Contacts of the strand formed by residues 220 - 228 (chain A) in PDB entry 4WRL
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 ALA 220 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LEU* 3.8 24.2 - - + -
214A ARG* 4.2 7.2 - - + +
219A ALA* 1.3 79.0 - - - +
221A GLN* 1.3 63.1 + - - +
263A LEU 4.1 0.5 - - - +
264A ASN* 4.2 2.4 - - - +
265A LEU* 3.3 36.4 + - + +
268A VAL* 5.3 1.8 - - + -
293A PHE* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL 4.2 0.3 - - - +
209A PRO* 3.5 22.0 - - - +
212A LEU* 4.6 6.4 - - - +
220A ALA* 1.3 78.5 - - - +
222A ILE* 1.3 62.0 + - - +
223A VAL* 3.9 27.3 - - + +
262A THR* 4.5 7.6 - - + +
263A LEU 3.6 10.8 - - - +
264A ASN* 3.8 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 5.2 7.2 - - + -
208A VAL 4.0 6.1 - - - +
209A PRO* 5.3 2.2 - - + -
212A LEU* 6.0 2.2 - - + -
221A GLN* 1.3 75.0 - - - +
223A VAL* 1.3 62.4 + - - +
224A CYS 4.0 0.6 + - - -
237A LEU* 4.5 12.6 - - + +
261A LEU 3.7 2.1 - - - +
263A LEU* 2.8 52.5 + - + +
276A TYR* 5.2 9.2 - - + -
291A MET* 5.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A THR 3.4 16.4 - - - +
207A LEU* 3.5 11.8 - - - +
208A VAL* 3.5 25.0 + - + +
221A GLN* 3.9 19.7 - - - +
222A ILE* 1.3 74.3 - - - +
224A CYS* 1.3 59.1 + - - +
225A SER* 4.1 4.2 + - - +
260A VAL* 4.6 11.2 - - + -
261A LEU 3.3 3.8 - - - +
262A THR* 3.7 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 3.9 3.3 - - - +
222A ILE 4.0 1.2 + - - -
223A VAL* 1.3 70.0 - - - +
225A SER* 1.3 62.1 + - - +
235A VAL* 3.7 19.7 - - - -
236A PHE 3.9 5.4 - - - -
237A LEU* 3.7 27.3 - - + +
259A LYS 3.9 0.9 - - - +
260A VAL* 3.4 0.5 - - - +
261A LEU* 2.6 53.3 + - + +
278A CYS* 2.0 52.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 3.3 13.0 - - - +
206A THR* 3.1 52.8 + - - -
223A VAL* 4.1 7.3 + - - +
224A CYS* 1.3 79.8 + - - +
226A ALA* 1.3 61.3 + - - +
235A VAL* 4.5 2.0 - - - -
258A GLN* 6.5 0.7 - - - -
259A LYS 3.5 4.9 - - - -
260A VAL* 3.5 28.8 - - - +
278A CYS* 3.9 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PRO* 3.8 6.3 - - + -
204A ALA 3.3 7.4 - - - -
205A LEU* 3.9 2.7 - - + -
225A SER* 1.3 77.0 - - - +
227A SER* 1.3 62.9 + - - +
233A PHE* 3.7 19.8 - - + -
235A VAL* 3.8 11.0 - - + +
258A GLN* 3.7 1.1 - - - +
259A LYS 3.0 30.8 + - - -
280A ALA* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PRO* 4.1 0.6 - - - +
204A ALA* 3.2 34.7 + - - +
226A ALA* 1.3 76.4 - - - +
228A SER* 1.3 61.8 + - - +
233A PHE* 4.3 2.0 - - - -
256A ARG* 2.9 25.5 + - - -
257A TYR 3.2 13.7 - - - -
258A GLN* 3.6 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ILE* 3.9 22.0 - - - +
200A PRO* 6.0 0.3 - - - +
201A GLY 5.1 1.2 + - - -
203A PRO* 4.6 10.8 - - - -
227A SER* 1.3 75.4 - - - +
229A VAL* 1.3 66.6 + - - +
230A ASP* 3.2 23.8 + - - +
233A PHE* 4.1 18.0 - - - -
256A ARG* 3.5 10.5 - - - +
257A TYR 3.0 26.8 + - - +
282A ASN* 4.9 2.9 + - - -
----------------------------------------------------------
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