413 LEU* 3.7 6.2 - - + +
1613 ILE* 5.1 0.2 - - + -
1803 VAL 3.1 7.1 + - - +
1813 ILE 3.0 9.9 + - - +
1833 ALA* 1.3 76.7 - - - +
1853 GLN* 1.3 59.9 + - - +
1873 GLN* 2.7 27.5 - - - +
1883 ASN 2.7 24.3 + - - -
1893 ILE* 2.8 23.8 + - + +
1913 ILE* 3.7 22.4 - - + -
2103 THR* 4.8 0.9 - - - +
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Residues in contact with GLN 185 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540 ARG* 5.2 9.6 - - - +
980 GLN* 3.6 8.7 + - - -
1813 ILE 2.9 11.9 + - - +
1823 PHE* 3.2 9.8 + - + +
1843 ALA* 1.3 74.7 - - - +
1863 LYS* 1.3 63.3 + - + +
1883 ASN* 2.8 35.3 + - - +
2093 ILE* 2.6 40.7 + - + +
2103 THR* 2.9 37.1 + - - +
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Residues in contact with LYS 186 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540 ARG* 4.4 24.4 - - - +
1823 PHE* 3.0 27.7 + - + +
1833 ALA* 3.6 10.0 - - - +
1853 GLN* 1.3 78.6 - - + +
1873 GLN* 1.3 62.9 + - - +
1883 ASN* 3.1 13.2 + - - +
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Residues in contact with GLN 187 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1413 LEU* 2.9 43.9 - - - +
1443 ILE* 4.2 15.6 - - - +
1613 ILE* 4.6 0.6 - - - +
1833 ALA 2.9 9.6 + - - +
1843 ALA* 2.7 31.2 + - - +
1863 LYS* 1.3 74.2 - - - +
1883 ASN* 1.3 71.6 + - - +
1893 ILE* 2.9 44.6 - - + +
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Residues in contact with ASN 188 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1593 SER 4.9 1.2 - - - +
1843 ALA 2.7 3.4 + - - -
1853 GLN* 2.8 26.6 + - - +
1863 LYS 3.0 13.5 + - - +
1873 GLN* 1.3 80.9 - - - +
1893 ILE* 1.3 64.1 + - - +
1903 LEU* 3.9 4.8 + - - +
2103 THR 5.8 0.4 - - - -
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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