Contacts of the helix formed by residues 159 - 176 (chain 3) in PDB entry 5LN3
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 ASP 159 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173 LYS* 3.6 15.1 + - - -
193 CYS* 4.8 2.0 - - - -
1573 ASN 5.1 0.5 - - - -
1583 MET* 1.4 80.4 - - - +
1603 PRO* 1.4 64.4 - - + +
1613 ASP* 3.1 8.3 - - - +
1623 HIS* 2.9 35.0 + - + +
1633 LEU* 2.7 33.0 + - - +
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Residues in contact with PRO 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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2492 LYS* 4.1 7.7 + - - +
173 LYS 5.5 1.3 - - - +
183 ASN 5.6 0.7 - - - +
193 CYS* 4.2 14.7 - - - -
1593 ASP* 1.4 87.9 - - + +
1613 ASP* 1.3 72.6 + - - +
1633 LEU* 3.7 10.6 - - + +
1643 PHE* 2.9 27.9 + - - +
1893 ILE* 4.5 12.6 - - + +
1913 GLU* 3.8 30.1 - - + +
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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
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2472 CYS 4.2 5.1 - - - +
2482 GLU* 5.1 7.6 - - + -
2492 LYS* 3.1 46.6 + - + +
1593 ASP* 4.8 4.5 - - + +
1603 PRO* 1.3 88.3 - - - +
1623 HIS* 1.4 67.5 + - + +
1643 PHE* 3.4 5.9 + - - +
1653 GLU 3.4 14.4 + - - -
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Residues in contact with HIS 162 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2442 ARG* 4.9 4.0 + - - +
2462 ARG* 3.2 56.2 + - + +
2472 CYS 4.7 5.4 - - - -
2482 GLU* 6.3 0.2 - - - -
1573 ASN 4.6 5.3 + - - -
1583 MET* 4.2 16.9 - - + -
1593 ASP* 2.9 43.7 + - + +
1613 ASP* 1.4 79.4 - - + +
1633 LEU* 1.3 64.8 + - - +
1643 PHE 3.2 0.2 - - - -
1653 GLU* 3.2 9.7 + - - +
1663 THR* 3.0 25.6 + - - -
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Residues in contact with LEU 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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143 MET* 4.0 17.3 - - + -
153 LYS 3.4 24.5 - - - +
163 GLY* 3.8 24.0 - - - +
193 CYS* 4.1 13.7 - - + -
203 VAL 4.2 2.7 - - - +
213 ALA* 3.6 33.0 - - + +
1583 MET* 4.1 22.6 - - + +
1593 ASP 2.7 20.5 + - - +
1603 PRO* 3.7 7.9 - - + +
1623 HIS* 1.3 71.9 - - - +
1643 PHE* 1.3 62.8 + - - +
1663 THR* 3.2 3.9 + - - -
1673 ILE* 3.1 26.7 + - + +
1893 ILE* 5.3 5.8 - - + -
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Residues in contact with PHE 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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2492 LYS* 3.4 50.9 - - + +
2522 THR* 4.6 6.1 - - + -
2542 VAL* 4.2 15.3 - - + -
1603 PRO 2.9 18.8 + - - +
1613 ASP 3.5 6.7 - - - +
1623 HIS 3.2 0.2 - - - -
1633 LEU* 1.3 74.6 - - - +
1653 GLU* 1.4 60.3 + - - +
1673 ILE* 3.3 10.0 - - + +
1683 SER* 2.8 48.5 + - - -
1873 VAL* 4.0 13.0 - - + -
1893 ILE* 4.1 21.7 - - + +
1983 ARG* 3.8 24.7 - - - -
2003 LEU* 3.7 28.0 - - + -
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Residues in contact with GLU 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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2442 ARG* 4.5 14.6 - - - +
2452 TYR 5.3 2.2 - - - +
2462 ARG* 5.7 0.4 - - - -
2472 CYS* 3.6 34.1 - - - +
2482 GLU 3.8 9.1 - - - +
2492 LYS* 4.9 1.7 - - - +
2512 THR* 3.2 25.7 + - - -
2522 THR* 3.3 15.9 + - - -
1613 ASP 3.4 4.0 + - - +
1623 HIS* 3.2 10.2 + - - +
1643 PHE* 1.4 79.3 - - - +
1663 THR* 1.3 66.4 + - - +
1683 SER* 3.3 4.5 + - - -
1693 GLN* 3.1 32.9 + - + +
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Residues in contact with THR 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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2442 ARG* 3.7 18.7 - - - +
143 MET* 4.6 22.4 - - + -
1533 LEU* 4.2 32.7 - - + +
1543 TRP* 5.0 2.0 - - - +
1583 MET* 3.3 24.5 - - + +
1623 HIS 3.0 12.6 + - - -
1633 LEU* 3.2 9.6 + - + -
1653 GLU* 1.3 79.0 - - - +
1673 ILE* 1.4 64.1 + - - +
1693 GLN* 3.4 3.7 + - - +
1703 ALA* 3.1 20.8 + - + +
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Residues in contact with ILE 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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123 MET* 4.7 10.1 - - + -
133 ALA* 6.0 0.2 - - - -
143 MET* 3.8 35.2 - - + +
213 ALA* 4.3 12.8 - - + -
223 ILE 5.5 0.2 - - - +
233 ALA* 4.7 13.7 - - + -
1633 LEU 3.1 12.2 + - - +
1643 PHE* 3.3 15.9 - - + +
1663 THR* 1.4 74.9 - - - +
1683 SER* 1.3 59.6 + - - +
1703 ALA* 3.1 7.7 + - + +
1713 MET* 2.8 36.2 + - - +
1873 VAL* 3.6 40.8 - - + -
1883 HIS 5.3 0.4 - - - +
1893 ILE* 3.7 17.7 - - + -
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Residues in contact with SER 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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2522 THR* 3.9 27.7 + - - +
1643 PHE* 2.8 51.9 + - - -
1653 GLU 3.7 4.0 - - - -
1663 THR 3.3 0.2 - - - -
1673 ILE* 1.3 78.1 - - - +
1693 GLN* 1.4 59.6 + - - +
1713 MET* 3.3 4.0 + - - +
1723 LEU* 2.9 33.6 + - - +
2003 LEU* 4.3 17.0 - - - +
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Residues in contact with GLN 169 (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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1533 LEU* 5.2 14.1 - - + -
1653 GLU* 3.1 24.3 + - + +
1663 THR* 3.9 3.8 - - - +
1683 SER* 1.4 80.3 - - - +
1703 ALA* 1.4 51.5 + - - +
1723 LEU* 3.1 20.2 + - - +
1733 ASN* 2.8 63.5 + - - +
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Residues in contact with ALA 170 (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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123 MET* 4.9 15.5 - - + -
143 MET* 5.9 4.3 - - + -
1493 MET* 3.4 34.4 - - + +
1533 LEU* 4.3 10.9 - - + +
1663 THR 3.1 14.0 + - - +
1673 ILE* 3.1 13.9 + - + +
1693 GLN* 1.4 73.9 - - - +
1713 MET* 1.4 57.2 - - - +
1733 ASN* 3.4 2.5 + - - -
1743 ALA* 3.0 33.7 + - - +
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Residues in contact with MET 171 (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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103 ALA* 5.2 1.3 - - + +
113 VAL* 4.9 2.7 - - - -
123 MET* 3.6 33.7 - - + +
233 ALA* 3.7 24.0 - - + +
243 ALA* 3.6 20.2 - - - +
253 ASP* 4.3 5.1 - - - +
1463 MET* 5.1 10.5 - - + -
1673 ILE 2.8 21.4 + - - +
1683 SER 3.4 6.5 - - - +
1703 ALA* 1.4 77.3 - - + +
1723 LEU* 1.4 61.7 + - + +
1743 ALA* 3.3 5.4 + - + +
1753 VAL* 3.2 29.4 + - - +
1853 VAL* 3.4 33.9 - - + -
1863 ILE 4.7 0.4 - - - +
1873 VAL* 4.8 0.2 - - + -
2003 LEU* 4.2 21.3 - - + -
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Residues in contact with LEU 172 (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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2522 THR* 4.7 17.5 - - + -
1683 SER* 2.9 22.4 + - - +
1693 GLN* 3.1 24.7 + - - +
1713 MET* 1.4 74.4 - - + +
1733 ASN* 1.3 64.4 + - - +
1743 ALA 3.5 0.2 + - - -
1753 VAL* 3.7 9.5 + - + +
1763 ASP* 2.8 20.4 + - - +
2003 LEU* 6.3 2.5 - - + -
2013 LYS 4.1 11.0 - - - +
2023 ALA* 4.0 29.4 - - + -
2033 ARG 5.3 0.9 - - - +
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Residues in contact with ASN 173 (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 MET* 4.2 15.1 - - - +
1533 LEU* 5.3 3.6 - - - +
1693 GLN* 2.8 46.7 + - - +
1703 ALA* 3.7 8.3 + - - +
1723 LEU* 1.3 78.2 - - - +
1743 ALA* 1.3 61.2 + - - +
1763 ASP* 3.5 21.0 + - - +
1773 ARG* 3.8 16.1 + - - +
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Residues in contact with ALA 174 (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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103 ALA* 5.3 4.9 - - + -
253 ASP* 5.3 5.4 - - - +
1423 CYS* 5.0 2.6 - - - -
1463 MET* 3.5 29.2 - - + -
1703 ALA 3.0 17.2 + - - +
1713 MET* 3.5 13.0 - - + +
1723 LEU 3.3 0.6 - - - -
1733 ASN* 1.3 73.4 - - - +
1753 VAL* 1.3 59.6 + - + +
1773 ARG* 3.1 33.7 + - - +
1783 ASP* 3.2 12.5 - - - +
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Residues in contact with VAL 175 (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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253 ASP* 4.0 17.5 - - - +
1713 MET 3.2 15.6 + - - +
1723 LEU* 4.3 7.0 - - + +
1733 ASN 3.5 0.6 - - - -
1743 ALA* 1.3 74.2 - - - +
1763 ASP* 1.4 60.8 + - - +
1783 ASP* 3.3 25.8 + - - +
1813 SER* 5.6 1.0 - - - -
1823 GLY 3.5 24.0 + - - +
1833 MET* 4.3 28.0 - - + -
1843 GLY 5.2 0.9 - - - +
1853 VAL* 4.2 12.6 - - + -
2023 ALA* 5.2 13.7 - - + -
2033 ARG* 5.2 9.9 - - + -
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Residues in contact with ASP 176 (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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1723 LEU 2.8 25.5 - - - +
1733 ASN* 3.6 11.5 + - - +
1743 ALA 3.3 0.8 - - - -
1753 VAL* 1.4 74.8 - - - +
1773 ARG* 1.4 62.6 + - + +
1783 ASP 3.3 5.6 + - - +
2033 ARG* 4.9 13.5 + - - -
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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
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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