Contacts of the helix formed by residues 172 - 185 (chain 5) in PDB entry 3EXG
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 172 (chain 5).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1773 GLU* 4.1 4.5 + - - +
574 ILE* 3.4 26.0 + - - +
584 SER* 4.1 4.2 - - - +
594 GLU* 3.6 11.3 + - - +
884 GLN* 3.4 24.6 + - - +
1385 VAL* 3.2 28.0 + - + +
1395 GLY* 4.0 5.8 - - - -
1695 ALA 2.7 16.4 + - - +
1705 ALA 3.4 0.4 - - - -
1715 ASN* 1.3 78.3 - - - +
1735 GLY* 1.3 60.0 + - - +
1745 GLN* 2.7 34.2 + - + +
1755 ILE* 2.9 39.4 + - + +
1765 PHE* 3.9 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 173 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1733 GLY* 3.4 36.3 - - - -
1773 GLU* 2.9 25.4 + - - +
1715 ASN 3.3 3.6 + - - -
1725 GLN* 1.3 67.7 - - - +
1745 GLN* 1.3 66.6 + - - +
1765 PHE* 2.9 21.7 + - - +
1775 GLU 3.2 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 174 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1733 GLY* 4.4 0.6 - - - -
1773 GLU* 4.5 1.8 + - - +
884 GLN* 3.3 14.5 + - - -
1385 VAL 3.5 0.2 + - - -
1395 GLY* 3.3 28.8 - - - +
1405 ALA* 3.3 5.5 - - - +
1435 PRO* 3.3 18.9 - - + +
1725 GLN* 2.7 31.8 + - + +
1735 GLY* 1.3 72.9 - - - +
1755 ILE* 1.3 62.9 + - - +
1775 GLU* 3.1 14.9 + - - +
1785 ALA* 3.0 23.4 + - - +
606 MET* 3.7 28.9 - - + +
926 GLN* 3.3 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1395 GLY* 4.8 3.6 - - - +
1425 VAL* 3.7 34.8 - - + -
1655 TYR* 3.9 25.4 - - + +
1695 ALA* 3.2 36.1 - - + +
1705 ALA* 4.2 5.8 - - - +
1725 GLN* 2.9 21.0 + - + +
1745 GLN* 1.3 78.3 - - - +
1765 PHE* 1.3 58.8 + - + +
1785 ALA* 3.3 4.2 + - - +
1795 TYR* 2.9 61.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 176 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1713 ASN 5.1 1.1 - - - -
1763 PHE* 3.5 66.8 - + + -
1705 ALA 3.8 17.9 - - - -
1715 ASN* 4.7 5.4 - - + -
1725 GLN 3.9 12.3 - - - -
1735 GLY* 2.9 8.3 + - - +
1755 ILE* 1.3 75.5 - - + +
1775 GLU* 1.3 67.4 + - - +
1795 TYR* 3.3 21.9 + + - +
1805 ASN* 3.2 21.5 + - - +
2165 ARG* 3.4 55.9 - - + -
2195 PHE* 5.5 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 177 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1713 ASN 3.6 10.3 - - - +
1723 GLN* 3.3 11.4 - - - +
1733 GLY* 2.4 39.2 + - - +
1735 GLY 3.2 9.8 + - - +
1745 GLN* 3.1 9.2 + - - +
1765 PHE* 1.3 78.0 - - - +
1785 ALA* 1.3 64.1 + - - +
1805 ASN* 3.2 5.3 + - - +
1815 MET* 3.2 27.9 + - - +
586 SER* 3.3 27.0 - - - +
596 GLU 4.7 0.2 + - - -
606 MET* 3.5 13.5 + - - +
616 GLY* 2.5 42.7 + - - -
886 GLN* 4.8 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1425 VAL* 3.8 23.3 - - + +
1435 PRO* 4.2 18.4 - - + -
1465 ALA* 4.4 6.9 - - + +
1745 GLN 3.0 12.2 + - - +
1755 ILE 3.4 8.3 - - - +
1775 GLU* 1.3 76.5 - - - +
1795 TYR* 1.3 66.4 + - - +
1815 MET* 3.4 7.7 + - - +
1825 ALA* 3.0 27.0 + - - +
1915 PHE* 4.2 8.3 - - + -
616 GLY* 5.1 0.4 - - - -
656 ILE* 5.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 179 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1655 TYR* 2.5 27.1 + - - -
1755 ILE* 2.9 39.6 + - + +
1765 PHE* 3.3 32.1 + + + +
1785 ALA* 1.3 75.2 - - - +
1805 ASN* 1.3 53.5 + - - +
1825 ALA* 3.7 0.3 - - - +
1835 ALA* 2.8 31.0 + - - +
1915 PHE* 3.8 25.8 - + - -
2165 ARG* 3.8 21.0 - - + +
2175 GLY* 3.9 10.5 + - - +
2195 PHE* 4.0 9.4 - - + -
2205 ILE* 3.2 31.8 - - + +
2525 LEU* 3.7 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 180 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1713 ASN* 3.5 35.0 + - + +
2073 ALA 3.6 6.6 + - - +
2083 ALA* 3.7 1.2 - - - -
2093 ALA* 3.2 28.2 + - - +
2163 ARG* 5.0 2.1 + - - +
1765 PHE 3.2 8.4 + - - +
1775 GLU* 3.6 9.6 + - - +
1785 ALA 3.2 0.6 - - - -
1795 TYR* 1.3 75.8 - - - +
1815 MET* 1.3 61.4 + - - +
1835 ALA* 3.3 2.4 + - - +
1845 LEU* 2.8 31.2 + - - +
2195 PHE* 3.8 18.8 - - + -
566 PRO* 3.7 27.1 - - - +
586 SER* 4.5 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 181 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1775 GLU 3.2 22.5 + - - +
1785 ALA 4.3 0.7 - - - +
1805 ASN* 1.3 73.2 - - - +
1825 ALA* 1.3 60.8 + - - +
1845 LEU* 3.5 6.2 - - - +
1855 TRP* 2.9 61.1 + - + +
1875 LEU* 4.2 2.2 - - - -
566 PRO* 3.4 35.0 - - + -
586 SER* 4.0 14.6 - - - -
616 GLY* 3.6 13.2 - - - -
626 PHE* 3.4 39.9 - - - +
656 ILE* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1465 ALA* 4.8 4.7 - - + -
1785 ALA 3.0 19.1 + - - +
1795 TYR 3.8 1.1 - - - +
1815 MET* 1.3 76.4 - - - +
1835 ALA* 1.3 63.0 + - - +
1865 LYS 3.2 2.3 + - - -
1875 LEU* 2.9 48.9 + - + +
1895 CYS* 4.9 1.6 - - + -
1915 PHE* 3.7 28.0 - - + -
2505 PRO* 3.3 13.6 - - + +
656 ILE* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2093 ALA* 3.9 7.2 - - + -
1795 TYR 2.8 19.4 + - - +
1805 ASN 3.6 1.8 - - - +
1825 ALA* 1.3 75.2 - - - +
1845 LEU* 1.3 66.1 + - - +
1865 LYS* 2.9 23.9 + - - +
2195 PHE* 3.6 29.4 - - + -
2205 ILE* 4.2 6.3 - - + -
2505 PRO* 3.6 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2053 GLU 4.6 2.7 - - - +
2063 ARG* 3.3 28.5 - - - +
2073 ALA 3.7 13.9 - - - +
2083 ALA 3.6 11.2 - - - +
2093 ALA* 3.6 34.7 - - - +
1805 ASN* 2.8 18.1 + - - +
1815 MET* 3.2 6.5 + - - +
1835 ALA* 1.3 73.9 - - - +
1855 TRP* 1.3 82.1 + - + +
1865 LYS* 3.6 4.3 + - - +
546 ASP 5.4 0.7 - - - +
566 PRO* 4.3 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 185 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1505 LEU* 4.2 16.4 - - + -
1535 LYS* 3.0 30.7 + - - +
1815 MET* 2.9 51.1 + - + +
1845 LEU* 1.3 99.7 - - + +
1865 LYS* 1.3 71.4 + - - +
1875 LEU* 3.5 27.6 - - + -
266 LEU* 4.9 5.8 - - + -
536 ILE* 3.6 31.4 - - + +
546 ASP 3.9 15.4 + - - -
556 THR* 4.2 13.2 - - + -
566 PRO* 4.3 1.3 - - + -
656 ILE* 4.0 23.1 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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