Contacts of the helix formed by residues 1109 - 1113 (chain F) in PDB entry 2BT4
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 ASN1109 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108F SER* 1.3 72.2 - - - +
1110F ILE* 1.3 61.2 + - - +
1111F HIS* 3.0 29.8 + - - +
1112F GLN* 2.9 35.0 + - - +
1113F ARG* 3.5 11.3 - - - +
1131F ALA* 4.4 1.8 - - - +
1132F GLY* 3.4 11.0 - - - +
1523H SER 3.0 19.3 + - - -
1526H ALA 2.9 27.3 + - - -
1527H ASP 3.7 15.2 + - - +
1529H VAL* 4.1 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1110 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085F HIS* 4.7 5.4 - - + -
1106F HIS* 3.8 34.1 - - + +
1108F SER* 3.1 10.9 + - - +
1109F ASN* 1.3 72.5 + - - +
1111F HIS* 1.3 82.6 + - + +
1112F GLN 3.1 0.2 - - - -
1113F ARG* 3.2 20.2 + - - +
1117F ARG* 3.4 26.3 - - + +
1118F HIS* 3.1 29.5 - - - +
1120F SER* 5.1 5.2 - - - -
1129F VAL* 6.1 1.8 - - + -
1131F ALA* 4.6 4.4 - - + +
1160F CA2 3.9 33.0 - - + +
2418F GOL 4.7 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1111 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109F ASN* 2.9 21.9 + - - +
1110F ILE* 1.3 93.2 - - + +
1112F GLN* 1.3 59.1 + - - +
1113F ARG 3.3 1.6 - - - -
1118F HIS* 3.4 37.9 + - - -
1129F VAL* 6.3 0.6 - - - +
1131F ALA* 4.6 10.1 - - + +
2418F GOL 4.3 1.8 - - - -
1511H HIS* 4.0 29.8 + + - -
1523H SER* 3.9 28.8 + - - +
1524H GLN* 4.7 11.8 - - + +
1529H VAL* 4.6 12.3 - - + +
2411H GOL 3.0 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1112 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109F ASN* 2.9 28.4 + - - +
1111F HIS* 1.3 76.7 - - - +
1113F ARG* 1.3 64.7 + - + +
1523H SER 3.6 10.7 + - - +
1524H GLN* 3.3 29.0 + - - +
1525H ARG* 3.6 9.1 + - - +
1526H ALA 3.0 25.7 + - - -
1527H ASP* 4.8 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1113 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024F GLN* 4.7 8.3 + - - +
1027F ILE* 4.8 16.4 - - - +
1028F TYR* 2.9 31.0 + - - -
1108F SER* 3.3 30.2 + - - -
1109F ASN 3.5 14.8 - - - +
1110F ILE* 3.2 13.6 + - - +
1111F HIS 4.5 0.2 - - - +
1112F GLN* 1.3 86.1 - - + +
1114F GLU* 1.3 78.4 + - - +
1115F PRO* 3.6 2.1 - - - +
1117F ARG* 3.8 38.2 - - + +
1118F HIS* 2.9 18.3 + - - -
1160F CA2 3.9 10.3 + - - +
----------------------------------------------------------
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