Contacts of the strand formed by residues 185 - 192 (chain A) in PDB entry 2ZPS
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 GLU 185 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 4.2 0.9 - - - -
104A ALA* 3.3 14.1 - - + +
105A LEU 3.7 11.1 - - - +
106A PRO* 3.5 7.5 - - + +
107A SER* 2.7 49.1 + - - -
108A SER* 4.3 4.3 + - - +
181A VAL* 3.3 6.7 - - - +
182A CYS 2.9 31.5 + - - +
183A ASN* 3.6 12.3 - - - +
184A GLY* 1.3 85.1 - - - +
186A LEU* 1.3 59.3 + - - +
187A GLN* 3.1 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 3.5 35.7 - - - +
30A VAL* 4.2 11.2 - - + -
36A VAL* 4.1 27.1 - - + -
103A VAL* 3.9 10.7 - - + +
104A ALA 2.8 18.3 + - - +
105A LEU* 4.7 4.5 - - + -
106A PRO* 3.1 22.1 - - - +
179A PRO* 3.7 14.8 - - + -
180A VAL 3.7 5.2 - - - +
181A VAL* 4.4 5.4 - - + -
185A GLU* 1.3 69.2 - - - +
187A GLN* 1.3 58.2 + - - +
188A GLY 3.5 23.1 - - - +
189A VAL* 5.0 1.6 - - + -
208A VAL* 3.3 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PRO* 3.4 11.8 - - - +
108A SER* 2.9 24.0 + - - +
109A CYS* 3.9 0.2 - - - +
110A ALA* 3.2 35.5 + - + +
141A ILE* 5.0 1.7 - - + +
160A PHE* 3.3 18.9 - - + -
180A VAL 2.9 5.7 + - - -
182A CYS* 3.6 36.4 - - + +
185A GLU* 3.1 17.6 + - - +
186A LEU* 1.3 73.5 - - - +
188A GLY* 1.3 58.3 + - - +
207A LYS* 3.9 1.4 - - - +
208A VAL* 3.1 24.4 + - - -
209A CYS* 3.8 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PHE* 3.7 10.5 - - - -
178A GLY 3.7 1.2 - - - +
180A VAL* 3.0 39.6 + - - +
186A LEU* 3.5 12.9 - - - +
187A GLN* 1.3 81.9 - - - +
189A VAL* 1.3 64.9 + - - +
206A ALA 3.2 9.4 - - - -
208A VAL* 3.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 3.9 22.9 - - + -
37A SER 3.7 4.0 - - - +
38A ALA* 3.7 18.4 - - + +
84A ASP 4.3 2.2 - - - +
85A ILE* 4.5 3.8 - - + -
177A GLY* 3.5 32.3 - - - +
178A GLY 3.2 4.3 - - - +
186A LEU* 5.0 2.7 - - + -
188A GLY* 1.3 79.2 - - - +
190A VAL* 1.3 72.2 + - - +
191A SER* 3.1 1.7 + - - -
205A TYR* 3.2 5.4 - - - +
206A ALA* 2.9 40.6 + - + +
208A VAL* 3.7 18.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
38A ALA* 3.8 4.3 - - - +
118A VAL* 3.8 29.2 - - + -
119A SER 5.0 0.9 - - - +
171A SER* 3.6 20.9 - - - +
175A ASP* 3.4 25.4 - - + +
176A SER* 3.6 20.8 - - - +
177A GLY* 2.8 24.8 + - - +
178A GLY* 2.9 18.4 + - - +
179A PRO 4.6 0.7 - - - +
180A VAL* 4.7 0.2 - - - +
189A VAL* 1.3 72.4 - - - +
191A SER* 1.3 61.5 + - - +
204A VAL 5.4 0.2 - - - +
205A TYR* 3.5 12.0 - - + -
1001A BEN 3.7 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A HIS* 3.3 22.2 + - - -
81A ILE* 3.0 18.2 + - - +
84A ASP* 2.6 31.4 + - - +
159A MET* 6.1 1.2 - - - +
189A VAL 3.1 8.1 + - - -
190A VAL* 1.3 77.2 - - - +
192A TRP* 1.3 71.2 + - - +
204A VAL 3.2 14.3 + - - -
205A TYR* 4.1 6.1 - - - -
206A ALA* 4.1 6.5 - - - -
1001A BEN 3.9 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASN 4.9 4.5 - - - -
81A ILE* 3.7 22.2 - - + +
151A TYR* 3.8 22.9 - + + -
154A MET* 3.9 29.2 - - + -
155A ILE* 3.8 11.2 - - + -
159A MET* 3.8 16.8 - - + +
191A SER* 1.3 106.5 - - - +
193A GLY* 1.3 79.6 + - - +
194A TYR* 4.0 25.4 - + - -
203A GLY 3.7 0.9 - - - -
204A VAL* 2.8 70.0 + - + +
1001A BEN 3.7 23.5 + - + -
----------------------------------------------------------
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