Contacts of the strand formed by residues 215 - 220 (chain O) in PDB entry 3FKS
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 VAL 215 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92O LEU* 3.8 3.8 - - - +
93O GLY* 2.7 29.9 + - - -
182O SER* 3.1 24.2 - - - +
183O VAL 4.8 0.4 - - - -
184O PHE* 4.4 7.2 - - + +
201O MET* 5.2 7.6 - - + -
206O VAL* 3.7 28.5 - - + +
207O ILE* 3.4 26.5 - - + +
213O SER 3.7 1.6 - - - -
214O LYS* 1.3 80.9 - - - +
216O ALA* 1.3 61.5 + - - +
217O LEU* 3.6 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91O THR* 3.8 33.4 - - - +
92O LEU* 3.6 12.4 - - + +
93O GLY 4.2 0.2 - - - +
94O ARG 5.1 0.2 - - - +
96O ILE* 5.4 3.4 - - + -
182O SER 2.9 8.7 + - - -
183O VAL* 3.2 25.4 - - + +
184O PHE 3.0 23.2 + - - -
215O VAL* 1.3 73.6 - - - +
217O LEU* 1.3 62.4 + - - +
218O VAL* 4.9 1.1 - - + -
239O ILE* 4.4 7.4 - - + -
243O PHE* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94O ARG 3.1 16.1 + - - +
95O ILE* 3.4 13.4 - - + -
96O ILE* 2.8 34.7 + - - +
184O PHE* 3.6 19.5 - - + -
197O LEU* 5.4 8.5 - - + -
198O TYR* 3.7 38.1 - - + -
201O MET* 5.6 6.7 - - + -
207O ILE* 4.4 13.0 - - + -
215O VAL* 3.6 31.6 + - + +
216O ALA* 1.3 71.9 - - - +
218O VAL* 1.3 56.6 + - - +
219O PHE* 4.0 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96O ILE* 4.0 17.9 - - + +
97O ASN 4.5 7.9 - - - +
183O VAL* 4.3 14.4 - - + -
184O PHE 2.9 12.4 + - - +
185O THR* 3.2 5.7 - - + +
186O GLY 2.8 25.6 + - - -
216O ALA* 4.6 2.5 - - + +
217O LEU* 1.3 77.7 - - - +
219O PHE* 1.3 66.5 + - - +
232O VAL* 4.1 15.9 - - + +
235O THR* 4.1 13.0 - - + -
236O GLY* 3.6 39.9 - - - +
239O ILE* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 219 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138K ILE* 3.7 38.8 - - + -
95O ILE* 4.4 11.4 - - + -
96O ILE 3.4 18.2 + - - +
97O ASN* 4.4 4.5 - - - +
98O VAL* 4.1 11.6 + - - +
103O ILE* 6.3 0.2 - - + -
184O PHE* 4.6 22.4 - + - -
186O GLY* 4.0 4.0 - - - -
191O THR 5.6 0.2 - - - -
194O GLY* 3.8 30.3 - - - -
197O LEU* 5.1 6.1 - - + -
198O TYR* 6.2 1.1 - - + -
217O LEU* 4.0 27.8 - - + -
218O VAL* 1.3 85.0 - - - +
220O GLY* 1.3 57.2 + - - +
221O GLN* 3.1 34.8 - - + -
224O GLU* 4.5 3.6 - - - +
232O VAL* 3.6 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 220 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98O VAL* 5.6 1.6 - - - -
186O GLY 2.9 14.0 + - - +
187O VAL* 3.6 2.8 - - - -
188O GLY* 2.8 27.2 + - - -
219O PHE* 1.3 74.6 - - - +
221O GLN* 1.3 57.4 + - - +
224O GLU* 3.8 16.6 - - - -
228O ALA* 5.4 2.5 - - - -
229O ARG* 3.7 9.8 - - - +
232O VAL* 3.5 15.9 - - - +
----------------------------------------------------------
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