Contacts of the helix formed by residues 1109 - 1116 (chain D) in PDB entry 5YWB
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 PRO1109 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510D LYS* 4.9 2.0 - - - -
1108D ALA* 1.3 90.3 - - + +
1110D MET* 1.3 66.4 + - - +
1111D ARG* 4.3 8.3 - - + +
1112D PHE* 3.0 26.1 + - + +
1113D PHE* 3.3 11.2 + - - -
1322D GLU* 4.1 14.6 - - + -
1323D ALA* 4.1 6.3 - - + +
1325D SER* 3.4 26.7 - - - +
1397D ASP* 5.7 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506D MET* 4.2 6.3 - - - +
507D LYS* 3.6 54.7 - - + +
510D LYS* 4.6 6.2 - - + +
1108D ALA 4.0 0.4 + - - -
1109D PRO* 1.3 73.9 - - - +
1111D ARG* 1.3 61.4 + - - +
1113D PHE* 3.2 21.4 + - + +
1114D GLU* 2.9 35.5 + - + +
1395D MET* 3.6 48.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109D PRO* 3.2 8.8 - - + +
1110D MET* 1.3 77.7 - - - +
1112D PHE* 1.3 54.2 + - - +
1114D GLU* 4.0 13.4 + - - +
1115D THR* 2.7 53.0 + - - +
1354D TYR* 3.6 25.0 - - - +
1355D ASP* 3.6 41.0 + - - +
1358D LEU* 5.1 3.0 - - - +
1395D MET 5.3 2.2 + - - +
1397D ASP* 4.7 15.0 - - - +
2502D ADP 3.3 36.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1105D ILE* 4.5 20.4 - - + -
1108D ALA* 3.6 26.2 - - + -
1109D PRO* 3.0 23.6 + - + +
1111D ARG* 1.3 80.0 - - - +
1113D PHE* 1.3 68.5 + + - +
1115D THR* 4.4 4.7 - - + -
1116D THR* 2.8 58.7 + - + -
1121D ILE* 4.8 12.1 - - + -
1318D LEU* 5.4 6.5 - - + -
1321D THR* 3.6 37.5 - - + -
1322D GLU* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503D LEU* 4.0 8.5 - - + -
506D MET* 3.6 48.0 - - + -
510D LYS* 4.3 2.0 - - + -
828D ILE* 4.9 1.4 - - - +
1105D ILE* 3.1 48.5 - - + -
1108D ALA* 3.7 20.9 - - + -
1109D PRO 3.3 17.4 + - - -
1110D MET* 3.2 23.8 + - + +
1112D PHE* 1.3 86.0 - + - +
1114D GLU* 1.3 62.6 + - - +
1116D THR* 3.4 16.6 - - - +
1118D LEU* 3.9 26.9 - - + +
1121D ILE* 5.0 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828D ILE* 3.3 49.4 - - + +
829D ASN* 4.5 10.7 + - - +
830D LEU 5.2 1.6 - - - +
1110D MET* 2.9 24.6 + - + +
1111D ARG* 4.1 12.8 + - - +
1113D PHE* 1.3 74.8 - - - +
1115D THR* 1.3 67.7 + - - +
1116D THR 3.8 2.1 - - - +
2502D ADP 2.5 40.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111D ARG* 2.7 47.1 + - - +
1112D PHE* 4.0 6.1 - - + -
1113D PHE 3.4 0.2 - - - -
1114D GLU* 1.3 79.8 - - - +
1116D THR* 1.3 66.0 + - - +
1117D PRO* 3.5 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828D ILE* 4.6 2.6 - - - +
1112D PHE* 2.8 42.9 + - + -
1113D PHE 3.4 13.6 - - - +
1114D GLU 3.8 2.8 - - - +
1115D THR* 1.3 78.8 - - - +
1117D PRO* 1.3 78.5 - - + +
1118D LEU* 3.3 6.4 + - - +
1120D SER* 4.1 4.3 - - - +
1121D ILE* 3.7 34.3 - - + -
1318D LEU* 6.5 0.2 - - + -
----------------------------------------------------------
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