Contacts of the helix formed by residues 188 - 198 (chain A) in PDB entry 2WXW
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 GLN 188 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PRO* 3.1 39.1 + - + +
34A PHE* 3.6 22.9 - - - -
186A LEU 3.9 0.2 + - - -
187A LYS* 1.3 67.2 - - - +
189A PRO* 1.4 69.4 - - + +
190A PHE 3.1 2.0 - - - -
191A VAL* 2.7 32.0 + - - +
192A GLN* 3.2 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 4.1 26.2 - - + +
32A PRO* 4.4 3.1 - - + -
115A LEU* 5.5 0.3 - - - +
145A HIS* 4.5 11.7 + - + +
187A LYS* 3.8 6.3 - - + -
188A GLN* 1.4 97.6 - - + +
190A PHE* 1.3 61.3 + - - +
192A GLN* 3.4 15.3 + - + +
193A GLY* 3.1 17.3 + - - -
380A LYS 5.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER 3.4 24.2 - - - -
113A LEU* 5.2 0.9 - - - -
115A LEU* 3.6 26.0 - - + +
116A GLY 3.7 10.3 - - - -
178A VAL* 4.8 6.7 - - + -
186A LEU* 5.0 4.0 - - + -
187A LYS 3.8 9.6 - - - +
188A GLN 3.1 0.4 - - - -
189A PRO* 1.3 80.2 - - - +
191A VAL* 1.3 70.2 + - + +
193A GLY* 3.1 4.0 + - - -
194A LEU* 3.0 64.0 + - + +
245A PHE* 4.0 11.7 - + - -
380A LYS* 3.6 17.9 + - + +
381A LEU* 3.3 47.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 3.5 21.3 - - + -
186A LEU* 3.3 24.2 - - + -
187A LYS 3.2 19.5 - - - +
188A GLN* 2.7 17.8 + - - +
190A PHE* 1.3 76.3 - - + +
192A GLN* 1.3 58.9 + - + +
194A LEU* 3.3 8.2 + - + +
195A ALA* 3.0 24.6 + - - +
201A VAL* 4.3 20.4 - - + +
203A PRO* 4.7 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A HIS* 5.2 3.4 - - + -
188A GLN* 3.2 39.7 + - - +
189A PRO* 3.7 13.7 - - - +
191A VAL* 1.3 73.0 - - + +
193A GLY* 1.3 62.4 + - - +
195A ALA* 3.2 17.7 - - + +
196A LEU* 2.9 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 3.7 12.1 - - - -
145A HIS* 4.3 16.9 - - - -
148A LEU* 3.2 23.9 - - - +
189A PRO 3.1 9.8 + - - -
190A PHE 3.1 9.1 + - - -
192A GLN* 1.3 74.1 - - - +
194A LEU* 1.3 64.1 + - - +
196A LEU* 3.1 18.3 + - - +
197A TYR 3.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER* 4.4 11.4 - - - -
115A LEU* 3.6 12.3 - - + -
148A LEU* 4.9 0.9 - - - -
176A VAL* 4.7 4.9 - - + -
178A VAL* 3.6 31.4 - - + -
190A PHE* 3.0 54.6 + - + +
191A VAL* 3.3 12.1 + - + +
193A GLY* 1.3 74.2 - - - +
195A ALA* 1.3 62.0 + - - +
197A TYR* 3.1 12.0 + - + +
198A THR* 3.0 24.8 + - + +
201A VAL* 3.5 25.5 - - + +
245A PHE* 3.8 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLN* 4.8 3.6 + - - -
191A VAL 3.0 13.6 + - - +
192A GLN* 3.2 18.4 - - + +
194A LEU* 1.3 77.0 - - - +
196A LEU* 1.3 60.2 + - + +
198A THR 3.1 22.4 - - - +
199A PRO* 4.0 6.0 - - + +
201A VAL* 3.8 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A HIS* 3.2 47.8 - - + +
148A LEU* 4.0 3.1 - - + -
149A SER* 3.6 25.8 - - - +
152A GLN* 3.1 27.9 + - - +
192A GLN* 2.9 30.7 - - + +
193A GLY* 3.1 11.5 + - - +
195A ALA* 1.3 81.7 - - + +
197A TYR* 1.3 57.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A THR 4.0 0.9 + - - -
105A ALA* 3.8 21.3 + - - +
108A GLY* 3.6 31.9 - - - -
109A THR* 4.2 4.5 - - - -
112A SER* 4.8 7.9 - - - -
148A LEU* 3.5 36.7 - - + +
151A LEU* 3.4 34.5 - - + -
152A GLN* 3.0 18.2 - - - +
155A GLN* 3.6 20.0 + - - -
174A THR* 5.3 6.4 - - - +
176A VAL* 4.1 28.5 - - + -
193A GLY 3.5 1.8 + - - -
194A LEU* 3.1 12.4 + - + +
196A LEU* 1.3 79.7 - - - +
198A THR* 1.3 59.1 - - + +
245A PHE* 6.0 0.2 - + - -
247A THR* 4.5 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 5.4 0.5 - - - +
152A GLN* 4.1 0.4 - - - +
174A THR* 2.5 33.1 + - - +
176A VAL* 3.2 35.0 - - + -
194A LEU* 3.0 10.4 + - + +
195A ALA* 3.1 13.8 - - - +
197A TYR* 1.3 83.3 - - + +
199A PRO* 1.3 75.9 - - - +
200A VAL* 3.3 17.1 + - - +
201A VAL* 3.1 15.2 - - + +
----------------------------------------------------------
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