Contacts of the strand formed by residues 112 - 116 (chain C) in PDB entry 1FSK
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 THR 112 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLN* 3.6 15.5 + - - +
7C PRO* 2.3 37.2 + - + +
8C GLY 3.6 0.2 - - - -
9C THR 4.1 4.9 - - - -
10C GLU* 3.6 31.9 - - + -
20C LEU* 4.3 18.0 - - + +
21C SER 5.0 0.7 + - - -
92C ALA 3.4 2.1 - - - +
93C VAL* 3.0 7.9 - - - +
94C TYR* 2.9 37.4 + - - -
111C GLY* 1.3 72.6 - - - -
113C LEU* 1.3 68.0 + - - +
114C VAL* 3.5 1.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLY 2.7 19.1 + - - +
9C THR* 3.1 10.8 - - + +
10C GLU 2.7 25.2 + - - +
41C PRO* 5.9 6.7 - - + -
91C SER* 6.2 0.2 - - - -
92C ALA* 3.5 21.8 - - - +
93C VAL* 4.3 9.2 - - + +
111C GLY 4.2 0.2 + - - -
112C THR* 1.3 72.7 - - - +
114C VAL* 1.3 65.9 + - - +
115C THR* 4.2 9.2 - - - +
153C GLU* 3.9 37.0 - - + +
154C PRO* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLU* 3.1 16.2 - - + +
12C VAL* 5.9 1.1 - - + -
18C VAL* 4.3 14.1 - - + -
20C LEU* 3.8 28.5 - - + -
90C ASP* 3.2 26.7 - - + +
91C SER* 3.3 7.3 - - - -
92C ALA 2.8 31.4 + - - +
94C TYR* 3.4 18.4 - - + -
112C THR* 4.4 2.9 - - + -
113C LEU* 1.3 80.3 - - - +
115C THR* 1.3 62.7 + - - +
116C VAL* 5.4 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C THR* 4.5 0.9 - - - +
10C GLU 2.7 10.6 + - - +
11C LEU* 3.2 22.3 - - + +
12C VAL* 2.7 33.4 + - - +
91C SER* 3.3 6.5 - - - +
113C LEU* 4.2 14.9 + - - +
114C VAL* 1.3 76.7 + - - +
116C VAL* 1.3 55.8 + - - +
117C SER* 3.8 5.6 - - - -
151C PHE* 4.1 19.7 - - + -
152C PRO* 4.1 15.6 - - + +
153C GLU* 4.3 6.7 + - + +
180C TYR* 5.2 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C VAL* 3.0 18.6 - - + +
14C PRO* 4.2 9.8 - - + +
18C VAL* 5.3 0.7 - - + -
86C PRO* 3.4 34.3 - - + -
87C THR* 3.1 35.9 - - - +
88C SER* 3.4 10.9 - - - +
90C ASP* 4.6 6.1 - - + -
91C SER* 2.7 32.0 + - - +
114C VAL* 5.4 3.6 - - + -
115C THR* 1.3 72.0 - - - +
117C SER* 1.3 64.5 + - - +
----------------------------------------------------------
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