Contacts of the strand formed by residues 155 - 160 (chain 3) in PDB entry 1AFB
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 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1473 ILE* 5.3 1.1 - - + -
1513 ALA* 3.8 15.7 - - + -
1533 THR 3.2 0.6 + - - +
1543 SER* 1.3 76.9 - - - +
1563 PHE* 1.3 65.1 + - - +
2023 THR* 3.0 7.5 - - - -
2033 ILE* 2.9 39.0 + - + +
2183 HIS* 4.2 0.4 - - - -
2193 THR* 3.4 19.5 - - - +
2213 VAL* 3.7 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193 MET 3.2 27.4 - - - -
1213 PHE* 3.3 40.6 - + + -
1243 VAL* 4.0 12.7 - - + +
1353 VAL* 3.7 13.0 - - + +
1363 ALA* 4.3 6.4 - - - +
1473 ILE* 5.8 0.2 - - - +
1553 ALA* 1.3 78.9 - - - +
1573 LEU* 1.3 64.2 + - - +
2003 CYS* 3.7 21.1 - - + -
2013 VAL 3.3 13.5 - - - -
2023 THR* 3.7 4.7 - - + -
2123 ILE* 3.6 23.6 - - + -
2133 SER 3.9 7.0 - - - -
2143 CYS 4.1 1.3 - - - -
2163 ALA 3.1 21.5 - - - -
2183 HIS* 3.6 24.7 - + + -
2193 THR 3.3 9.6 + - - +
2213 VAL* 4.8 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1213 PHE* 3.4 15.6 - - - -
1353 VAL* 3.6 3.6 - - - -
1363 ALA 3.2 13.5 - - - +
1383 PRO* 3.9 20.9 - - + -
1473 ILE* 4.3 10.8 - - + -
1563 PHE* 1.3 80.8 - - - +
1583 GLY* 1.3 59.8 + - - +
1593 ILE* 2.9 26.4 + - + +
2013 VAL* 2.8 32.3 + - + +
2033 ILE* 3.9 30.7 - - + +
2093 TRP* 3.7 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 158 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1213 PHE* 4.5 0.4 - - - -
1353 VAL* 3.4 17.5 - - - +
1363 ALA 2.9 14.1 + - - -
1373 ILE* 3.4 20.6 - - - +
1573 LEU* 1.3 67.3 - - - +
1593 ILE* 1.3 61.8 + - - +
1703 TYR* 3.4 0.3 - - - -
1713 VAL* 2.8 45.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1373 ILE* 4.6 1.3 - - + -
1383 PRO* 4.3 9.0 - - + -
1573 LEU* 2.9 26.4 + - + +
1583 GLY* 1.3 80.4 - - - +
1603 THR* 1.3 70.8 + - - +
1683 PHE* 3.8 22.4 - - + -
1693 MET 3.2 11.9 - - - +
1703 TYR* 3.8 19.7 - - + -
1713 VAL* 3.9 1.2 - - - +
1763 LEU* 3.6 25.6 - - + -
2013 VAL* 3.5 31.7 + - + +
2093 TRP* 3.7 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 160 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1213 PHE* 3.6 34.3 - - + -
1593 ILE* 1.3 82.1 - - - +
1613 ASP* 1.3 58.5 + - - +
1623 GLU* 3.5 24.5 + - - +
1633 VAL* 5.0 2.8 + - - +
1673 GLN 3.9 0.5 - - - +
1683 PHE* 3.6 7.4 - - - -
1693 MET* 2.8 32.6 + - - +
1713 VAL* 4.1 9.2 - - + +
1993 ASP 3.0 17.7 - - - +
2003 CYS* 4.0 9.2 - - - -
----------------------------------------------------------
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