Contacts of the strand formed by residues 221 - 229 (chain U) in PDB entry 2FD6
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 GLN 221 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194U CYS* 4.1 0.9 - - - -
220U ASN* 1.3 78.6 - - - +
222U CYS* 1.3 61.8 + - - +
223U LEU 3.3 0.5 + - - -
241U CYS* 3.3 5.7 - - - -
242U ALA* 2.7 44.2 + - - +
243U THR 3.8 11.4 - - - +
244U ALA* 3.9 3.7 - - - +
247U CYS* 3.9 19.3 - - - -
265U CYS* 3.3 23.1 - - - +
266U CYS* 3.8 4.8 + - - -
267U THR* 3.3 20.3 - - - +
402U PG4 2.8 49.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 222 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192U ARG* 4.2 6.7 - - - -
193U GLN 3.5 13.2 - - - -
194U CYS* 2.0 46.7 - - - -
220U ASN 3.8 0.2 + - - -
221U GLN* 1.3 68.7 - - - +
223U LEU* 1.3 60.2 + - - +
224U VAL* 5.1 0.2 - - - +
240U GLY 3.6 1.6 - - - -
264U SER 3.7 0.2 - - - +
265U CYS* 3.3 5.1 - - - -
266U CYS* 2.8 37.4 + - - +
268U LYS 3.5 18.6 - - - -
270U GLY 4.1 2.0 - - - -
271U CYS* 3.6 8.3 - - - -
272U ASN* 3.5 23.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159U PHE* 3.8 20.6 - - + -
221U GLN 3.3 0.6 + - - -
222U CYS* 1.3 73.4 - - - +
224U VAL* 1.3 64.1 + - - +
225U ALA* 3.7 21.8 - - + +
238U VAL 4.0 5.2 - - - +
239U ARG* 3.2 14.7 - - - -
240U GLY 2.8 14.8 + - - +
242U ALA* 3.7 28.3 - - + -
246U MET* 4.1 19.7 - - + +
256U PHE* 4.1 20.6 - - + -
263U VAL* 4.6 7.9 - - + -
264U SER 3.3 6.5 - - - +
265U CYS* 3.9 14.4 - - - -
272U ASN* 2.8 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223U LEU* 1.3 73.0 - - - +
225U ALA* 1.3 60.7 + - - +
226U THR* 4.4 13.7 - - - +
237U MET* 4.5 4.9 - - + -
238U VAL 3.4 5.2 - - - +
239U ARG* 3.3 44.6 - - + +
262U ASP 3.6 1.9 - - - +
263U VAL* 3.3 2.4 - - - -
264U SER* 2.8 50.7 + - - +
266U CYS* 6.4 0.2 - - - -
272U ASN* 3.0 31.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223U LEU* 3.7 15.9 - - + +
224U VAL* 1.3 73.8 - - - +
226U THR* 1.3 61.6 + - - +
237U MET* 3.0 5.5 - - - +
238U VAL* 2.8 38.2 + - + +
256U PHE* 4.6 5.4 - - + -
258U MET* 3.4 26.3 - - + +
261U ILE* 3.9 19.7 - - + -
262U ASP 3.5 4.5 - - - -
263U VAL* 4.0 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 226 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224U VAL* 4.2 7.5 - - - +
225U ALA* 1.3 75.0 + - - +
227U GLY* 1.3 66.4 + - - +
235U SER* 5.6 4.9 - - - -
236U TYR 3.3 12.3 - - - +
237U MET* 3.9 23.3 - - + +
258U MET* 4.2 2.9 - - - -
260U HIS 3.6 0.5 - - - +
261U ILE 3.7 0.2 - - - -
262U ASP* 2.8 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 227 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226U THR* 1.3 79.6 - - - +
228U THR* 1.3 67.3 + - - +
235U SER* 3.3 9.9 - - - -
236U TYR* 2.8 30.6 + - - -
258U MET* 3.8 8.4 - - - -
260U HIS 3.1 16.6 - - - -
262U ASP* 5.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 228 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227U GLY* 1.3 81.0 - - - +
229U HIS* 1.3 59.3 + - - +
232U LYS 4.7 0.2 - - - -
233U ASN* 3.8 45.7 + - - +
234U GLN 3.0 7.0 - - - -
235U SER* 4.9 0.9 - - - -
236U TYR* 4.2 2.2 - - - +
258U MET* 3.3 6.2 - - - +
259U ASN* 2.9 51.5 + - - +
260U HIS* 3.9 11.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 229 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228U THR* 1.3 74.2 - - - +
230U GLU* 1.3 102.1 + - + +
232U LYS 2.9 17.7 - - - +
234U GLN* 3.1 11.0 + - - +
236U TYR* 3.3 56.0 - + + +
257U SER* 3.1 41.7 - - - +
259U ASN* 4.5 2.3 + - - +
----------------------------------------------------------
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