Contacts of the strand formed by residues 304 - 311 (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 304 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150O GLY* 2.9 24.0 - - - +
151O GLY 3.9 0.9 - - - +
152O LYS* 5.7 0.5 - - - +
237O LEU* 6.5 0.2 - - + -
240O ALA* 5.4 5.8 - - + +
244O ARG* 3.5 31.6 - - + +
251O VAL* 3.5 19.3 - - + +
253O LEU* 4.7 13.2 - - + -
296O ILE* 5.0 3.8 - - + -
297O THR* 3.4 34.5 - - - +
298O THR* 2.7 11.6 + - - -
303O SER* 1.3 78.7 + - - +
305O THR* 1.3 70.6 + - - +
306O SER* 3.7 8.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 305 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134O LEU* 4.2 17.2 - - + +
148O ALA 3.8 19.7 - - - +
149O ARG* 3.9 4.2 - - - +
150O GLY 3.0 16.7 + - - +
151O GLY 3.8 6.1 - - - +
153O ILE* 4.3 7.2 - - + -
174O ILE* 6.2 0.7 - - + -
178O HIS* 4.5 10.2 - - - -
251O VAL 2.9 13.2 + - - -
252O LEU* 3.4 19.9 - - + +
253O LEU* 2.6 35.0 + - - +
303O SER* 4.2 0.5 + - - -
304O VAL* 1.3 72.4 - - - +
306O SER* 1.3 56.0 + - - +
307O VAL* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 306 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151O GLY 3.2 6.7 + - - +
152O LYS* 3.4 28.4 - - - +
153O ILE* 2.6 35.8 + - - +
253O LEU* 3.3 11.7 - - - -
255O ILE* 6.1 0.4 - - - -
296O ILE* 3.4 30.3 - - - +
297O THR* 5.9 0.2 - - - -
304O VAL* 3.7 4.7 + - - -
305O THR* 1.3 74.7 - - - +
307O VAL* 1.3 59.7 + - - +
308O GLN* 4.3 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 307 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134O LEU* 6.2 2.0 - - + -
147O TYR* 5.6 4.0 - - + -
153O ILE* 3.3 33.2 - - + -
155O LEU* 4.6 13.7 - - + -
167O ILE* 5.8 3.7 - - + +
170O LEU* 4.2 24.5 - - + -
252O LEU* 4.7 3.8 - - + -
253O LEU 2.7 10.0 + - - +
254O PHE* 3.4 32.6 - - + +
255O ILE 3.1 20.7 + - - +
305O THR* 4.7 9.9 - - + -
306O SER* 1.3 75.5 - - - +
308O GLN* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 308 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152O LYS* 4.0 19.4 - - - +
153O ILE 2.8 15.6 + - - +
154O GLY* 3.0 7.5 - - - -
155O LEU* 3.0 30.3 + - - +
167O ILE* 5.9 0.4 - - - -
255O ILE* 3.6 20.6 - - + +
258O ILE* 3.6 24.9 - - + +
293O GLN* 3.0 41.4 + - - +
296O ILE* 4.2 13.8 - - - +
306O SER* 4.3 11.3 + - - +
307O VAL* 1.3 77.9 - - - +
309O ALA* 1.3 60.6 + - - +
310O VAL* 4.0 2.4 + - + -
325O THR* 4.9 1.0 - - - +
329O LEU* 4.0 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155O LEU* 3.8 13.5 - - + +
163O LYS* 4.8 5.6 - - + -
167O ILE* 3.5 31.2 - - + +
255O ILE 2.9 11.1 + - - +
256O ASP* 3.7 7.2 - - - +
257O ASN* 2.6 40.0 - - - +
258O ILE* 3.0 14.0 + - - +
307O VAL 4.2 0.2 + - - -
308O GLN* 1.3 72.3 - - - +
310O VAL* 1.3 55.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 310 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154O GLY* 5.1 0.2 - - - -
155O LEU 3.0 11.5 + - - +
156O PHE* 3.4 45.3 - - + -
157O GLY 3.4 22.7 + - - +
163O LYS* 3.8 3.0 - - - +
257O ASN* 3.4 4.2 - - - +
258O ILE* 3.6 18.6 - - + -
259O PHE* 4.5 7.2 - - + -
308O GLN* 4.5 9.0 - - + +
309O ALA* 1.3 76.3 - - - +
311O TYR* 1.3 70.4 + - - +
312O VAL* 4.0 0.7 - - - +
321O ALA 5.6 0.2 - - - -
322O PRO* 4.2 7.0 - - + -
325O THR* 3.8 24.9 - - + +
329O LEU* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 311 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301K PHE* 5.8 0.7 - + - -
342K THR* 3.5 37.6 + - - -
343K ASN* 3.8 12.0 + - - -
346K SER* 3.5 24.7 - - - -
157O GLY 3.7 3.1 - - - -
158O GLY 4.2 0.2 - - - -
159O ALA* 3.7 15.9 - - + +
163O LYS* 3.5 20.4 - - - +
189O GLU* 5.3 0.2 - - - -
257O ASN* 3.0 22.8 + - - +
259O PHE* 3.6 41.3 - + + +
260O ARG* 3.9 21.1 - - - -
263O GLN* 5.7 1.1 - - - -
310O VAL* 1.3 79.0 - - - +
312O VAL* 1.3 68.0 + - - +
313O PRO* 3.5 33.7 - - + +
322O PRO* 4.4 2.6 - - - +
----------------------------------------------------------
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