Contacts of the helix formed by residues 157 - 168 (chain 3) in PDB entry 5KZ5
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 LYS 157 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1553 GLU 3.7 1.0 + - - -
1563 HIS* 1.3 71.3 - - - +
1583 CYS* 1.4 62.1 + - - +
1603 LEU* 3.8 14.0 - - + +
1613 ASP* 3.1 46.3 + - - +
3823 THR* 6.2 6.1 - - + -
3833 SER 5.5 1.8 - - - +
3843 ALA* 3.6 25.3 - - + +
3873 GLU* 3.1 34.6 + - - +
3883 PRO 3.7 19.3 - - - -
3893 SER* 3.7 28.3 - - - +
3903 TYR* 5.1 2.5 - - - +
3913 VAL* 5.0 4.4 - - + +
449O LEU* 3.8 13.6 - - + +
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Residues in contact with CYS 158 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1283 THR* 5.3 8.1 - - - -
1323 ASN* 3.5 23.7 + - - +
1563 HIS* 4.9 4.0 - - + -
1573 LYS* 1.4 78.1 - - - +
1593 VAL* 1.3 59.8 + - + +
1613 ASP* 3.7 0.7 + - - -
1623 SER* 3.0 25.8 + - - -
1054 ARG* 5.9 3.1 - - - -
1084 GLN* 3.8 16.6 - - - +
1094 GLN* 4.9 6.2 - - + +
447O ILE 4.4 0.9 - - - +
449O LEU* 3.6 35.0 - - - +
450O LYS 4.6 7.9 - - - -
452O ILE* 5.7 4.7 - - - -
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Residues in contact with VAL 159 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1313 ASN* 3.8 13.7 - - + +
1323 ASN* 3.3 40.2 - - - +
1353 ILE* 3.6 14.8 - - + -
1363 LYS* 3.1 29.9 + - + +
1553 GLU* 3.5 29.2 - - + +
1563 HIS* 3.0 21.5 + - + +
1583 CYS* 1.3 71.2 - - - +
1603 LEU* 1.4 63.9 + - - +
1623 SER* 3.2 2.8 + - - -
1633 CYS* 3.1 20.6 + - - -
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Residues in contact with LEU 160 (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 THR 4.1 10.1 - - - +
1533 GLN* 4.2 16.8 - - + +
1553 GLU* 3.9 25.8 - - + +
1563 HIS 2.9 15.6 + - - +
1573 LYS* 3.8 16.6 - - + +
1583 CYS 3.4 0.2 - - - -
1593 VAL* 1.4 76.5 - - - +
1613 ASP* 1.4 59.9 + - - +
1633 CYS* 3.1 11.8 - - - -
1643 ARG* 3.4 3.5 + - + +
1753 TYR* 3.0 55.7 + - + +
3873 GLU* 4.5 11.7 - - - +
3903 TYR* 4.1 27.8 - - + +
3913 VAL* 5.8 2.0 - - + -
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Residues in contact with ASP 161 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1573 LYS* 3.1 36.7 + - - +
1603 LEU* 1.4 80.1 - - - +
1623 SER* 1.4 62.9 + - - +
1643 ARG* 3.4 4.1 + - - +
1653 SER 3.1 7.4 + - - -
3873 GLU* 3.2 24.2 - - - +
3134 GLN* 3.4 16.7 + - - +
444O GLN 3.8 10.6 - - - +
446O GLY 2.7 26.3 - - - +
447O ILE 3.3 16.6 - - - +
449O LEU* 3.2 19.2 - - + +
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Residues in contact with SER 162 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1323 ASN* 3.9 9.9 + - - -
1363 LYS* 3.7 26.9 - - - +
1583 CYS 3.0 14.6 + - - -
1593 VAL* 3.2 10.6 + - - -
1613 ASP* 1.4 78.2 - - - +
1633 CYS* 1.4 60.2 + - - +
1653 SER* 3.3 20.2 + - - -
1663 LEU* 3.7 10.4 + - - +
1094 GLN* 5.1 4.3 + - - +
1124 SER* 5.2 1.3 + - - -
447O ILE* 3.6 18.2 + - - +
448O ASP* 5.1 1.9 + - - -
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Residues in contact with CYS 163 (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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1363 LYS* 3.7 19.0 - - - +
1493 LEU* 6.3 0.7 - - + -
1513 THR* 3.9 19.3 - - + -
1553 GLU* 3.5 22.2 - - - -
1593 VAL 3.1 8.4 + - - -
1603 LEU* 3.1 24.7 - - - -
1623 SER* 1.4 74.0 - - - +
1643 ARG* 1.3 60.0 + - - +
1663 LEU* 3.3 21.2 + - + +
1673 GLU 3.4 8.5 + - - -
1733 VAL* 3.4 15.5 - - + +
1753 TYR* 3.6 22.2 - - - -
1993 LEU* 5.8 0.9 - - + -
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Residues in contact with ARG 164 (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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1603 LEU* 3.4 8.8 + - + +
1613 ASP* 3.4 11.4 + - - +
1623 SER 3.3 0.2 - - - -
1633 CYS* 1.3 75.8 - - - +
1653 SER* 1.4 57.5 + - - +
1673 GLU* 3.2 31.6 + - - +
1683 ALA* 2.9 41.4 + - - +
1753 TYR* 3.3 27.4 - - + +
441O GLU* 4.7 7.7 + - - +
444O GLN* 3.2 52.0 + - + +
445O ASP* 3.2 29.2 + - - +
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Residues in contact with SER 165 (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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1613 ASP 3.1 6.6 + - - -
1623 SER 3.4 12.1 - - - -
1633 CYS 3.3 0.4 - - - -
1643 ARG* 1.4 76.2 - - - +
1663 LEU* 1.4 58.3 + - - +
1683 ALA* 3.4 3.2 + - - +
1693 GLU* 3.1 45.2 + - - +
3154 MET* 5.7 2.6 - - - +
445O ASP 3.5 6.2 + - - -
446O GLY 3.4 18.2 + - - -
447O ILE* 3.5 32.1 - - - +
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Residues in contact with LEU 166 (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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1363 LYS* 5.1 7.9 - - + -
1393 ALA* 5.0 5.6 - - + -
1403 ARG* 3.9 38.6 - - - +
1493 LEU* 4.4 22.2 - - + -
1623 SER 3.9 10.8 - - - +
1633 CYS* 3.3 18.1 + - + +
1643 ARG 3.3 0.4 - - - -
1653 SER* 1.4 76.3 - - - +
1673 GLU* 1.4 59.4 + - - +
1693 GLU* 3.3 15.3 + - - +
1703 GLY 3.6 0.3 + - - -
1713 PHE* 3.1 40.7 + - + +
1733 VAL* 4.1 6.1 - - + -
1993 LEU* 6.4 0.4 - - + -
2414 PRO* 3.7 27.1 - - + -
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Residues in contact with GLU 167 (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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1633 CYS 3.4 2.4 + - - +
1643 ARG* 3.2 42.5 + - - +
1663 LEU* 1.4 79.4 - - - +
1683 ALA* 1.3 55.9 + - - +
1703 GLY* 3.2 15.2 + - - -
1713 PHE 3.2 22.6 - - - +
1723 GLN* 4.9 0.4 - - - -
1733 VAL* 3.1 44.5 - - + +
1753 TYR* 4.0 14.2 - - - -
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Residues in contact with ALA 168 (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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1643 ARG* 2.9 22.3 + - - +
1653 SER 3.4 4.7 + - - +
1673 GLU* 1.3 71.2 - - - +
1693 GLU* 1.3 58.0 + - + +
1703 GLY* 3.1 8.9 + - - -
3164 GLU* 4.0 32.4 - - + +
3194 HIS* 4.9 0.5 + - - -
3204 LYS* 4.3 8.5 + - - -
445O ASP* 3.4 30.7 - - - +
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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