Contacts of the strand formed by residues 221 - 225 (chain X) in PDB entry 2W6C
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 ARG 221 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193X THR* 4.2 9.3 - - - +
194X VAL 3.4 2.0 + - - -
195X THR* 3.3 13.2 - - - +
196X ILE 3.0 22.7 + - - -
219X PHE* 3.5 10.9 - - - -
220X ARG* 1.3 109.3 - - + +
222X ALA* 1.3 62.8 + - - +
317X THR* 4.0 4.0 - - - +
318X GLN* 2.6 49.1 + - - +
476X PHE* 3.1 29.2 + - + -
477X ALA 3.0 27.6 + - - -
478X LYS 3.3 18.4 + - - -
479X THR* 3.5 4.8 + - - +
480X GLY* 3.1 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 222 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195X THR* 4.4 0.4 - - - -
196X ILE* 3.3 9.0 - - + +
206X VAL* 3.4 25.1 - - + -
210X ILE* 3.8 25.8 - - + -
219X PHE* 4.5 1.6 - - + -
221X ARG* 1.3 79.5 - - - +
223X ILE* 1.3 62.9 + - - +
224X LEU* 4.2 2.5 - - + -
317X THR* 5.5 0.9 - - + -
318X GLN 3.6 4.4 + - - -
319X ILE* 3.2 12.7 - - + +
320X LEU 3.1 21.0 + - - -
476X PHE* 3.6 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 223 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112X MET* 4.4 3.6 - - + -
195X THR* 4.0 13.7 - - + -
196X ILE 2.9 6.7 + - - +
197X PHE* 3.2 33.4 - - + -
198X GLY 3.4 4.7 + - - -
206X VAL* 3.9 6.2 - - - +
222X ALA* 1.3 77.9 - - - +
224X LEU* 1.3 66.1 + - - +
225X GLN* 4.0 13.9 - - + +
320X LEU* 3.0 21.8 - - + +
321X LEU* 5.2 0.2 - - - -
473X TRP* 3.5 55.2 - - + +
476X PHE* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198X GLY 4.0 2.7 - - - -
203X GLY* 3.3 25.6 - - - +
206X VAL* 3.8 15.7 - - + -
207X GLY* 3.8 16.6 - - - +
210X ILE* 4.7 4.0 - - + -
222X ALA* 4.2 8.7 - - + +
223X ILE* 1.3 83.0 - - - +
225X GLN* 1.3 64.1 + - - +
227X GLY 3.6 19.1 - - - +
228X SER* 4.4 2.2 - - - -
229X PRO* 4.2 5.8 - - + -
319X ILE* 4.6 11.9 - - + -
320X LEU 3.0 9.0 + - - +
321X LEU* 3.0 38.9 - - + +
322X GLY 3.2 5.2 + - - +
404X LEU* 4.5 1.1 - - + +
407X PHE* 4.1 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 225 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114X TRP* 3.9 15.6 - - - -
197X PHE* 3.6 16.8 - - - -
198X GLY 2.9 16.3 + - - +
199X GLU* 3.1 11.1 - - - +
200X SER 2.8 21.8 + - - -
203X GLY* 4.3 0.7 - - - -
223X ILE* 4.0 10.8 - - + +
224X LEU* 1.3 72.9 - - - +
226X SER* 1.3 69.7 + - - +
227X GLY* 3.1 2.2 + - - -
421X TYR* 3.2 22.7 - - + +
443X GLU* 2.9 31.0 + - - +
444X ILE* 4.2 3.8 - - - +
447X VAL* 3.9 12.8 - - - +
473X TRP* 2.8 29.3 + - + -
----------------------------------------------------------
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