Contacts of the strand formed by residues 205 - 210 (chain B) 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 ILE 205 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA* 4.8 9.6 - - + -
113B PRO* 4.4 27.1 - - + +
115B VAL* 3.6 31.0 - - + +
194B CYS 3.8 0.9 - - - +
196B ALA* 2.9 42.6 + - + +
198B HIS* 5.0 6.7 - - + +
200B THR* 5.4 0.7 - - - +
201B SER* 3.9 20.2 - - - +
203B SER 4.4 0.7 - - - +
204B PRO* 1.3 72.1 - - + +
206B VAL* 1.3 66.2 + - - +
207B LYS* 5.1 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 5.5 0.2 - - - -
149B LYS* 6.3 0.2 - - - -
193B THR* 3.4 24.5 - - - +
194B CYS 3.4 7.0 - - - +
195B GLU* 2.8 30.7 - - - +
204B PRO* 3.6 12.9 + - + +
205B ILE* 1.3 78.4 - - - +
207B LYS* 1.3 85.6 + - - +
208B SER* 5.2 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 3.6 49.8 + - + +
116B SER* 4.8 1.7 - - - +
117B ILE* 3.9 18.0 - - + +
194B CYS* 2.6 41.8 + - + +
205B ILE* 5.1 7.9 - - - -
206B VAL* 1.3 92.9 - - - +
208B SER* 1.3 58.3 + - - +
138C ASN* 5.1 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 3.8 12.7 - - - +
191B SER* 5.7 3.5 - - - -
192B TYR 2.7 22.0 - - - -
193B THR* 3.0 27.1 + - - -
206B VAL* 5.2 2.5 - - - +
207B LYS* 1.3 71.6 - - - +
209B PHE* 1.3 61.2 + - - +
134C ALA 5.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 3.9 19.1 - - + -
119B PRO* 3.3 38.8 - - + -
120B PRO* 4.5 1.8 - - + -
132B VAL* 3.7 22.7 - - + -
186B TYR* 3.3 21.8 - - - -
191B SER* 3.4 4.3 - - - -
192B TYR* 2.9 73.2 + + + +
208B SER* 1.3 76.8 - - - +
210B ASN* 1.3 62.9 + - - +
211B ARG* 3.9 11.2 - - - -
214B CYS* 5.7 4.5 - - - -
132C GLY* 6.4 1.3 - - - -
134C ALA* 5.0 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ASN* 3.7 3.8 - - - +
191B SER* 3.6 21.6 - - - +
209B PHE* 1.3 77.8 - - - +
211B ARG* 1.3 66.2 + - - +
212B ASN* 2.9 39.1 + - - +
213B GLU* 2.8 45.0 + - + +
214B CYS* 3.4 8.5 + - - -
134C ALA* 5.2 4.5 - - - +
----------------------------------------------------------
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