Contacts of the strand formed by residues 19 - 25 (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 CYS 19 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153 LYS* 4.2 0.2 - - - +
163 GLY* 2.8 35.0 + - - +
173 LYS 3.1 26.9 - - - -
183 ASN* 1.4 76.6 - - - +
203 VAL* 1.3 71.8 + - - +
1123 LEU* 3.5 14.4 - - - +
1193 PRO* 4.8 0.5 - - - +
1583 MET 4.8 0.9 - - - -
1603 PRO* 4.2 23.8 - - - -
1633 LEU* 4.1 11.7 - - + -
1893 ILE* 5.5 0.2 - - + -
1903 ILE 3.2 17.0 - - - +
1913 GLU* 3.3 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143 MET 4.1 4.9 - - - +
153 LYS* 4.0 13.9 - - + -
163 GLY 4.3 2.7 - - - +
193 CYS* 1.3 82.7 - - - +
213 ALA* 1.4 64.6 + - - +
1103 ALA* 5.5 5.2 - - + -
1113 GLY* 4.1 27.1 - - - +
1123 LEU* 4.1 4.5 - - + -
1193 PRO* 3.7 29.2 - - + -
1203 PHE 4.7 4.7 - - - +
1213 ILE* 5.6 6.1 - - + -
1633 LEU* 4.2 3.3 - - - +
1893 ILE* 3.9 0.9 - - - +
1903 ILE* 2.9 54.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133 ALA* 3.2 7.2 - - - +
143 MET 2.9 35.2 + - - +
203 VAL* 1.4 77.0 - - - +
223 ILE* 1.4 60.5 - - - +
1103 ALA* 5.3 2.5 - - - +
1633 LEU* 3.6 24.7 - - + -
1673 ILE* 4.3 15.7 - - + -
1883 HIS 3.5 12.1 - - - +
1893 ILE* 4.0 14.4 - - + -
1903 ILE* 4.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113 VAL* 4.4 8.5 - - + -
123 MET 3.6 9.9 - - - +
133 ALA* 4.1 6.3 - - + +
213 ALA* 1.4 73.5 - - - +
233 ALA* 1.4 66.2 + - - +
423 ILE* 4.0 33.2 - - + +
503 TYR* 4.2 30.1 - - + +
523 GLY* 4.6 11.9 - - - +
1083 VAL* 5.0 7.4 - - + +
1103 ALA* 4.5 16.4 - - + -
1873 VAL* 3.8 0.7 - - - -
1883 HIS* 3.0 40.4 + - + +
1903 ILE* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113 VAL* 3.1 6.9 - - - +
123 MET* 2.7 34.9 + - + +
133 ALA* 4.7 0.2 - - - +
223 ILE* 1.4 75.3 - - - +
243 ALA* 1.3 63.5 + - - +
423 ILE* 5.6 0.7 - - - -
1673 ILE* 4.7 12.8 - - + -
1713 MET* 3.7 24.5 - - + -
1863 ILE* 3.2 12.6 - - - +
1873 VAL* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103 ALA 4.0 7.2 - - - -
113 VAL* 3.9 10.3 - - + +
233 ALA* 1.3 78.3 - - - +
253 ASP* 1.3 65.7 + - - +
413 LYS* 5.6 2.5 - - + +
423 ILE* 3.9 28.5 - - + +
1713 MET* 3.6 9.1 - - - +
1853 VAL* 3.2 7.3 - - - +
1863 ILE* 2.9 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 GLY* 4.0 8.5 - - - -
103 ALA* 3.1 42.4 + - - +
243 ALA* 1.3 83.4 - - - +
263 ARG* 1.4 74.7 + - - +
393 PHE 4.1 1.4 - - - +
403 GLN* 5.4 0.2 - - - -
413 LYS* 4.0 18.5 + - - +
1713 MET* 4.3 6.1 - - - +
1743 ALA* 5.3 5.5 - - - +
1753 VAL* 4.0 10.4 - - - +
1783 ASP* 4.6 9.4 - - - +
1823 GLY* 4.7 11.2 - - - +
1843 GLY 3.5 7.2 - - - +
1853 VAL* 3.0 19.3 - - - +
1863 ILE* 5.0 1.0 - - - +
----------------------------------------------------------
Back to top of page
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