Contacts of the strand formed by residues 118 - 126 (chain 3) in PDB entry 1ZBE
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 118 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1113 PHE* 5.1 0.4 - - - -
1153 THR 4.2 16.0 + - - +
1163 ASP* 3.9 6.6 + - - +
1173 SER* 1.3 80.1 - - - +
1193 ALA* 1.3 64.7 + - - +
1503 THR* 4.0 20.2 - - + +
1923 HIS* 3.1 5.1 - - - +
1933 GLY* 2.8 39.7 + - - +
1953 ALA* 3.5 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1113 PHE* 4.8 2.0 - - + -
1183 LYS* 1.3 78.8 - - - +
1203 ARG* 1.3 62.2 + - - +
1213 TYR* 3.7 34.7 - - + +
1493 ASP* 3.3 5.4 - - - +
1503 THR* 3.0 36.2 + - - +
1893 GLN* 5.2 0.4 - - - +
1913 THR 3.5 13.5 - - - +
1923 HIS* 3.9 9.2 - - + +
1953 ALA* 4.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193 ALA* 1.3 78.9 - - - +
1213 TYR* 1.3 64.2 + - - +
1473 GLU* 2.7 38.8 + - - +
1483 TRP* 3.5 13.1 - - - +
1493 ASP* 2.9 44.5 + - + +
1893 GLN* 3.7 2.8 - - - -
1903 ILE* 2.9 43.7 + - + -
1913 THR* 3.1 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 121 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663 THR* 3.4 22.5 - - + +
743 LEU* 3.6 25.6 - - + -
1113 PHE* 3.5 25.9 - + + -
1193 ALA* 3.7 22.4 - - + +
1203 ARG* 1.3 80.8 - - - +
1223 MET* 1.3 62.7 + - - +
1473 GLU* 3.1 9.0 - - - +
1483 TRP* 2.9 72.6 + + + -
1493 ASP* 5.7 0.4 - - - -
1503 THR* 4.4 5.6 - - - -
1873 VAL* 5.2 0.9 - - + -
1883 TYR 3.5 15.3 - - - +
1893 GLN* 4.1 12.3 - - + -
1903 ILE* 4.3 2.9 - - - -
1993 THR 5.1 0.2 + - - -
2003 LEU* 3.8 29.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 122 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1213 TYR* 1.3 79.5 - - - +
1233 VAL* 1.3 65.9 + - - +
1243 ALA* 4.1 3.6 - - + -
1373 PRO* 3.7 26.2 - - + +
1403 ALA* 3.6 33.0 - - + -
1413 ALA* 3.6 21.3 - - - +
1453 HIS* 3.8 26.9 - - + -
1463 ALA 3.2 12.1 - - - +
1473 GLU* 3.8 12.3 - - + +
1483 TRP* 3.9 3.8 - - - -
1863 CYS 3.8 0.7 - - - +
1873 VAL* 3.4 3.3 - - - +
1883 TYR* 2.7 40.8 + - + +
1903 ILE* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073 LEU* 4.8 0.7 - - + -
1093 PHE* 3.9 26.5 - - + -
1223 MET* 1.3 74.8 - - - +
1243 ALA* 1.3 65.6 + - - +
1453 HIS* 3.2 4.3 - - - +
1463 ALA* 2.9 39.9 + - + +
1483 TRP* 3.8 12.5 - - + -
1563 PHE* 4.5 0.4 - - + -
1583 PHE* 3.6 47.5 - - + -
1853 VAL* 3.9 19.1 - - + -
1863 CYS 3.3 9.4 - - - +
1873 VAL* 4.5 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1223 MET* 4.1 13.2 - - + -
1233 VAL* 1.3 79.7 - - - +
1253 TYR* 1.3 60.3 + - - +
1263 ILE* 3.6 8.3 - - + +
1403 ALA* 4.2 18.4 - - + +
1433 CYS* 4.6 2.7 - - + -
1443 ILE 3.4 7.2 - - - +
1453 HIS* 3.7 14.6 - - + -
1583 PHE* 5.1 2.7 - - - -
1853 VAL* 3.4 7.2 - - - +
1863 CYS 3.0 33.2 + - - +
1883 TYR* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 125 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2122 GLY* 5.8 0.9 - - - -
793 VAL* 3.8 14.8 - - + -
1243 ALA* 1.3 72.7 - - - +
1263 ILE* 1.3 64.6 + - - +
1273 PRO* 3.2 40.8 - - + +
1283 PRO* 3.8 5.9 - - - +
1433 CYS* 3.4 14.8 - - - +
1443 ILE* 3.1 26.8 + - + +
1583 PHE* 5.0 7.6 - - + -
1603 ILE* 3.9 20.4 - - + -
1613 PRO* 3.8 41.1 + - + -
1633 VAL* 3.9 25.6 + - + -
1823 GLN* 2.8 29.6 + - - +
1843 TRP 3.6 9.0 - - - -
1853 VAL* 4.7 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2152 PRO* 3.9 22.0 - - + -
1243 ALA* 3.6 21.5 - - + +
1253 TYR* 1.3 74.8 - - - +
1273 PRO* 1.3 74.3 - - - +
1303 VAL* 4.5 6.1 - - + -
1333 PRO* 5.1 0.2 - - + -
1343 PRO* 3.9 20.2 - - + -
1403 ALA* 5.2 0.7 - - + -
1433 CYS* 4.3 12.1 - - - -
1833 GLY* 3.3 1.9 - - - -
1843 TRP* 2.8 62.9 + - + +
1863 CYS* 3.4 34.5 - - + -
1883 TYR* 4.7 1.8 - - - +
----------------------------------------------------------
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