Contacts of the helix formed by residues 149 - 163 (chain 4) 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 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54 VAL* 3.7 4.0 - - - -
1484 TRP* 1.3 109.2 - - + +
1504 SER* 1.3 63.9 + - - +
1514 GLU* 2.8 26.5 + - - +
1524 ASP* 3.1 18.5 + - - +
1534 ALA* 3.0 20.3 + - - +
1804 PHE* 3.5 41.6 - - + +
1994 LYS* 5.2 3.0 - - - +
2014 GLU* 3.6 13.1 + - - -
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Residues in contact with SER 150 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34 VAL* 3.0 34.5 + - - -
54 VAL* 3.5 13.9 + - - +
84 ALA* 3.4 27.7 - - - +
1494 ASN* 1.3 74.4 + - - +
1514 GLU* 1.3 60.5 + - - -
1534 ALA* 2.9 2.6 + - - -
1544 LYS* 2.9 29.1 + - - +
1804 PHE* 3.4 22.1 - - - +
1814 GLU 5.8 0.2 - - - -
1824 PHE* 4.1 5.4 - - - -
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Residues in contact with GLU 151 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1494 ASN* 2.8 14.3 + - - +
1504 SER* 1.3 71.2 - - - +
1524 ASP* 1.3 67.8 + - - +
1544 LYS* 4.0 0.2 - - - -
1554 GLY 2.9 20.4 + - - -
1814 GLU 4.7 3.3 + - - +
1824 PHE* 3.8 13.1 - - + -
1834 PRO* 3.0 32.2 - - + +
1864 ALA* 3.9 12.1 - - + -
1914 PHE* 3.3 31.6 - - + -
1934 ILE* 3.6 3.0 - - - +
1994 LYS* 4.0 24.5 + - - -
2394 ARG* 4.3 7.6 + - - -
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Residues in contact with ASP 152 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1474 PRO* 3.7 8.2 - - + +
1484 TRP* 2.9 27.9 + - - +
1494 ASN* 3.1 25.9 + - - +
1514 GLU* 1.3 78.4 + - - +
1534 ALA* 1.3 57.3 + - - +
1554 GLY* 3.6 0.3 - - - -
1564 LEU* 2.9 35.1 + - + +
1934 ILE* 3.5 8.8 - - - +
1994 LYS* 5.0 0.2 - - - -
2014 GLU* 4.3 1.2 - - - +
2374 ASN* 2.8 26.0 - - - +
2394 ARG* 2.8 40.5 + - + +
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Residues in contact with ALA 153 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54 VAL* 3.6 30.3 - - + -
84 ALA* 4.5 1.8 - - + -
94 ILE* 3.7 21.0 - - + +
1474 PRO* 3.7 20.0 - - + -
1494 ASN 3.0 4.2 + - - +
1504 SER* 2.9 11.5 + - - +
1524 ASP* 1.3 76.2 - - - +
1544 LYS* 1.3 62.1 + - - +
1564 LEU* 4.6 0.8 - - - +
1574 ILE* 3.2 26.9 + - - +
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Residues in contact with LYS 154 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84 ALA* 3.0 27.7 + - + +
114 GLN* 2.8 30.1 + - + +
124 GLY* 4.1 3.1 - - - +
154 GLU* 3.2 27.9 + - - -
1504 SER 2.9 13.8 + - - +
1514 GLU 4.1 1.6 - - - +
1534 ALA* 1.3 76.7 - - - +
1554 GLY* 1.3 63.6 + - - +
1574 ILE* 3.2 5.8 - - - +
1584 LYS* 3.0 38.9 + - + +
1824 PHE* 3.7 12.3 - - + -
1864 ALA 3.0 28.1 + - - +
1874 GLN* 3.4 14.8 + - - +
1884 SER 3.9 4.3 - - - -
1914 PHE* 4.1 5.4 - - + -
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Residues in contact with GLY 155 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1514 GLU 2.9 15.3 + - - -
1524 ASP 3.6 3.1 - - - -
1544 LYS* 1.3 73.9 - - - +
1564 LEU* 1.3 56.0 + - - +
1584 LYS* 4.6 0.4 - - - -
1594 SER* 3.3 18.4 + - - -
1914 PHE* 3.6 27.7 - - - -
1924 LEU* 3.9 1.6 - - - -
1934 ILE* 3.0 33.2 + - - +
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Residues in contact with LEU 156 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1454 VAL* 4.0 33.2 - - + +
1474 PRO* 4.1 27.1 - - + -
1524 ASP 2.9 18.8 + - - +
1534 ALA* 4.6 1.3 - - - +
1554 GLY* 1.3 75.7 - - - +
1574 ILE* 1.3 62.0 + - - +
1584 LYS 3.2 1.1 - - - -
1594 SER* 3.8 2.1 - - - -
1604 ALA* 2.7 32.6 + - - +
1694 VAL* 5.1 2.0 - - + +
1934 ILE* 3.4 41.5 - - + +
1944 PRO 4.9 2.0 - - - +
1954 ILE* 4.6 15.8 - - + +
2394 ARG* 4.3 21.8 - - + +
2404 THR* 5.2 1.1 - - - +
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Residues in contact with ILE 157 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94 ILE* 4.3 13.5 - - + +
124 GLY* 4.0 19.1 - - - -
134 MET* 4.4 12.3 - - + -
774 ILE* 5.2 1.1 - - + -
1134 VAL* 4.5 10.5 - - + -
1154 ARG* 3.7 31.0 - - + +
1534 ALA 3.2 16.7 + - - +
1544 LYS* 3.2 16.2 - - - +
1564 LEU* 1.3 80.0 - - - +
1584 LYS* 1.3 65.1 + - - +
1604 ALA* 4.0 1.5 - - + -
1614 ILE* 3.1 44.7 + - + +
1694 VAL* 4.4 22.3 - - + +
1714 GLU* 4.8 4.0 - - - +
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Residues in contact with LYS 158 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124 GLY* 3.6 18.6 - - - +
154 GLU* 3.3 31.0 + - - +
164 GLU* 2.7 39.9 + - - +
1544 LYS* 3.0 32.3 + - + +
1554 GLY 4.4 0.4 - - - +
1574 ILE* 1.3 79.4 - - - +
1594 SER* 1.3 60.2 + - - +
1614 ILE* 3.2 4.0 + - - +
1624 ARG* 2.9 38.4 + - - +
1894 LYS 3.1 24.9 + - - -
1914 PHE 3.1 37.2 - - - +
1924 LEU* 3.8 6.1 - - + -
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Residues in contact with SER 159 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1554 GLY 3.3 17.4 + - - -
1564 LEU* 3.4 3.8 + - - -
1584 LYS* 1.3 77.3 - - - +
1604 ALA* 1.3 56.9 + - - +
1624 ARG* 3.4 7.2 + - - +
1634 ASP* 3.0 28.9 + - - +
1924 LEU* 3.8 17.9 - - - +
1934 ILE 3.2 24.6 + - - -
1944 PRO* 4.2 4.9 - - - +
1954 ILE* 4.1 16.9 + - - +
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Residues in contact with ALA 160 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1134 VAL* 3.3 15.6 - - + +
1454 VAL* 5.4 1.1 - - + -
1564 LEU 2.7 22.0 + - - +
1574 ILE* 4.2 2.2 - - - +
1594 SER* 1.3 70.6 - - - +
1614 ILE* 1.3 66.1 + - - +
1634 ASP* 3.2 12.6 + - - +
1674 VAL* 3.4 32.6 - - + +
1694 VAL* 4.3 13.0 - - + -
1954 ILE* 4.1 9.1 - - + +
10164 K 3.0 12.3 - - - -
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Residues in contact with ILE 161 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124 GLY 4.9 0.2 - - - +
134 MET* 4.5 6.3 - - - -
164 GLU* 3.7 35.2 - - + +
234 VAL* 3.8 30.3 - - + -
754 ARG* 3.6 16.0 + - + +
774 ILE* 3.4 35.9 - - + -
1134 VAL* 3.8 10.5 - - + +
1574 ILE* 3.1 32.8 + - + +
1584 LYS 3.7 3.4 - - - +
1604 ALA* 1.3 73.7 - - - +
1624 ARG* 1.3 59.7 + - - +
1634 ASP 3.6 0.2 - - - +
10164 K 2.7 19.9 - - - -
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Residues in contact with ARG 162 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164 GLU* 2.5 46.3 + - - +
194 ARG* 3.3 47.8 - - - +
754 ARG* 3.4 10.9 + - - +
1584 LYS* 2.9 32.5 + - - +
1594 SER* 3.8 7.0 - - - +
1614 ILE* 1.3 75.6 - - - +
1634 ASP* 1.3 61.1 + - - +
1644 ASN* 3.8 3.8 + - - +
1894 LYS* 4.4 7.3 + - - +
1904 ASP* 5.1 9.3 + - - +
1924 LEU* 3.8 33.9 - - + +
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Residues in contact with ASP 163 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3433 ASP* 4.3 4.9 - - - +
754 ARG* 3.3 2.1 + - - -
1434 LYS* 2.8 28.7 + - - +
1594 SER 3.0 17.0 + - - +
1604 ALA* 3.2 11.9 + - - +
1624 ARG* 1.3 78.1 - - - +
1644 ASN* 1.3 64.7 + - - +
1654 ASN* 2.6 39.6 + - - +
1674 VAL* 4.2 12.6 - - + -
1954 ILE* 4.3 8.7 - - + +
10164 K 2.5 29.5 - - - -
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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