Contacts of the helix formed by residues 140 - 156 (chain 3) 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 ALA 140 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1353 ASN* 5.1 7.9 - - + -
1373 ILE* 3.2 22.5 + - + +
1393 GLY* 1.3 78.1 - - - +
1413 GLN* 1.3 62.9 + - - +
1423 VAL 3.2 0.9 + - - -
1433 PRO* 3.4 4.7 - - - +
1443 LEU* 3.3 21.8 + - + +
1743 GLN* 3.3 14.7 - - - +
914 ASP* 3.9 20.9 - - - +
924 GLN* 3.4 7.6 + - - +
964 SER* 4.0 15.9 - - - +
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Residues in contact with GLN 141 (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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863 ILE* 3.7 13.4 - - + +
873 THR* 3.6 13.0 - - - +
883 ALA* 3.2 30.2 - - - +
1353 ASN* 3.4 26.3 - - - +
1373 ILE 4.0 3.8 - - - +
1393 GLY* 3.2 13.5 + - - +
1403 ALA* 1.3 83.9 + - - +
1423 VAL* 1.3 62.5 + - - +
1433 PRO 3.5 0.2 - - - -
1443 LEU* 3.6 12.0 - - - +
1453 GLY* 2.7 22.7 + - - -
1633 THR* 3.4 5.8 - - + +
1643 LEU 2.9 28.7 + - - +
1653 TYR* 3.7 13.1 - - - +
1693 ALA* 5.9 0.8 - - - +
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Residues in contact with VAL 142 (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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1393 GLY* 3.1 10.1 + - - +
1413 GLN* 1.3 77.6 - - - +
1433 PRO* 1.3 69.8 - - + +
1453 GLY* 3.1 2.4 + - - -
1463 ALA* 2.8 27.4 + - - +
1633 THR* 3.4 17.1 - - + +
1653 TYR* 3.9 27.6 - - + -
1753 ILE* 3.6 40.8 - - + +
1783 ALA* 4.2 9.6 - - + -
1793 TYR* 5.5 0.2 - - + -
1913 PHE* 4.1 20.4 - - + -
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Residues in contact with PRO 143 (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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1393 GLY 3.1 15.0 - - - +
1403 ALA 3.4 4.3 - - - +
1423 VAL* 1.3 92.7 - - + +
1443 LEU* 1.3 57.5 + - - +
1463 ALA* 2.9 3.9 + - + +
1473 GLY* 2.7 27.2 + - - -
1743 GLN* 3.4 40.6 - - + +
1783 ALA* 4.1 10.8 - - + -
614 GLY* 3.7 26.9 - - - +
644 GLY* 3.8 14.4 - - - -
654 ILE* 3.7 6.1 - - + +
924 GLN* 4.0 2.5 - - - +
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Residues in contact with LEU 144 (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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863 ILE* 3.7 15.9 - - + -
1353 ASN* 3.6 25.4 - - - +
1403 ALA 3.3 16.2 + - - +
1413 GLN* 3.6 7.2 - - - +
1423 VAL 3.2 0.8 - - - -
1433 PRO* 1.3 77.0 - - - +
1453 GLY* 1.3 63.9 + - - +
1473 GLY* 3.0 2.4 + - - -
1483 ILE* 2.9 28.9 + - + +
644 GLY* 3.7 19.3 - - - +
674 VAL* 4.0 13.7 - - + -
684 GLY* 3.6 8.7 - - - +
714 MET* 4.2 19.7 - - + -
924 GLN* 4.0 18.4 - - - +
964 SER* 4.0 20.2 - - - +
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Residues in contact with GLY 145 (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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863 ILE* 3.8 10.7 - - - +
1413 GLN 2.7 18.8 + - - -
1423 VAL 3.1 1.8 + - - -
1443 LEU* 1.3 73.1 - - - +
1463 ALA* 1.3 62.5 + - - +
1483 ILE* 3.2 8.4 + - - +
1493 ALA* 2.8 23.2 + - - +
1613 CYS* 4.0 3.1 - - - -
1633 THR* 3.3 25.3 + - - -
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Residues in contact with ALA 146 (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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1423 VAL 2.8 17.2 + - - +
1433 PRO 2.9 6.0 + - - +
1453 GLY* 1.3 72.6 - - - +
1473 GLY* 1.3 61.5 + - - +
1493 ALA* 3.2 9.1 - - - +
1503 LEU* 3.0 19.4 + - - +
1633 THR* 4.2 0.2 + - - -
1783 ALA* 4.0 20.4 - - + +
1823 ALA* 4.9 0.2 - - + -
1873 LEU* 3.6 15.8 - - + +
1893 CYS* 4.3 5.1 - - - -
1913 PHE* 4.3 11.7 - - + -
654 ILE* 4.0 18.9 - - + +
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Residues in contact with GLY 147 (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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1433 PRO 2.7 11.5 + - - -
1443 LEU 3.4 4.7 - - - -
1453 GLY 2.9 0.2 - - - -
1463 ALA* 1.3 78.1 - - - +
1483 ILE* 1.3 61.0 + - - +
1503 LEU* 3.0 15.8 + - - +
1513 ALA* 3.1 9.5 + - - +
654 ILE* 3.2 34.7 - - - +
684 GLY* 4.1 0.2 - - - -
694 ALA* 3.6 13.0 + - - -
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Residues in contact with ILE 148 (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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843 HIS* 3.6 38.8 - - + +
863 ILE* 4.3 9.0 - - + -
1323 TYR* 3.3 43.7 - - + -
1443 LEU* 2.9 26.2 + - + +
1453 GLY* 3.7 9.4 - - - +
1473 GLY* 1.3 73.7 - - - +
1493 ALA* 1.3 65.1 + - - +
1513 ALA* 3.2 9.9 + - - +
1523 CYS* 3.3 12.9 + - - -
1613 CYS* 3.7 8.1 - - + -
684 GLY* 3.6 21.1 - - - +
714 MET* 5.6 1.6 - - + -
724 ALA* 4.2 14.1 - - + -
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Residues in contact with ALA 149 (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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1453 GLY 2.8 11.7 + - - +
1463 ALA* 3.2 11.7 - - - +
1483 ILE* 1.3 77.0 - - - +
1503 LEU* 1.3 64.4 + - - +
1523 CYS* 3.0 23.0 + - - +
1533 LYS 3.2 4.2 + - - -
1613 CYS* 4.0 11.4 - - + +
1873 LEU* 4.2 3.1 - - + -
1883 PRO* 3.6 16.2 - - + +
1893 CYS* 3.3 37.9 - - + -
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Residues in contact with LEU 150 (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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1463 ALA 3.0 12.0 + - - +
1473 GLY* 3.0 9.9 + - - +
1493 ALA* 1.3 75.9 - - - +
1513 ALA* 1.3 64.6 + - - +
1533 LYS* 3.1 17.6 + - + +
1543 TYR* 2.9 31.0 + - + +
1853 TRP* 4.6 13.7 - - + -
1873 LEU* 3.5 29.8 - - + +
244 PHE* 4.2 29.6 - - + -
264 LEU* 5.5 0.7 - - + -
504 LYS 6.2 0.2 - - - +
534 ILE* 4.6 15.3 - - + -
654 ILE* 4.3 20.2 - - + -
694 ALA* 4.8 3.1 - - + -
744 LEU* 6.0 0.4 - - + -
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Residues in contact with ALA 151 (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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1473 GLY 3.1 9.3 + - - +
1483 ILE 3.3 10.5 - - - +
1493 ALA 3.1 0.4 - - - -
1503 LEU* 1.3 77.8 - - - +
1523 CYS* 1.3 62.6 + - - +
1543 TYR* 3.1 4.3 - - - +
1553 ASN* 2.9 31.9 + - - +
694 ALA* 4.3 6.3 - - - +
724 ALA* 3.8 26.0 - - + +
744 LEU* 3.7 27.4 - - + -
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Residues in contact with CYS 152 (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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843 HIS* 3.9 19.7 - - - -
1483 ILE 3.3 12.8 + - - -
1493 ALA* 3.0 11.3 + - - +
1513 ALA* 1.3 71.4 - - - +
1533 LYS* 1.3 70.8 + - - +
1553 ASN* 2.7 21.0 + - - +
1563 GLY* 3.1 9.5 + - - -
1573 LYS* 4.3 4.0 + - - +
1583 ASP 6.0 0.4 - - - -
1593 GLU* 3.5 51.1 - - + +
1603 VAL 4.4 6.7 - - - -
1613 CYS* 5.1 0.2 - - - -
1883 PRO* 4.1 4.5 - - + -
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Residues in contact with LYS 153 (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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1493 ALA 3.2 2.6 + - - +
1503 LEU* 3.1 19.0 + - + +
1523 CYS* 1.3 76.7 - - - +
1543 TYR* 1.3 58.5 + - - +
1563 GLY* 3.0 21.3 + - - +
1853 TRP* 3.4 41.2 + - - +
1863 LYS 4.2 7.6 - - - +
1873 LEU* 4.3 7.6 - - + -
1883 PRO* 4.2 19.8 - - + +
504 LYS* 5.1 6.8 + - - +
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Residues in contact with TYR 154 (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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1503 LEU* 2.9 22.4 + - + +
1513 ALA* 3.1 13.0 - - - +
1533 LYS* 1.3 79.4 - - - +
1553 ASN* 1.3 64.1 + - - +
1563 GLY 3.4 0.2 - - - -
214 GLU* 2.3 38.6 + - + +
224 LYS* 4.1 3.5 + - + -
234 VAL 3.8 4.3 + - - -
244 PHE* 4.0 20.4 - + + +
504 LYS* 2.9 73.6 + - + +
514 ARG* 3.0 21.1 + - - -
744 LEU* 3.6 30.1 - - + -
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Residues in contact with ASN 155 (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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1513 ALA* 2.9 22.6 + - - +
1523 CYS* 2.7 15.9 + - - +
1543 TYR* 1.3 87.6 - - - +
1563 GLY* 1.3 66.6 + - - +
1573 LYS* 3.1 23.6 + - + +
1593 GLU* 5.7 3.0 + - - -
224 LYS* 5.4 4.9 - - - +
504 LYS* 5.6 0.2 - - - -
724 ALA 5.3 4.9 + - - -
744 LEU* 4.0 14.8 - - - +
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Residues in contact with GLY 156 (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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1523 CYS 3.1 4.2 + - - -
1533 LYS* 3.0 16.5 + - - -
1543 TYR 3.4 1.0 + - - -
1553 ASN* 1.3 78.9 - - - +
1573 LYS* 1.3 66.0 + - - +
1583 ASP* 3.5 3.8 - - - -
504 LYS* 5.6 0.2 - - - +
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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