Contacts of the strand formed by residues 250 - 255 (chain A) in PDB entry 3CFV
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 LYS 250 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A HIS* 3.7 7.6 + - - -
245A VAL* 3.9 2.3 - - - +
246A ALA 3.6 21.5 + - - -
248A ASP* 2.9 45.3 + - + +
249A GLN* 1.3 80.4 - - - +
251A LEU* 1.3 60.1 + - - +
252A MSE 4.0 19.5 - - + -
267A LEU* 3.9 26.7 - - + +
268A VAL 3.0 12.8 - - - +
269A ASP* 4.0 26.5 + - - +
270A ALA* 4.7 1.3 - - - -
275A VAL* 4.7 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLY* 4.9 0.7 - - - -
244A SER 3.3 18.4 - - - +
245A VAL* 3.7 17.9 - - + -
250A LYS* 1.3 73.4 - - - +
252A MSE 1.3 69.8 + - - +
253A ILE* 5.0 4.2 - - + +
267A LEU* 3.7 0.5 - - - -
268A VAL* 2.8 48.4 + - + +
270A ALA* 4.0 16.2 - - + +
278A LEU* 3.9 18.2 - - + -
288A LEU* 3.8 24.0 - - + -
290A THR* 3.9 14.4 - - + +
300A TRP* 3.9 22.2 - - + +
305A LEU* 4.8 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A GLY* 3.2 28.3 - - - +
225A HIS* 3.6 30.1 - - + +
243A GLY* 3.1 4.3 - - - -
244A SER* 2.8 39.1 + - - +
248A ASP* 4.1 7.4 - - - +
250A LYS* 4.2 12.1 - - + -
251A LEU* 1.3 79.6 - - - +
253A ILE* 1.3 65.0 + - - +
254A TRP* 3.5 34.7 - - - +
264A PRO* 3.8 16.8 - - + -
266A HIS 3.6 7.2 - - - +
267A LEU* 4.0 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU* 4.1 24.0 - - + -
242A PHE 3.5 7.9 - - - +
243A GLY* 4.7 5.2 - - - -
251A LEU* 5.0 11.4 - - + -
252A MSE 1.3 79.3 - - - +
254A TRP* 1.3 65.1 + - - +
264A PRO* 3.2 3.8 - - - +
265A SER* 3.0 28.3 + - - -
266A HIS* 3.2 28.2 + - + +
268A VAL* 5.2 1.6 - - + -
280A PHE* 5.5 3.6 - - + -
288A LEU* 5.2 5.2 - - + -
302A LEU* 3.3 35.2 - - + -
305A LEU* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A VAL* 6.0 1.6 - - + -
222A PHE* 3.4 39.5 - + + -
224A GLY* 3.5 32.8 - - - -
225A HIS* 4.8 4.0 - - - -
240A SER 4.4 0.9 - - - -
241A LEU* 3.4 15.2 - - - +
242A PHE* 2.7 71.9 + + + +
244A SER* 2.7 27.1 + - - -
252A MSE 3.5 30.4 - - - +
253A ILE* 1.3 78.5 - - - +
255A ASP* 1.3 62.5 + - - +
260A THR 4.8 3.6 - - - -
261A THR* 4.2 6.1 - - - -
262A SER 4.3 0.7 - - - -
263A LYS 3.9 12.1 - - - -
264A PRO* 3.7 33.2 - - + -
265A SER* 4.6 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A PHE* 4.9 7.2 - - - -
240A SER* 3.5 6.8 - - - -
241A LEU* 4.5 11.1 - - + +
242A PHE* 5.3 0.2 - - - -
254A TRP* 1.3 79.6 - - - +
256A THR* 1.3 68.7 + - - +
257A ARG* 2.8 50.8 + - - +
258A SER* 3.5 28.6 + - - +
260A THR 5.1 2.3 - - - +
265A SER* 3.8 20.4 + - - +
----------------------------------------------------------
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