Contacts of the helix formed by residues 149 - 163 (chain 6) 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 ASN 149 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56 VAL* 3.9 4.7 - - - -
1486 TRP* 1.3 107.8 - - + +
1506 SER* 1.3 66.5 + - - +
1516 GLU* 3.2 12.5 + - - +
1526 ASP* 2.7 39.5 + - - +
1536 ALA* 2.8 24.6 + - - +
1806 PHE* 3.4 36.6 - - + -
1996 LYS* 5.3 2.8 - - - +
2016 GLU* 3.7 10.7 + - - -
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Residues in contact with SER 150 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36 VAL* 2.6 45.8 + - - -
46 THR 3.2 13.5 - - - -
56 VAL* 3.4 5.8 + - - +
86 ALA* 3.6 16.3 - - - +
1496 ASN* 1.3 73.6 - - - +
1516 GLU* 1.3 66.0 + - - +
1536 ALA* 2.9 2.0 + - - -
1546 LYS* 2.8 24.4 + - - +
1806 PHE* 3.6 17.0 - - - -
1826 PHE* 3.9 8.7 - - - -
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Residues in contact with GLU 151 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1496 ASN* 3.3 14.1 - - - +
1506 SER* 1.3 79.9 - - - +
1526 ASP* 1.3 63.7 + - - +
1556 GLY 3.1 16.8 + - - -
1806 PHE* 5.5 0.8 - - + +
1816 GLU 5.0 3.8 + - - +
1826 PHE* 4.0 10.1 - - + -
1836 PRO* 3.4 37.7 - - + +
1856 GLU* 5.2 1.2 - - - +
1866 ALA* 4.4 2.9 - - + -
1916 PHE* 3.3 33.3 - - + -
1936 ILE* 3.5 2.9 - - - +
1996 LYS* 4.7 16.9 + - - -
2396 ARG* 4.8 6.0 + - - +
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Residues in contact with ASP 152 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1476 PRO* 3.9 6.7 - - + -
1486 TRP* 2.7 32.4 + - - +
1496 ASN* 2.7 35.1 + - - +
1516 GLU* 1.3 70.1 - - - +
1536 ALA* 1.3 67.7 + - - +
1566 LEU* 2.8 36.0 + - + +
1936 ILE* 3.5 10.1 - - + -
1996 LYS* 4.3 1.2 - - - +
2016 GLU* 4.2 2.9 - - - +
2376 ASN* 3.0 22.6 - - - +
2396 ARG* 3.4 27.3 + - - -
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Residues in contact with ALA 153 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56 VAL* 4.1 16.4 - - + -
86 ALA* 4.4 2.9 - - + -
96 ILE* 3.9 26.7 - - + +
1476 PRO* 3.6 22.4 - - + +
1486 TRP 5.6 0.2 - - - +
1496 ASN 2.8 20.5 + - - +
1506 SER 3.6 3.4 - - - +
1526 ASP* 1.3 76.3 - - - +
1546 LYS* 1.3 63.4 + - - +
1566 LEU* 4.2 0.3 - - - +
1576 ILE* 3.2 25.0 + - - +
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Residues in contact with LYS 154 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86 ALA* 3.6 28.8 - - + +
116 GLN* 2.6 33.1 + - + +
126 GLY 4.1 4.0 - - - +
156 GLU* 3.3 25.5 + - - -
1506 SER 2.8 14.8 + - - +
1516 GLU 4.3 1.6 - - - +
1536 ALA* 1.3 78.3 - - - +
1556 GLY* 1.3 61.6 + - - +
1576 ILE* 3.2 9.4 - - - +
1586 LYS* 3.1 32.1 - - + +
1826 PHE* 3.9 11.7 - - + -
1866 ALA 2.8 27.3 + - - +
1876 GLN 3.5 3.6 + - - -
1886 SER 3.1 16.4 + - - -
1916 PHE* 4.7 5.8 - - + -
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Residues in contact with GLY 155 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1516 GLU 3.1 9.9 + - - -
1546 LYS* 1.3 77.5 - - - +
1566 LEU* 1.3 62.0 + - - +
1586 LYS* 3.4 2.9 + - - +
1596 SER* 3.1 18.2 + - - -
1916 PHE* 3.7 18.1 - - - -
1926 LEU* 4.1 0.3 - - - -
1936 ILE* 3.5 38.3 + - - -
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Residues in contact with LEU 156 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1456 VAL* 4.1 33.2 - - + +
1476 PRO* 3.8 33.0 - - + -
1526 ASP* 2.8 31.6 + - + +
1536 ALA 4.2 1.1 - - - +
1556 GLY* 1.3 69.0 - - - +
1576 ILE* 1.3 61.3 + - - +
1586 LYS 3.0 0.3 + - - -
1596 SER* 3.2 4.6 + - - -
1606 ALA* 2.8 32.2 + - - +
1696 VAL* 5.5 0.9 - - + -
1936 ILE* 3.9 27.4 - - + +
1946 PRO 4.8 0.4 - - - +
1956 ILE* 4.7 8.4 - - + +
2396 ARG* 4.4 22.7 - - + +
2406 THR* 4.4 7.6 - - - +
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Residues in contact with ILE 157 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96 ILE* 4.3 13.2 - - + +
126 GLY* 3.9 15.3 - - - -
136 MET* 4.1 19.1 - - + -
776 ILE* 5.2 2.2 - - + -
1136 VAL* 4.8 7.9 - - + -
1156 ARG* 3.7 34.1 - - + -
1536 ALA 3.2 13.1 + - - +
1546 LYS* 3.2 18.2 - - - +
1566 LEU* 1.3 78.2 - - - +
1586 LYS* 1.3 68.0 + - + +
1606 ALA* 3.4 4.9 - - - +
1616 ILE* 3.1 33.6 + - + +
1696 VAL* 4.5 17.1 - - + +
1716 GLU* 4.4 8.5 - - - +
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Residues in contact with LYS 158 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126 GLY* 3.7 18.6 - - - +
156 GLU* 3.2 22.5 + - - +
166 GLU* 2.7 41.3 + - - +
1546 LYS* 3.1 39.7 - - - +
1556 GLY 3.4 6.7 + - - +
1566 LEU 3.0 0.6 - - - -
1576 ILE* 1.3 78.8 - - + +
1596 SER* 1.3 61.3 - - - +
1606 ALA 3.1 1.1 - - - -
1616 ILE* 3.0 5.4 + - - +
1626 ARG* 2.8 34.5 + - - +
1896 LYS 3.6 15.0 + - - -
1916 PHE 2.8 30.3 - - - +
1926 LEU* 3.7 11.0 - - + -
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Residues in contact with SER 159 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1556 GLY 3.1 3.9 + - - -
1566 LEU 3.7 6.5 - - - -
1586 LYS* 1.3 77.9 - - - +
1606 ALA* 1.3 56.8 + - - +
1626 ARG* 3.2 8.5 + - - +
1636 ASP* 2.9 29.5 + - - +
1926 LEU* 3.6 16.9 - - - +
1936 ILE 3.0 39.5 + - - -
1946 PRO* 4.3 1.7 - - - +
1956 ILE* 4.3 16.6 - - - +
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Residues in contact with ALA 160 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136 VAL* 3.6 12.9 - - + +
1456 VAL* 5.7 1.8 - - + -
1566 LEU 2.8 20.5 + - - +
1576 ILE* 3.4 7.6 - - - +
1596 SER* 1.3 75.0 - - - +
1616 ILE* 1.3 61.7 + - - +
1636 ASP* 3.2 14.6 + - - +
1676 VAL* 4.1 19.0 - - + +
1696 VAL* 4.0 25.4 - - + -
1956 ILE* 4.6 4.5 - - + +
10076 K 3.0 14.7 - - - -
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Residues in contact with ILE 161 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126 GLY 5.0 0.2 - - - +
136 MET* 4.6 10.5 - - - +
166 GLU* 3.5 41.5 - - + +
196 ARG* 6.1 0.9 - - - +
236 VAL* 4.0 28.5 - - + -
756 ARG* 3.2 16.8 + - + +
776 ILE* 3.5 34.8 - - + -
1136 VAL* 4.0 9.0 - - + -
1576 ILE* 3.1 22.5 + - + +
1586 LYS 3.0 7.2 + - - +
1606 ALA* 1.3 74.8 - - - +
1626 ARG* 1.3 65.6 + - - +
10076 K 3.1 14.7 - - - -
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Residues in contact with ARG 162 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166 GLU* 2.4 49.3 + - - -
196 ARG* 3.3 48.3 - - - +
756 ARG* 3.3 10.5 + - - +
1586 LYS* 2.8 23.1 + - - +
1596 SER* 3.6 9.9 - - - +
1616 ILE* 1.3 80.2 - - - +
1636 ASP* 1.3 62.4 + - - +
1646 ASN* 4.6 5.0 + - - +
1896 LYS 4.6 3.0 + - - -
1906 ASP* 4.8 15.8 + - - +
1926 LEU* 3.9 34.2 - - + +
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Residues in contact with ASP 163 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3435 ASP* 4.3 3.0 - - - +
756 ARG* 2.9 13.0 + - - -
1116 PRO* 4.3 0.5 - - - +
1436 LYS* 3.2 24.5 + - - -
1596 SER 2.9 11.6 + - - +
1606 ALA* 3.3 14.8 - - - +
1616 ILE 3.1 0.4 - - - -
1626 ARG* 1.3 78.4 - - - +
1646 ASN* 1.3 59.7 + - - +
1656 ASN* 2.8 42.4 + - - +
1676 VAL* 4.1 14.7 - - + +
1956 ILE* 4.2 9.5 - - + +
10076 K 2.9 17.7 - - - -
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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