Contacts of the helix formed by residues 230 - 241 (chain A) in PDB entry 3W5D
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 THR 230 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN* 4.9 1.1 - - - +
161A ALA* 4.8 1.1 - - - -
162A ASP* 3.3 28.5 - - - +
210A SER* 4.3 8.2 - - - +
225A THR* 3.6 12.6 - - - +
226A THR* 3.6 33.2 - - - -
227A GLY 3.3 6.7 + - - +
228A VAL 3.4 0.2 - - - -
229A SER* 1.3 81.1 - - - +
231A GLU* 1.3 59.9 + - - +
232A ILE* 3.3 13.6 - - - +
233A GLY 3.1 15.9 + - - -
234A LYS* 2.8 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ASP* 3.0 23.8 + - - +
180A LEU* 4.2 16.2 - - + -
201A ASN* 2.8 43.3 + - - +
204A LYS* 3.7 13.2 + - - -
209A PHE* 3.7 14.1 - - + -
229A SER 5.4 0.2 - - - +
230A THR* 1.3 72.7 - - - +
232A ILE* 1.3 61.5 + - - +
234A LYS* 2.8 36.5 + - - +
235A ILE* 3.1 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.7 16.9 - - + +
119A LEU* 4.4 14.5 - - + +
122A TYR* 5.0 14.8 - - + +
123A GLU* 5.7 6.1 - - + +
162A ASP* 5.3 0.4 + - - -
179A ILE* 5.3 6.1 - - + -
180A LEU* 3.6 28.9 - - + -
210A SER* 3.6 40.2 - - - +
211A GLY* 4.8 4.3 - - - +
230A THR* 3.3 11.2 - - - +
231A GLU* 1.3 72.8 - - - +
233A GLY* 1.3 64.7 + - - +
235A ILE* 3.1 13.5 + - - +
236A ARG* 2.8 27.4 + - - +
705A VAL* 4.4 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.7 23.1 - - - -
227A GLY 3.8 6.5 - - - -
228A VAL* 3.1 17.3 - - - +
230A THR* 3.0 14.5 + - - -
232A ILE* 1.3 76.1 - - - +
234A LYS* 1.3 63.7 + - - +
236A ARG* 3.2 4.0 + - - +
237A ASP* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLU* 6.2 3.3 - - + +
198A ARG* 5.5 8.0 - - - +
204A LYS* 5.4 1.0 - - - +
228A VAL 3.2 8.9 + - - +
229A SER* 3.6 15.6 + - - +
230A THR 2.8 24.6 + - - +
231A GLU* 2.8 37.6 + - - +
233A GLY* 1.3 72.4 - - - +
235A ILE* 1.3 61.7 + - - +
237A ASP* 3.4 7.8 + - - +
238A GLN* 2.8 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 4.6 2.7 - - + -
180A LEU* 4.0 13.5 - - + -
231A GLU* 3.1 19.1 + - + +
232A ILE* 3.1 9.6 + - - +
234A LYS* 1.3 74.0 - - + +
236A ARG* 1.3 65.3 + - - +
238A GLN* 3.6 15.2 + - - +
239A MET* 3.2 38.5 + - - +
705A VAL* 3.4 50.0 - - + +
706A ASN* 3.8 15.7 - - + -
709A PRO* 4.2 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.2 19.1 - - + -
42A PRO* 3.3 47.1 + - - +
43A ALA 5.1 4.0 + - - -
44A GLU* 6.3 0.2 - - - +
116A ILE* 4.0 24.9 - - + +
119A LEU* 3.5 25.1 - - + -
228A VAL* 4.8 1.1 - - - -
232A ILE 2.8 12.8 + - - +
233A GLY* 3.4 12.3 - - - +
235A ILE* 1.3 76.3 - - - +
237A ASP* 1.3 88.7 + - - +
239A MET* 3.4 4.3 + - - +
240A ALA* 2.9 50.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A VAL* 3.8 30.0 - - - +
233A GLY 3.0 15.4 + - - +
234A LYS* 3.8 7.8 - - - +
235A ILE 3.3 0.2 - - - -
236A ARG* 1.3 105.3 + - - +
238A GLN* 1.3 60.8 + - + +
240A ALA* 3.3 1.2 + - - +
241A ALA* 2.8 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LYS* 2.8 34.4 + - - +
235A ILE* 3.6 17.1 - - - +
236A ARG 3.4 0.2 - - - -
237A ASP* 1.3 77.1 - - + +
239A MET* 1.3 55.0 + - - +
241A ALA* 3.3 7.2 + - - +
242A THR* 2.7 32.0 + - - -
685A SER* 5.3 4.7 + - - -
709A PRO* 4.2 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ALA* 3.2 42.6 - - + +
116A ILE* 4.0 10.5 - - + +
119A LEU* 3.9 20.6 - - - -
235A ILE* 3.2 21.2 + - - +
236A ARG 3.6 4.0 - - - +
238A GLN* 1.3 80.7 - - - +
240A ALA* 1.3 58.9 + - - +
242A THR* 3.2 8.0 + - - -
708A ALA* 3.6 27.8 - - + +
709A PRO* 4.1 20.6 - - + +
712A LYS* 3.1 45.7 + - + +
726A VAL* 5.2 2.2 - - + -
730A ALA* 4.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 3.5 19.7 - - + +
236A ARG* 2.9 45.5 + - - +
237A ASP 3.8 2.7 - - - +
238A GLN 3.3 0.2 - - - -
239A MET* 1.3 72.7 - - - +
241A ALA* 1.3 58.1 + - - +
242A THR 3.1 13.9 + - - +
243A GLU* 5.8 0.3 - - - +
712A LYS* 5.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASP 2.8 18.2 + - - +
238A GLN* 3.3 7.8 + - - +
240A ALA* 1.3 75.1 - - - +
242A THR* 1.3 57.5 + - - +
243A GLU* 3.5 12.6 + - - +
----------------------------------------------------------
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