Contacts of the helix formed by residues 173 - 185 (chain 2) 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 GLY 173 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442 THR 3.9 3.8 + - - -
452 THR* 3.7 18.8 - - - +
1712 GLY* 3.1 1.4 - - - -
1722 SER* 1.3 78.6 - - - +
1742 SER* 1.3 62.1 + - - +
1752 LEU* 3.3 2.7 - - - -
1762 ALA* 3.1 17.5 + - - +
1772 ALA* 3.2 11.3 + - - +
2052 GLY* 5.1 3.0 - - - -
2092 ASP* 3.3 26.1 - - - +
2122 SER* 4.9 2.7 + - - -
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Residues in contact with SER 174 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591 TYR* 4.8 9.3 + - - -
452 THR* 4.9 0.7 - - - -
1692 THR* 3.4 34.2 + - - +
1702 MET* 3.7 11.0 - - - -
1712 GLY* 3.3 29.1 + - - +
1722 SER 3.3 3.4 - - - -
1732 GLY* 1.3 74.4 - - - +
1752 LEU* 1.3 62.2 + - - +
1772 ALA* 3.4 1.9 + - - +
1782 MET* 3.1 24.5 + - - +
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Residues in contact with LEU 175 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591 TYR* 3.8 36.1 - - + -
1722 SER 4.8 3.2 + - - +
1732 GLY 3.1 1.2 + - - -
1742 SER* 1.3 79.1 - - - +
1762 ALA* 1.4 61.5 + - - +
1782 MET* 3.5 6.2 - - + +
1792 ALA* 3.4 19.9 + - - +
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Residues in contact with ALA 176 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1732 GLY 3.1 10.0 + - - +
1752 LEU* 1.4 76.2 - - - +
1772 ALA* 1.4 64.7 + - - +
1792 ALA* 3.3 14.6 + - - +
1802 VAL* 3.5 15.9 + - - +
2042 ALA* 4.8 4.0 - - - +
2052 GLY* 4.8 2.0 - - - -
2082 ASN* 3.8 28.2 + - + +
2092 ASP* 3.6 21.3 + - - +
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Residues in contact with ALA 177 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452 THR* 4.4 10.5 - - + -
1692 THR* 4.2 13.0 - - + +
1732 GLY 3.2 9.5 + - - +
1742 SER 4.0 5.2 - - - +
1762 ALA* 1.4 77.6 - - - +
1782 MET* 1.4 58.0 + - - +
1802 VAL* 3.1 12.0 + - - +
1812 PHE* 3.0 49.4 + - + -
2012 ALA* 4.4 17.0 - - + +
2042 ALA* 5.2 2.0 - - - -
2052 GLY* 5.4 3.6 - - - +
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Residues in contact with MET 178 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591 TYR* 3.9 31.4 - - + +
601 ILE* 5.8 9.6 - - + -
631 ARG* 3.3 39.9 - - + +
1672 TYR* 4.6 5.2 - - - -
1692 THR* 4.5 10.5 - - + -
1742 SER 3.1 17.9 + - - +
1752 LEU* 3.5 9.6 - - - +
1762 ALA 3.3 0.2 - - - -
1772 ALA* 1.4 75.0 - - - +
1792 ALA* 1.3 64.6 + - - +
1812 PHE* 3.3 16.6 + - - +
1822 GLU* 3.3 36.7 + - + +
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Residues in contact with ALA 179 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1752 LEU 3.4 7.3 + - - +
1762 ALA* 3.3 12.0 + - - +
1772 ALA 3.3 0.6 - - - -
1782 MET* 1.3 80.2 - - - +
1802 VAL* 1.3 63.4 + - + +
1822 GLU* 3.6 9.4 + - - +
1832 ASP* 3.1 21.5 + - - +
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Residues in contact with VAL 180 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1762 ALA 3.5 15.0 - - - +
1772 ALA* 3.1 7.1 + - - +
1792 ALA* 1.3 74.9 - - + +
1812 PHE* 1.4 60.8 + - - +
1822 GLU 3.5 0.2 + - - -
1832 ASP* 3.5 7.5 + - + +
1842 LYS* 3.0 53.8 + - + +
2002 GLU* 4.3 14.4 - - + +
2012 ALA* 5.7 0.2 - - - -
2042 ALA* 3.8 27.6 - - + -
2082 ASN* 5.5 2.7 - - - +
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Residues in contact with PHE 181 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472 ALA* 3.9 18.2 - - + -
492 VAL* 3.7 26.7 - - + -
1672 TYR* 3.9 32.3 - + + -
1682 VAL 5.1 3.4 - - - -
1692 THR* 4.1 18.4 - - + -
1772 ALA* 3.0 38.7 + - + -
1782 MET* 3.3 13.7 + - - +
1802 VAL* 1.4 62.1 - - - +
1822 GLU* 1.4 55.8 + - - +
1842 LYS* 3.6 23.1 - - - +
1852 PHE* 2.9 36.3 + - + +
1972 LEU* 5.4 1.3 - - + -
1982 VAL* 5.1 1.1 - - + -
2012 ALA* 3.6 28.3 - - + -
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Residues in contact with GLU 182 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631 ARG* 3.6 7.6 + - - -
1672 TYR* 2.7 39.1 + - - -
1782 MET* 3.3 39.8 + - + +
1792 ALA* 3.6 6.7 + - - +
1802 VAL 3.5 0.6 - - - -
1812 PHE* 1.4 64.2 - - - +
1832 ASP* 1.4 65.8 + - - +
1852 PHE* 3.7 14.4 + - - +
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Residues in contact with ASP 183 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1792 ALA 3.1 20.1 - - - +
1802 VAL* 3.5 8.6 + - + +
1822 GLU* 1.4 79.3 - - - +
1842 LYS* 1.4 64.0 + - - +
1852 PHE 3.6 5.4 + - - +
1862 ARG* 3.0 21.5 + - - +
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Residues in contact with LYS 184 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1802 VAL* 3.0 38.6 - - + +
1812 PHE* 3.6 26.6 - - - +
1832 ASP* 1.4 82.6 - - - +
1852 PHE* 1.4 61.8 + - - +
1862 ARG* 3.0 28.4 + - - +
1892 MET* 5.7 0.2 - - - +
1972 LEU* 3.2 63.4 + - + +
2002 GLU* 4.3 15.9 - - - +
2012 ALA* 3.4 25.9 - - - +
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Residues in contact with PHE 185 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492 VAL* 6.4 1.6 - - + -
1662 PRO* 4.3 20.2 - - + -
1672 TYR* 3.5 48.0 - + + +
1812 PHE* 2.9 23.4 + - + +
1822 GLU 3.9 7.0 - - - +
1832 ASP 3.5 7.7 - - - +
1842 LYS* 1.4 57.8 - - - +
1862 ARG* 1.4 77.3 + - - +
1872 PRO* 3.8 30.7 - - + -
1892 MET* 5.7 3.4 - - + -
1972 LEU* 5.4 4.5 - - - -
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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