Contacts of the helix formed by residues 132 - 154 (chain 3) in PDB entry 5IY6
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 LEU 132 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623 SER* 3.3 9.9 + - - -
633 HIS 2.8 11.5 + - - +
643 ILE 3.5 16.4 - - - +
653 GLN 2.7 27.6 - - - +
663 GLU* 3.1 20.6 - - + -
673 SER* 4.1 4.2 - - - +
1283 HIS* 5.5 1.3 - - - +
1303 GLU* 4.4 13.7 - - - +
1313 THR* 1.4 81.4 + - - +
1333 LEU* 1.3 60.9 + - - +
1343 ALA* 3.3 3.4 - - + +
1353 GLY* 3.4 9.1 + - - +
1363 SER* 3.2 15.2 + - - -
1733 GLN* 5.2 1.3 - - + +
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Residues in contact with LEU 133 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623 SER* 3.5 5.2 - - - +
1313 THR* 2.7 49.5 + - + +
1323 LEU* 1.3 71.3 - - - +
1343 ALA* 1.3 84.2 + - + +
1363 SER* 2.6 25.3 + - - +
1373 LEU* 2.8 19.8 + - + +
1633 VAL* 5.9 5.8 - - + -
1673 ALA* 5.8 0.2 - - + -
1683 GLU 5.4 2.9 - - - +
1693 ASP* 4.8 8.3 - - - +
1733 GLN* 3.8 16.2 - - - +
1763 ASN* 4.3 2.9 - - - +
1773 PHE* 2.9 44.6 - - + -
2033 LEU* 4.8 14.6 - - + -
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Residues in contact with ALA 134 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1323 LEU* 3.3 1.9 - - + -
1333 LEU* 1.3 84.5 - - + +
1353 GLY* 1.3 62.2 + - - +
1373 LEU* 3.4 0.8 + - - -
1383 ALA* 3.0 20.4 + - - +
1763 ASN* 2.7 53.8 - - + +
1773 PHE* 3.8 8.1 - - - +
1803 VAL* 3.4 14.0 - - + +
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Residues in contact with GLY 135 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673 SER* 3.7 11.0 - - - -
1323 LEU* 3.4 14.4 + - - +
1333 LEU 3.2 0.4 - - - -
1343 ALA* 1.3 81.2 - - - +
1363 SER* 1.3 60.9 + - - +
1383 ALA* 3.2 8.1 + - - +
1393 LYS* 3.0 27.7 + - - +
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Residues in contact with SER 136 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143 VAL* 4.1 16.5 - - - +
603 ILE* 3.7 14.0 - - - +
623 SER* 2.8 28.4 + - - -
673 SER* 3.0 21.6 - - - -
1323 LEU 3.2 4.9 + - - -
1333 LEU* 2.6 21.5 + - - +
1353 GLY* 1.3 76.4 - - - +
1373 LEU* 1.3 59.2 + - - +
1393 LYS* 3.2 5.0 + - - +
1403 ALA* 2.9 27.1 + - - +
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Residues in contact with LEU 137 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143 VAL* 4.7 3.1 - - + -
1333 LEU* 2.8 16.3 + - + +
1343 ALA 3.8 0.7 - - - +
1363 SER* 1.3 78.2 + - - +
1383 ALA* 1.3 59.4 + - - +
1403 ALA* 3.1 3.2 + - + +
1413 LEU* 2.7 35.6 + - + +
1613 ILE* 4.1 33.4 - - + -
1633 VAL* 4.5 13.9 - - + -
1773 PHE* 2.9 43.3 - - + -
1803 VAL* 2.9 31.6 - - + -
1813 ILE* 4.6 2.7 - - + -
1913 ILE* 4.4 18.4 - - + -
2033 LEU* 5.5 0.4 - - + -
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Residues in contact with ALA 138 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1343 ALA 3.0 14.2 + - - +
1353 GLY* 3.5 11.7 - - - +
1373 LEU* 1.3 78.3 - - - +
1393 LYS* 1.3 63.7 + - + +
1413 LEU* 3.3 4.8 + - - +
1423 CYS* 3.0 23.1 + - - +
1803 VAL* 4.0 12.3 - - + +
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Residues in contact with LYS 139 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603 ILE* 4.0 6.1 - - + -
673 SER* 4.2 21.5 - - - +
693 PHE* 3.0 48.4 - - + -
1353 GLY 3.0 19.3 + - - +
1363 SER* 3.2 6.9 + - - +
1383 ALA* 1.3 76.9 - - + +
1403 ALA* 1.3 63.7 + - - +
1423 CYS* 3.2 8.2 + - + +
1433 TYR* 3.0 22.5 + - - +
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Residues in contact with ALA 140 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123 VAL* 4.1 19.6 - - + +
143 VAL* 5.0 2.0 - - + -
603 ILE* 3.8 15.9 - - + -
1363 SER 2.9 13.4 + - - +
1373 LEU* 3.1 11.0 + - - +
1393 LYS* 1.3 78.2 - - - +
1413 LEU* 1.3 57.2 + - - +
1433 TYR* 3.2 7.3 + - - +
1443 ILE* 2.9 29.2 + - - +
1613 ILE* 4.1 24.0 - - + -
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Residues in contact with LEU 141 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1373 LEU* 2.7 32.9 + - + +
1383 ALA* 4.0 4.5 - - - +
1403 ALA* 1.3 73.5 - - - +
1423 CYS* 1.3 63.7 + - - +
1443 ILE* 2.7 24.8 - - + +
1453 HIS* 2.9 11.1 + - - +
1613 ILE* 3.8 21.8 - - + -
1803 VAL* 3.6 19.5 - - + +
1833 ALA* 3.8 15.5 - - + -
1843 ALA* 3.7 20.9 - - + +
1873 GLN* 2.9 40.3 - - - +
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Residues in contact with CYS 142 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693 PHE* 6.2 0.7 - - + -
1383 ALA 3.0 13.5 + - - +
1393 LYS* 3.2 12.1 + - + +
1413 LEU* 1.3 76.8 - - - +
1433 TYR* 1.3 58.5 + - - +
1453 HIS* 3.2 8.0 + - - +
1463 ARG* 2.9 32.9 + - - +
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Residues in contact with TYR 143 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103 LEU* 3.0 48.9 - - + +
123 VAL* 4.6 2.2 - - + -
563 LYS* 4.9 6.4 - - - +
573 LEU 5.4 1.6 + - - -
583 ALA* 4.4 17.5 - - + -
693 PHE* 5.1 9.2 - - + -
723 PRO* 4.2 30.5 - - + +
1393 LYS 3.0 12.9 + - - +
1403 ALA* 3.2 9.2 + - - +
1423 CYS* 1.3 74.1 - - - +
1443 ILE* 1.3 61.4 + - - +
1463 ARG* 2.7 47.6 - - + +
1473 MET* 2.9 22.3 + - + +
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Residues in contact with ILE 144 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103 LEU* 4.1 5.6 - - + -
123 VAL* 5.6 2.2 - - + -
1403 ALA 2.9 10.4 + - - +
1413 LEU* 2.7 37.5 - - - +
1433 TYR* 1.3 78.4 - - - +
1453 HIS* 1.3 58.6 + - + +
1473 MET* 2.8 40.3 - - + +
1483 ASN* 2.8 24.7 + - + +
1573 MET* 3.2 20.4 - - + -
1593 SER* 2.8 31.2 - - - +
1613 ILE* 6.1 4.0 - - + -
1873 GLN* 4.2 18.4 - - - +
1893 ILE* 4.3 7.4 - - + -
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Residues in contact with HIS 145 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1413 LEU 2.9 13.4 + - - +
1423 CYS* 3.2 8.0 + - - +
1443 ILE* 1.3 85.2 - - + +
1463 ARG* 1.3 59.0 + - - +
1483 ASN* 3.1 10.0 + - + +
1493 LYS* 2.8 36.1 + - + +
1873 GLN* 6.1 0.2 - - - +
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Residues in contact with ARG 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 CYS* 2.9 16.6 + - - +
1433 TYR* 2.7 55.0 - - + +
1453 HIS* 1.3 77.9 - - - +
1473 MET* 1.3 65.8 + - - +
1493 LYS* 2.8 52.9 + - - +
1503 GLU* 3.2 8.0 + - - +
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Residues in contact with MET 147 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103 LEU* 3.7 20.4 - - + -
563 LYS* 4.0 15.3 - - - +
1433 TYR* 2.9 33.3 + - + +
1443 ILE* 2.8 52.3 - - + +
1463 ARG* 1.3 76.5 - - - +
1483 ASN* 1.3 68.3 + - - +
1503 GLU* 3.3 8.5 + - - +
1513 VAL* 2.7 37.1 + - + +
1573 MET* 3.1 35.0 - - + -
1583 LYS 4.9 0.2 - - - +
1593 SER* 3.7 9.4 - - - -
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Residues in contact with ASN 148 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1443 ILE 2.8 13.9 + - - +
1453 HIS* 3.1 11.2 + - + +
1473 MET* 1.3 80.9 - - - +
1493 LYS* 1.3 55.7 + - - +
1513 VAL* 3.1 4.3 + - - +
1523 LYS* 2.6 43.3 + - - +
1553 GLN 5.1 0.8 + - - -
1563 GLU* 5.1 2.0 - - - +
1573 MET* 3.0 53.2 - - + +
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Residues in contact with LYS 149 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1453 HIS* 2.8 20.6 + - + +
1463 ARG* 2.8 58.9 + - - +
1483 ASN* 1.3 76.0 - - - +
1503 GLU* 1.3 93.5 + - - +
1523 LYS* 2.9 34.5 + - - +
1533 ASP* 3.3 8.8 + - - +
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Residues in contact with GLU 150 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1463 ARG* 3.2 14.5 + - - +
1473 MET* 3.6 8.1 - - - +
1483 ASN 3.2 0.4 - - - -
1493 LYS* 1.3 103.1 + - + +
1513 VAL* 1.3 64.6 + - + +
1533 ASP* 3.1 36.9 + - - +
1543 ASN* 3.9 1.2 + - - +
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Residues in contact with VAL 151 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83 LEU* 4.0 27.8 - - + -
563 LYS* 4.7 4.7 - - - +
1473 MET* 2.7 35.8 + - + +
1483 ASN* 3.4 9.4 - - - +
1503 GLU* 1.3 75.4 - - + +
1523 LYS* 1.3 52.7 + - - +
1533 ASP 3.0 2.2 - - - -
1543 ASN* 2.6 29.1 + - + +
1553 GLN* 2.6 50.6 - - + +
1563 GLU* 3.9 10.8 - - - +
1573 MET* 4.0 11.0 - - + +
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Residues in contact with LYS 152 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1483 ASN* 2.6 24.2 + - - +
1493 LYS* 2.9 28.9 + - - +
1513 VAL* 1.3 69.6 - - - +
1533 ASP* 1.3 65.7 + - - +
1543 ASN 2.7 17.5 - - - +
1553 GLN 4.2 5.2 - - - -
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Residues in contact with ASP 153 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1493 LYS 3.9 6.4 - - - +
1503 GLU* 3.2 30.1 - - - +
1523 LYS* 1.3 84.5 + - - +
1543 ASN* 1.3 60.1 + - + +
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Residues in contact with ASN 154 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83 LEU* 5.3 8.8 - - + +
1503 GLU 3.9 1.3 + - - +
1513 VAL* 2.6 20.4 + - + +
1523 LYS 2.7 18.0 - - - +
1533 ASP* 1.3 81.4 - - - +
1553 GLN* 1.3 82.3 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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