Contacts of the strand formed by residues 155 - 160 (chain 2) in PDB entry 1KZB
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 ALA 155 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1512 ALA* 4.1 7.2 - - + -
1532 ASP 3.2 7.8 + - - +
1542 VAL* 1.3 75.0 - - - +
1562 PHE* 1.3 63.1 + - - +
1572 LEU* 6.0 0.2 - - + -
1972 VAL* 3.1 5.1 - - - -
1982 LEU* 2.6 44.5 + - + +
2132 PHE* 4.4 0.4 - - - -
2142 LEU* 3.3 20.6 - - + +
2162 VAL* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192 MET 3.3 26.7 - - - -
1202 PRO 4.4 0.2 - - - -
1212 LEU* 3.4 46.4 - - + -
1242 ALA* 4.4 5.6 - - + -
1352 VAL* 4.0 4.7 - - + +
1552 ALA* 1.3 75.8 - - - +
1572 LEU* 1.3 65.9 + - - +
1952 CYS* 3.8 24.5 - - + -
1962 VAL 3.4 15.3 - - - -
1972 VAL* 3.6 5.3 - - + +
2072 VAL* 3.8 14.1 - - + -
2082 PRO 4.2 2.5 - - - -
2092 CYS 4.2 4.0 - - - -
2112 ASP 3.3 18.8 - - - -
2132 PHE* 3.5 22.8 - + + +
2142 LEU 2.9 15.1 + - - +
2152 VAL* 4.5 9.0 - - + -
2162 VAL* 3.8 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212 LEU* 4.5 7.3 - - - +
1352 VAL* 3.5 6.7 - - - +
1362 ALA* 3.3 15.7 - - + +
1382 PRO* 4.0 17.3 - - + -
1472 ILE* 4.2 19.5 - - + -
1552 ALA 4.5 0.7 - - - +
1562 PHE* 1.3 83.6 - - - +
1582 GLY* 1.3 60.0 + - - +
1592 ILE* 2.8 24.0 + - + +
1952 CYS* 6.0 0.2 - - - +
1962 VAL* 2.9 25.6 + - + +
1982 LEU* 4.1 29.2 - - + +
2042 TRP* 3.7 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 158 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212 LEU* 5.7 0.2 - - - -
1352 VAL* 3.4 16.3 - - - +
1362 ALA 2.8 14.8 + - - -
1372 THR* 3.0 20.3 + - - -
1572 LEU* 1.3 68.7 - - - +
1592 ILE* 1.3 59.7 + - - +
1702 ASP* 3.1 19.9 - - - -
1712 LEU* 3.2 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212 LEU* 5.1 0.2 - - - +
1372 THR* 3.9 21.1 - - + -
1382 PRO* 4.6 2.9 - - + +
1572 LEU* 2.8 21.3 + - + +
1582 GLY* 1.3 82.8 - - - +
1602 THR* 1.3 74.2 + - - +
1682 PHE* 3.7 26.2 - - + -
1692 GLU 3.3 12.6 - - - +
1712 LEU* 4.0 1.2 - - - +
1762 VAL* 4.4 13.2 - - + -
1952 CYS* 3.9 0.5 - - - +
1962 VAL* 3.5 38.1 + - + -
2042 TRP* 3.6 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 160 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212 LEU* 3.9 5.8 - - + -
1592 ILE* 1.3 82.9 - - - +
1612 ASP* 1.3 58.5 + - - +
1622 GLN* 3.5 32.4 + - - +
1672 VAL 3.8 0.2 - - - +
1682 PHE* 3.5 7.1 - - - -
1692 GLU* 2.9 36.5 + - - +
1702 ASP 5.4 1.0 + - - -
1712 LEU* 3.7 23.0 - - + +
1942 ASN 3.0 16.2 - - - -
1952 CYS* 3.8 20.0 - - - -
----------------------------------------------------------
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