Contacts of the strand formed by residues 218 - 228 (chain D) in PDB entry 1WUU
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 LEU 218 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D LEU* 5.2 10.5 - - + -
215D ASP* 3.2 33.6 + - + +
216D PRO* 4.0 1.9 - - - +
217D LYS* 1.3 80.6 - - - +
219D ALA* 1.3 80.4 + - - +
220D VAL* 5.7 1.1 - - + -
295D LEU* 4.9 5.2 - - + -
300D TYR* 3.2 44.6 - - + +
339D TYR* 3.9 13.5 - - + -
355D LEU* 3.5 33.4 - - + -
356D LEU 3.0 12.6 - - - +
358D ALA* 3.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D LEU* 1.3 83.2 - - - +
220D VAL* 1.3 64.1 + - - +
355D LEU* 3.3 9.9 - - - +
356D LEU* 2.7 54.0 + - + +
358D ALA* 3.7 17.7 - - + -
361D ALA* 5.7 2.0 - - + -
380D LEU* 5.1 7.9 - - + -
381D SER 5.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D VAL* 4.7 1.3 - - + -
40D LEU* 4.3 11.9 - - + -
55D MSE 4.2 27.8 - - + -
213D LEU* 6.1 3.6 - - + -
218D LEU* 5.7 1.3 - - + -
219D ALA* 1.3 78.2 - - - +
221D LEU* 1.3 61.3 - - - +
222D ILE* 4.3 12.3 - - + -
353D VAL* 3.6 28.5 - - + -
354D THR 3.3 2.0 - - - +
355D LEU* 3.9 16.4 - - + -
356D LEU* 4.5 0.2 - - - -
379D TYR 3.6 0.5 - - - +
380D LEU* 3.0 19.3 - - - +
381D SER* 3.2 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D ALA 4.0 0.4 - - - -
220D VAL* 1.3 72.2 - - - +
222D ILE* 1.3 75.0 + - - +
223D THR* 3.9 14.1 - - - +
353D VAL* 3.4 1.7 - - - -
354D THR* 2.4 69.2 + - + +
356D LEU* 4.1 11.9 - - + -
361D ALA 4.3 3.1 - - - +
364D ALA* 3.8 30.7 - - + -
365D MSE 4.0 24.9 - - + +
368D ILE* 5.1 5.8 - - + -
378D PHE* 4.7 1.8 - - + -
379D TYR 3.3 18.2 - - - +
380D LEU* 3.3 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D VAL* 3.8 30.1 - - + -
57D LEU* 4.2 10.8 - - + -
59D LEU* 6.1 1.6 - - + -
139D LEU* 4.2 8.1 - - + -
220D VAL* 4.3 12.3 - - + -
221D LEU* 1.3 73.7 - - - +
223D THR* 1.3 67.0 + - - +
351D CYS* 3.4 30.3 - - + -
352D THR 3.3 10.1 - - - +
353D VAL* 4.5 0.7 - - + -
377D THR 3.8 0.9 - - - +
378D PHE* 3.6 4.2 - - - -
379D TYR* 3.1 53.3 + - + +
381D SER* 3.8 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D LEU* 3.9 13.1 + - - +
222D ILE* 1.3 76.1 + - - +
224D ASN* 1.3 61.6 + - - +
225D SER 3.5 3.1 + - - -
328D LEU* 4.2 13.9 - - + +
351D CYS* 2.9 5.1 - - - -
352D THR* 2.6 51.0 + - - +
354D THR* 4.9 1.4 + - - -
368D ILE* 4.1 19.4 - - + +
376D ALA* 3.8 25.4 - - + -
377D THR 3.6 3.6 - - - +
378D PHE* 3.5 22.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D PRO* 4.2 25.1 - - - +
137D GLY* 4.8 6.0 - - - -
222D ILE 3.9 0.6 + - - -
223D THR* 1.3 70.6 - - - +
225D SER* 1.3 57.0 + - - +
226D ASN* 2.8 63.3 + - - +
350D GLY* 3.8 14.1 - - - -
351D CYS* 3.6 20.8 - - - -
376D ALA* 3.2 4.1 - - - -
377D THR* 2.7 38.7 + - + +
379D TYR* 4.6 6.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D THR 3.5 3.6 + - - -
224D ASN* 1.3 70.5 - - - +
226D ASN* 1.3 65.4 + - - +
227D VAL* 2.9 27.2 + - - +
324D GLU* 4.3 8.3 - - - -
325D LEU* 4.6 5.4 - - - -
328D LEU* 3.6 21.9 - - - +
349D GLY* 3.9 1.4 - - - -
350D GLY 2.6 30.6 + - - -
372D TYR* 2.5 37.9 + - - -
375D THR 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D ASN* 2.8 36.4 + - - -
225D SER* 1.3 79.1 - - - +
227D VAL* 1.3 60.0 - - - +
228D ARG* 3.9 4.1 + - - +
375D THR* 2.3 36.1 + - + +
377D THR* 2.3 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D ASN* 4.5 0.6 + - - -
225D SER* 2.9 13.4 + - - +
226D ASN* 1.3 80.2 - - - +
228D ARG* 1.3 62.4 + - - +
229D HIS* 3.2 37.5 - - + +
322D CYS* 4.6 0.4 - - - -
324D GLU* 3.6 28.0 - - + +
349D GLY* 3.2 10.3 - - - -
350D GLY* 2.6 33.5 + - - -
372D TYR* 3.8 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D GLY 4.9 4.7 + - - -
135D LEU* 2.8 55.5 + - - +
136D GLY* 2.8 30.1 - - - +
226D ASN 3.9 5.1 + - - +
227D VAL* 1.3 72.0 - - - +
229D HIS* 1.3 64.0 + - - +
230D SER 3.4 4.2 + - - -
349D GLY* 5.1 0.4 - - - -
350D GLY 4.9 0.7 - - - +
395D ANP 3.8 26.2 + - - -
----------------------------------------------------------
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