Contacts of the helix formed by residues 188 - 198 (chain A) in PDB entry 4F4W
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 GLY 188 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLY 3.7 4.4 + - - -
187A ILE* 1.3 76.3 - - - +
189A SER* 1.3 65.4 + - - -
190A VAL* 3.2 6.6 + - - -
191A LEU* 3.3 8.3 + - - +
192A ALA* 2.9 22.2 + - - +
12P G 3.4 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLY* 1.3 70.9 - - - -
190A VAL* 1.3 65.5 + - - +
192A ALA* 3.5 7.0 + - - +
193A ARG* 3.2 27.6 + - - +
12P G 5.5 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLY* 4.7 4.5 - - - +
189A SER* 1.3 80.7 + - - +
191A LEU* 1.3 79.7 + - + +
193A ARG* 3.0 28.9 + - + +
194A ARG* 3.0 24.6 + - + +
11P G 4.2 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLY 5.2 0.2 - - - +
187A ILE* 3.8 33.2 - - + -
188A GLY 3.3 9.1 + - - +
190A VAL* 1.3 84.8 - - + +
192A ALA* 1.3 68.7 + - - +
194A ARG* 3.1 13.6 + - + +
195A LEU* 2.8 32.5 + - + +
217A ILE 3.5 25.1 - - - +
218A THR* 4.0 28.9 - - + +
222A LYS* 4.6 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 4.4 9.1 - - + +
182A ASP* 4.1 29.8 - - + -
187A ILE* 4.0 13.9 - - + +
188A GLY 2.9 17.7 + - - +
189A SER* 3.6 8.7 - - - +
191A LEU* 1.3 78.9 - - - +
193A ARG* 1.3 52.3 + - - +
195A LEU* 3.3 3.9 + - - +
196A ASN* 2.7 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A SER* 3.2 10.8 + - - +
190A VAL* 3.0 38.3 + - + +
192A ALA* 1.3 78.4 - - - +
194A ARG* 1.3 58.1 + - + +
196A ASN* 3.0 10.8 + - + +
197A GLU* 2.5 50.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A VAL* 3.0 12.4 + - + +
191A LEU* 3.5 14.8 - - + +
193A ARG* 1.3 82.9 - - + +
195A LEU* 1.3 63.2 + - - +
197A GLU* 3.1 28.5 + - - +
198A LEU* 3.2 32.8 + - - +
216A LYS 3.4 24.0 + - - -
217A ILE* 3.6 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 4.0 23.3 - - + -
187A ILE* 4.3 10.5 - - + -
191A LEU* 2.8 36.7 + - + +
192A ALA* 3.6 5.2 - - - +
194A ARG* 1.3 72.6 - - - +
196A ASN* 1.3 57.9 + - - +
198A LEU* 2.9 21.2 + - - +
200A ILE* 3.0 44.3 + - + +
206A ILE* 4.7 0.9 - - + -
214A LEU* 3.9 17.0 - - + -
217A ILE* 3.7 22.2 - - + -
218A THR* 3.8 16.8 - - + -
226A LEU* 4.4 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 3.7 24.5 - - - +
182A ASP* 4.5 9.3 + - - -
192A ALA* 2.7 17.8 + - - +
193A ARG* 3.0 17.3 - - + +
195A LEU* 1.3 71.9 - - - +
197A GLU* 1.3 60.6 + - - +
199A GLY* 3.1 7.1 + - - -
200A ILE 3.3 10.3 + - - -
201A GLN* 2.7 51.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ARG* 2.5 25.3 + - - +
194A ARG* 3.1 27.1 + - - +
196A ASN* 1.3 72.6 - - - +
198A LEU* 1.3 64.2 + - + +
199A GLY 3.3 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ARG* 3.3 29.8 - - - +
195A LEU* 2.9 10.3 + - - +
197A GLU* 1.3 85.4 - - + +
199A GLY* 1.3 57.6 + - - -
200A ILE* 3.3 9.8 + - + +
209A LYS* 4.3 18.2 + - - +
217A ILE* 3.2 44.4 - - + -
----------------------------------------------------------
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