Contacts of the helix formed by residues 185 - 190 (chain G) in PDB entry 1ZWS
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 185 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G PHE 3.8 1.6 + - - -
184G VAL* 1.3 78.8 - - - +
186G PRO* 1.3 77.8 - - + +
187G GLU* 3.5 22.9 - - + +
188G ILE* 3.4 15.9 + - + +
189G VAL* 3.4 12.0 + - - +
198G ALA* 4.3 8.7 + - + +
201G TRP* 3.3 29.1 - - + -
202G SER* 5.4 0.4 + - - -
229G ILE* 4.0 1.3 - - - -
263G ARG* 3.7 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 186 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G ALA* 1.3 83.6 - - + +
187G GLU* 1.3 57.9 + - - +
188G ILE 2.6 17.4 + - - -
189G VAL* 2.8 11.8 + - + -
190G ASN* 2.6 30.3 + - - +
192G GLU* 4.9 0.2 - - - -
201G TRP* 3.3 29.8 - - + -
229G ILE* 3.5 33.4 - - + +
230G THR* 4.8 3.1 - - - -
232G VAL* 4.8 0.4 - - + -
258G LYS* 4.4 29.4 - - + +
263G ARG* 4.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 187 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G ALA* 3.5 10.1 - - + +
186G PRO* 1.3 75.9 - - - +
188G ILE* 1.3 61.6 - - + +
192G GLU* 2.8 54.5 + - + +
193G PRO 3.7 18.2 - - - +
194G LEU* 3.4 17.0 - - + -
195G GLY 4.5 0.2 - - - +
197G GLU* 3.7 8.0 - - - +
198G ALA* 3.0 34.5 + - + +
258G LYS 4.4 4.7 + - - +
260G THR* 4.6 13.2 - - + +
263G ARG* 2.7 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 188 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138G PHE* 5.3 1.8 - - + +
176G ASN 3.8 15.6 - - - +
177G ILE* 4.1 14.6 - - + +
178G PHE* 3.7 43.1 - - + +
184G VAL* 3.5 31.4 - - + -
185G ALA 3.5 14.4 - - - +
186G PRO 2.6 4.8 + - - -
187G GLU* 1.3 77.7 - - + +
189G VAL* 1.3 70.2 + - + +
190G ASN 3.1 1.3 - - - -
191G TYR* 2.8 17.2 + - - -
194G LEU* 3.5 24.0 - - + -
198G ALA* 4.7 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G ILE* 5.2 0.2 - - - +
184G VAL* 4.5 15.7 - - + -
185G ALA 3.4 15.5 - - - +
186G PRO 3.6 4.0 - - - +
188G ILE* 1.3 79.9 - - + +
190G ASN* 1.3 56.1 + - - +
191G TYR 3.2 2.4 + - - -
226G LEU* 4.2 21.1 - - + +
229G ILE* 3.9 21.8 - - + -
230G THR* 3.3 27.8 - - + -
177H ILE* 3.4 20.1 - - + +
189H VAL 5.0 0.5 - - - +
191H TYR* 3.2 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 190 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G PRO* 2.6 39.1 + - - +
187G GLU 4.1 0.7 - - - -
188G ILE 3.6 0.4 - - - -
189G VAL* 1.3 74.5 - - - +
191G TYR* 1.3 67.4 + - - +
192G GLU* 2.6 32.8 + - - +
230G THR* 3.1 30.2 - - - +
258G LYS* 5.0 11.9 - - - +
175H LYS* 5.4 1.4 - - - +
190H ASN* 5.5 2.5 - - - -
191H TYR* 3.7 21.2 + - + +
----------------------------------------------------------
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