Contacts of the strand formed by residues 112 - 117 (chain F) in PDB entry 1PQ3
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 SER 112 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F HIS* 3.5 21.2 + - - -
25F SER 3.0 15.8 + - - -
26F VAL* 3.5 6.1 - - - +
27F ALA 2.9 22.4 + - - +
110F GLY 3.9 0.2 + - - -
111F TYR* 1.3 70.0 - - - +
113F CYS* 1.3 61.5 + - - +
114F VAL* 4.4 0.8 - - - +
289F LEU 3.1 21.5 + - - -
290F SER* 2.9 12.8 + - - +
323F PHE* 3.9 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 113 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ALA* 3.7 4.9 - - - -
29F ILE* 3.3 36.1 - - - -
103F VAL* 4.0 19.1 - - + -
106F ALA* 4.3 14.4 - - + -
107F VAL* 4.2 16.2 - - + -
111F TYR 3.5 1.2 + - - -
112F SER* 1.3 72.3 - - - +
114F VAL* 1.3 56.3 + - - +
115F THR* 3.9 6.1 + - - -
290F SER 2.7 10.1 + - - -
291F ALA* 2.9 17.2 - - + +
292F LEU 2.6 34.3 + - - +
323F PHE* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F VAL* 3.7 14.1 - - + -
27F ALA 2.7 13.7 + - - +
28F VAL* 3.4 13.3 - - + +
29F ILE 2.9 24.6 + - - +
54F LEU* 5.0 0.9 - - + -
58F LEU* 5.6 0.4 - - + -
113F CYS* 1.3 75.3 - - - +
115F THR* 1.3 61.8 + - - +
116F LEU* 3.9 23.5 + - + -
292F LEU* 3.3 15.0 - - + +
319F ILE* 4.2 20.0 - - + -
323F PHE* 3.3 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F ILE* 3.3 12.6 - - - +
31F ALA* 4.0 22.4 - - + -
99F LEU* 4.4 8.3 - - + -
103F VAL* 4.2 10.9 - - - +
113F CYS* 3.9 7.5 + - - -
114F VAL* 1.3 74.4 - - - +
116F LEU* 1.3 68.7 + - - +
117F GLY* 3.7 1.4 + - - +
122F LEU* 5.1 4.9 - - + -
126F THR* 3.3 26.5 - - + +
292F LEU 2.7 10.3 + - - +
293F ASP* 3.6 16.8 + - + +
294F LEU 3.0 26.0 + - - -
295F VAL* 5.0 1.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F VAL* 4.1 15.0 - - + -
29F ILE 2.9 13.4 + - - +
30F GLY* 4.3 1.8 - - - -
31F ALA* 2.8 30.8 + - - +
46F PRO* 3.4 23.5 - - + +
49F ILE* 4.1 21.8 - - + -
50F ARG* 4.2 20.9 - - + +
54F LEU* 3.6 24.5 - - + -
114F VAL* 3.9 12.6 - - + -
115F THR* 1.3 74.9 - - - +
117F GLY* 1.3 62.7 + - - +
294F LEU* 3.8 4.5 - - + -
319F ILE* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F VAL 3.9 0.3 - - - +
45F GLY* 3.7 11.3 - - - -
46F PRO* 3.4 17.5 - - - +
49F ILE* 5.1 1.4 - - - +
115F THR* 3.7 2.2 + - - -
116F LEU* 1.3 72.9 - - - +
118F GLY* 1.3 71.5 + - - +
122F LEU* 3.6 13.9 - - - -
294F LEU 2.9 18.8 + - - +
295F VAL* 4.1 5.1 - - - +
297F VAL* 4.5 8.0 + - - +
----------------------------------------------------------
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