Contacts of the strand formed by residues 303 - 309 (chain M) 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 SER 303 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150M GLY* 4.9 10.2 - - - -
244M ARG* 4.1 0.8 - - - +
249M GLN 3.8 5.8 + - - +
250M ASP* 3.4 25.9 + - - +
251M VAL* 3.1 24.8 + - - +
298M THR* 3.5 21.8 - - - +
302M GLY* 1.3 73.5 - - - -
304M VAL* 1.3 65.2 + - - +
305M THR* 5.6 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 304 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150M GLY* 2.8 21.5 - - - +
151M GLY 3.9 1.6 - - - +
152M LYS* 5.7 1.4 - - - +
240M ALA* 5.2 5.6 - - + +
241M GLU* 6.0 0.7 - - + -
244M ARG* 3.6 35.4 - - + +
251M VAL* 3.6 15.5 - - + +
253M LEU* 4.1 26.0 - - + -
296M ILE* 4.1 20.6 - - + -
297M THR* 3.6 17.0 - - - +
298M THR* 3.1 10.9 + - - -
303M SER* 1.3 79.2 - - - +
305M THR* 1.3 65.5 + - - +
306M SER* 3.6 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 305 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134M LEU* 4.5 17.7 - - + -
148M ALA 4.2 7.2 - - - +
149M ARG* 4.4 7.3 - - + +
150M GLY* 2.9 29.4 + - - +
151M GLY 3.7 9.0 - - - +
153M ILE* 4.5 9.4 - - + -
174M ILE* 6.1 1.3 - - + -
178M HIS* 4.4 9.5 + - + -
251M VAL 3.1 13.5 + - - -
252M LEU* 3.3 21.4 - - + +
253M LEU 3.1 25.5 + - - +
303M SER* 4.2 1.8 + - - -
304M VAL* 1.3 70.0 - - - +
306M SER* 1.3 59.7 + - - +
307M VAL* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 306 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151M GLY 3.3 7.9 + - - +
152M LYS* 3.7 11.3 - - - +
153M ILE* 2.7 35.2 + - - +
253M LEU* 3.6 8.6 + - - +
255M ILE* 4.0 5.7 - - - +
296M ILE* 3.5 27.2 - - - +
304M VAL* 3.6 6.1 + - - -
305M THR* 1.3 70.7 - - - +
307M VAL* 1.3 57.8 + - - +
308M GLN* 3.1 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 307 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153M ILE* 3.5 41.3 - - + -
155M LEU* 5.3 3.8 - - + -
167M ILE* 4.7 10.3 - - + +
170M LEU* 3.5 28.9 - - + -
174M ILE* 4.8 8.7 - - + -
252M LEU* 4.7 6.5 - - + -
253M LEU 3.0 9.3 + - - +
254M PHE* 3.8 30.4 - - + +
255M ILE 3.4 18.8 + - - +
305M THR* 4.6 7.2 - - + +
306M SER* 1.3 71.8 - - - +
308M GLN* 1.3 62.6 + - - +
309M ALA 3.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 308 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152M LYS* 3.9 11.3 - - - +
153M ILE 3.0 13.0 + - - +
154M GLY* 3.6 1.4 - - - -
155M LEU* 2.8 27.3 + - - +
255M ILE* 3.4 25.8 - - + +
258M ILE* 3.7 18.9 - - + +
293M GLN* 3.0 42.0 + - - +
296M ILE* 3.4 15.6 - - - +
306M SER* 3.1 24.7 + - - +
307M VAL* 1.3 73.4 - - - +
309M ALA* 1.3 59.6 + - - +
310M VAL* 3.7 4.1 + - + +
325M THR* 5.1 2.6 - - - +
329M LEU* 4.6 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155M LEU* 3.4 18.2 - - + +
163M LYS* 4.8 5.8 - - + -
167M ILE* 4.2 18.6 - - + +
255M ILE 3.0 8.9 + - - +
256M ASP* 3.5 28.0 - - + +
257M ASN* 2.6 31.8 - - - +
258M ILE* 3.3 11.1 + - - +
307M VAL 3.9 1.2 + - - -
308M GLN* 1.3 71.7 - - - +
310M VAL* 1.3 56.2 + - - +
----------------------------------------------------------
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