Contacts of the strand formed by residues 184 - 189 (chain I) in PDB entry 2ZHX
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 CYS 184 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I ALA* 3.8 30.3 - - - -
163I LEU* 3.2 23.6 - - + +
179I LEU* 3.7 25.2 - - + +
180I ALA 3.7 14.6 - - - +
181I ALA* 3.2 27.9 - - - +
182I GLY 3.4 1.1 - - - +
183I ASN* 1.3 98.2 - - - +
185I VAL* 1.3 66.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163I LEU 3.3 5.4 + - - +
164I VAL* 3.6 5.4 - - - +
165I ALA* 3.2 23.2 + - - +
179I LEU* 4.4 1.8 - - - +
181I ALA* 5.6 1.1 - - - -
182I GLY 5.9 1.3 - - - +
183I ASN 5.5 0.2 - - - -
184I CYS* 1.3 80.1 - - - +
186I ALA* 1.3 70.2 + - - +
187I ILE* 4.3 2.2 - - + -
213I LEU* 3.8 40.8 - - + -
217I MET* 4.3 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165I ALA* 3.4 13.2 - - + +
167I LEU* 4.7 9.9 - - + -
176I LYS* 4.2 24.8 - - + +
179I LEU* 4.2 15.9 - - + -
181I ALA* 6.2 0.4 - - - +
185I VAL* 1.3 82.0 - - - +
187I ILE* 1.3 65.2 + - - +
188I GLU* 4.0 10.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 187 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I VAL* 4.7 2.2 - - + +
165I ALA 3.3 4.1 + - - +
166I ILE* 3.8 26.9 - - + +
167I LEU* 3.0 26.9 + - - +
168I TRP* 5.8 0.6 - - - +
185I VAL* 4.4 2.7 + - + -
186I ALA* 1.3 76.9 - - - +
188I GLU* 1.3 60.9 + - - +
206I PRO* 3.7 36.8 - - + +
209I ARG* 3.7 37.0 - - + +
210I ALA* 4.3 10.1 - - + +
213I LEU* 3.6 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 188 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167I LEU* 3.4 18.4 - - + +
168I TRP* 5.5 0.7 - - - -
170I ARG* 6.0 0.2 - - - -
173I SER* 3.1 32.6 + - - +
176I LYS* 2.9 44.6 + - - +
186I ALA 4.0 8.6 + - - +
187I ILE* 1.3 78.4 - - - +
189I SER* 1.3 65.3 + - - +
209I ARG* 4.2 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 189 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167I LEU 3.5 6.0 + - - +
168I TRP* 3.5 17.9 + - - -
169I GLY 3.0 21.5 + - - +
188I GLU* 1.3 78.1 - - - +
190I PRO* 1.3 80.4 + - - +
200I GLY 3.9 13.5 - - - -
201I PHE* 3.5 11.6 - - - -
204I SER* 4.0 13.5 + - - -
----------------------------------------------------------
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