Contacts of the helix formed by residues 172 - 190 (chain 5) in PDB entry 3J7Y
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 LYS 172 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1705 ILE* 4.5 7.9 - - + +
1715 PRO* 1.3 74.3 - - - +
1735 ARG* 1.3 61.0 + - - +
1745 GLU* 3.3 1.8 - - + +
1755 THR* 2.9 28.9 + - - +
1765 TYR* 3.1 15.0 + - - -
2985 ASN* 3.7 37.0 - - - +
2405A C 5.8 6.3 - - - -
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Residues in contact with ARG 173 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1725 LYS* 1.3 70.5 - - - +
1745 GLU* 1.3 64.4 + - - +
1755 THR 3.1 2.7 + - - -
1765 TYR* 3.3 36.9 + - + +
1775 CYS* 3.3 31.1 + - + +
1785 PRO* 3.8 1.6 - - - +
2955 ASP 4.1 1.8 - - - -
2965 LYS* 3.2 26.5 - - - +
2975 ALA 3.7 4.3 - - - +
2985 ASN* 3.1 13.9 + - - +
3035 ARG* 3.3 49.1 - - - +
3485 ASP* 2.6 39.4 + - - +
3505 ARG* 5.6 1.2 - - - +
2394A A 4.2 5.1 - - - -
2395A A 2.4 32.3 + - - -
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Residues in contact with GLU 174 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1725 LYS* 3.3 1.1 + - + -
1735 ARG* 1.3 72.4 - - - +
1755 THR* 1.3 60.0 + - - +
1785 PRO* 3.9 3.3 - - - +
2965 LYS* 3.5 46.2 - - + +
2975 ALA* 4.7 4.0 - - - +
2985 ASN* 2.8 29.9 + - - +
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Residues in contact with THR 175 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1655 GLN* 3.5 27.8 - - + +
1665 THR* 4.8 12.9 - - - +
1715 PRO* 4.6 2.3 - - + +
1725 LYS* 2.9 22.0 + - - +
1745 GLU* 1.3 78.8 - - - +
1765 TYR* 1.3 61.9 + - - -
1775 CYS 3.6 0.9 - - - -
1785 PRO* 3.3 11.1 - - - +
1795 VAL* 3.1 25.6 - - + +
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Residues in contact with TYR 176 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1615 ALA* 3.1 27.5 - - - +
1625 ARG* 3.5 47.8 + - - -
1655 GLN* 3.5 8.5 - - - +
1715 PRO* 3.7 14.4 - - + -
1725 LYS* 3.1 24.6 + - - +
1735 ARG* 3.3 55.7 + - + -
1755 THR* 1.3 78.7 - - - +
1775 CYS* 1.3 61.9 + - - +
1795 VAL* 3.2 2.8 + - - +
1805 ILE* 2.9 47.5 + - + +
3485 ASP* 4.6 0.5 + - - -
3495 GLY* 4.1 20.4 - - - -
3505 ARG* 5.5 0.9 + - - +
3835 TYR* 4.2 0.4 - - - -
2394A A 5.3 3.2 + - - -
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Residues in contact with CYS 177 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1735 ARG* 3.3 25.7 + - + +
1765 TYR* 1.3 85.8 - - + +
1785 PRO* 1.4 74.7 - - + +
1805 ILE* 3.6 3.1 + - - +
1815 VAL* 3.4 21.5 + - - +
2945 LEU* 4.2 7.6 - - - -
2955 ASP 3.5 22.0 - - - +
2965 LYS* 4.7 0.7 - - - -
3485 ASP* 3.4 37.5 - - - -
3495 GLY* 3.9 12.4 - - - +
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Residues in contact with PRO 178 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1735 ARG 3.8 3.1 - - - +
1745 GLU 3.9 3.6 - - - +
1755 THR 3.3 17.0 - - - +
1775 CYS* 1.4 96.1 - - + +
1795 VAL* 1.3 57.0 + - + +
1815 VAL* 3.2 6.7 + - + +
1825 ASP* 2.9 28.4 + - - +
2945 LEU* 3.8 32.3 - - + +
2965 LYS* 3.7 27.4 - - + -
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Residues in contact with VAL 179 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1605 HIS* 4.2 17.5 - - + +
1615 ALA* 4.3 9.9 - - + -
1655 GLN* 4.3 14.1 - - + +
1755 THR* 3.1 23.3 - - + +
1765 TYR* 3.2 10.5 + - - +
1785 PRO* 1.3 78.7 - - + +
1805 ILE* 1.3 56.9 + - - +
1825 ASP* 3.2 8.7 + - - +
1835 ASN* 2.9 50.6 + - - +
204s CYS* 5.9 4.5 - - - -
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Residues in contact with ILE 180 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1575 VAL* 3.9 8.0 - - + +
1585 ILE* 5.1 6.3 - - + +
1615 ALA* 3.0 29.6 - - + -
1625 ARG* 4.9 0.9 - - + -
1765 TYR* 2.9 29.6 + - + +
1775 CYS 3.7 4.9 - - - +
1795 VAL* 1.3 75.1 - - - +
1815 VAL* 1.3 60.8 + - - +
1835 ASN* 3.2 8.5 + - - +
1845 LEU* 2.9 49.0 + - + +
3495 GLY* 3.2 36.8 - - - +
3525 PHE* 4.4 12.1 - - + -
3825 LEU* 5.1 6.3 - - + -
3835 TYR* 3.8 12.1 - - + +
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Residues in contact with VAL 181 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1775 CYS* 3.4 18.6 + - - +
1785 PRO* 3.2 10.7 + - + +
1805 ILE* 1.3 79.5 - - - +
1825 ASP* 1.3 58.7 + - - +
1845 LEU* 3.2 11.2 + - - +
1855 ILE* 2.9 51.6 + - + +
2285 ALA* 6.4 0.4 - - + -
2925 TYR* 4.8 15.0 - - + +
2935 LEU 5.8 1.8 - - - +
2945 LEU* 5.0 15.5 - - + -
3455 VAL* 5.1 5.2 - - + -
3465 GLY 5.2 4.5 - - - +
3475 THR 5.8 0.2 - - - -
3485 ASP 5.1 4.0 - - - +
3525 PHE* 4.2 26.7 - - + -
4145 PHE* 4.5 7.8 - - + -
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Residues in contact with ASP 182 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1785 PRO 2.9 13.3 + - - +
1795 VAL* 3.3 13.0 - - - +
1815 VAL* 1.3 77.9 - - - +
1835 ASN* 1.3 59.1 + - - +
1855 ILE* 3.2 14.7 + - - +
1865 GLN* 2.9 32.2 + - - +
200s LEU 6.1 1.1 - - - -
202s TYR* 3.0 42.4 + - - -
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Residues in contact with ASN 183 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1575 VAL* 3.3 36.8 + - + +
1605 HIS* 3.6 21.1 + - - +
1795 VAL* 2.9 39.9 + - - +
1805 ILE* 3.4 5.6 - - - +
1825 ASP* 1.3 78.9 - - - +
1845 LEU* 1.3 57.3 + - - +
1865 GLN* 3.2 13.8 + - - +
1875 LEU* 2.9 33.3 + - - +
200s LEU 4.4 13.5 + - - +
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Residues in contact with LEU 184 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1545 VAL* 4.4 12.8 - - + -
1575 VAL* 4.3 11.0 - - + -
1805 ILE* 2.9 40.5 + - + +
1815 VAL* 3.2 11.9 + - - +
1835 ASN* 1.3 75.4 - - - +
1855 ILE* 1.3 58.3 + - - +
1875 LEU* 3.2 9.7 + - + +
1885 CYS* 2.9 34.5 + - - -
3525 PHE* 4.3 15.0 - - + -
3825 LEU* 4.8 13.2 - - + -
4115 PHE* 3.7 32.7 - - + -
4145 PHE* 3.9 28.0 - - + -
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Residues in contact with ILE 185 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1815 VAL* 2.9 41.2 + - + +
1825 ASP* 3.4 13.2 - - - +
1845 LEU* 1.3 77.2 - - - +
1865 GLN* 1.3 57.2 + - - +
1885 CYS* 3.2 10.5 + - - +
1895 LYS* 2.9 33.0 + - + +
2035 CYS* 4.7 22.0 - - + -
2285 ALA* 5.6 4.0 - - + -
2305 LEU* 5.7 0.2 - - + -
2925 TYR* 3.8 36.3 - - + +
4145 PHE* 4.2 11.2 - - + -
4185 TYR* 4.4 15.3 - - + +
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Residues in contact with GLN 186 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1825 ASP* 2.9 17.9 + - - +
1835 ASN* 3.2 16.8 + - - +
1855 ILE* 1.3 77.2 - - - +
1875 LEU* 1.3 59.1 + - + +
1895 LYS* 3.1 11.9 + - + +
1905 SER* 2.9 27.3 + - - -
182s SER* 5.7 3.4 + - - +
185s VAL* 4.7 12.4 - - + +
195s LEU 5.3 1.7 + - - +
196s ALA 5.8 3.8 - - - +
198s ALA 4.6 10.8 + - - +
199s ALA* 4.8 1.2 - - - -
200s LEU* 3.1 60.8 + - - +
202s TYR* 5.5 2.4 + - - -
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Residues in contact with LEU 187 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1535 CYS* 4.0 21.1 - - + -
1545 VAL* 4.2 16.2 - - - +
1575 VAL* 3.7 27.8 - - + -
1835 ASN 2.9 15.4 + - - +
1845 LEU* 3.3 12.8 - - + +
1865 GLN* 1.3 76.9 - - + +
1885 CYS* 1.3 61.5 + - - +
1905 SER* 2.5 31.0 + - - +
1915 GLN* 3.8 3.8 + - - +
4115 PHE* 4.1 31.2 - - + -
196s ALA 5.6 4.3 - - - +
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Residues in contact with CYS 188 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1845 LEU 2.9 23.2 + - - -
1855 ILE 3.2 7.6 + - - +
1875 LEU* 1.3 75.5 - - - +
1895 LYS* 1.3 63.0 + - - +
1915 GLN* 3.0 26.0 + - - +
1985 LEU* 4.1 1.6 - - - +
4115 PHE* 5.0 8.1 - - - -
4145 PHE* 3.7 30.7 - - - -
4155 LEU* 4.3 20.5 - - + +
4185 TYR* 3.5 42.5 - - + -
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Residues in contact with LYS 189 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1855 ILE* 2.9 18.2 + - + +
1865 GLN* 3.1 15.2 + - + +
1885 CYS* 1.3 79.5 - - - +
1905 SER* 1.3 50.7 + - - +
1925 ILE* 2.8 58.9 + - + +
1985 LEU* 3.8 20.2 + - - -
1995 ALA* 5.3 2.0 + - - +
2015 ARG* 4.6 16.6 + - - +
2025 ILE* 5.6 1.6 - - - +
4185 TYR* 3.8 22.3 + - - +
182s SER* 4.2 25.4 - - - +
183s THR* 4.9 7.1 - - - +
186s GLY* 4.2 15.0 - - - -
189s SER* 5.2 0.5 + - - -
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Residues in contact with SER 190 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1865 GLN 2.9 12.2 + - - -
1875 LEU* 2.5 26.8 + - - +
1895 LYS* 1.3 72.5 - - - +
1915 GLN* 1.3 60.4 + - - +
1925 ILE 3.2 3.9 + - - -
1935 LEU* 4.0 7.4 + - - +
189s SER* 4.0 14.4 + - - -
196s ALA* 3.7 39.3 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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