Contacts of the strand formed by residues 188 - 192 (chain K) in PDB entry 1ZUM
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 VAL 188 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66K ALA* 3.5 33.2 - - + +
69K ALA* 4.3 2.5 - - + -
70K PHE* 3.9 18.4 - - + +
76K TRP* 3.8 20.2 - - + -
160K GLY 3.0 14.4 + - - +
161K VAL* 3.7 16.4 - - + -
162K CYS* 2.8 27.2 + - - +
187K ASN* 1.3 79.1 - - - +
189K VAL* 1.3 66.3 + - - +
216K GLY 4.1 4.9 - - - +
217K VAL* 3.3 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66K ALA* 4.9 0.4 - - - -
162K CYS* 3.5 5.6 - - + +
164K GLN* 3.2 41.1 - - - +
179K LEU* 4.2 17.3 - - + -
182K ALA* 3.9 17.0 - - + -
183K LEU* 4.8 6.3 - - + -
188K VAL* 1.3 80.8 - - - +
190K VAL* 1.3 64.9 - - - +
191K MET* 3.7 20.9 - - + +
217K VAL 2.7 14.4 + - - +
218K VAL* 3.7 5.8 - - + -
219K ASN* 2.8 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K VAL* 4.7 2.5 - - + +
62K ALA* 3.8 29.6 - - + +
63K VAL* 3.9 36.1 - - + -
66K ALA* 4.0 3.1 - - + -
161K VAL* 3.9 17.9 - - + -
162K CYS 3.1 6.4 + - - +
163K GLY* 3.4 7.2 - - - -
164K GLN 3.0 21.5 + - - +
189K VAL* 1.3 77.7 - - - +
191K MET* 1.3 60.1 + - - +
219K ASN 3.3 4.9 - - - +
221K VAL* 4.6 7.9 - - + -
232K ILE* 4.0 25.5 - - + +
238K VAL* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 191 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164K GLN* 3.2 37.2 - - + +
166K ILE* 4.3 13.7 - - + -
175K GLN* 3.9 36.1 - - + +
178K LYS* 3.9 15.3 - - + -
179K LEU* 3.8 19.3 - - + -
189K VAL* 3.8 8.5 - - + -
190K VAL* 1.3 73.6 - - - +
192K LYS* 1.3 60.2 + - - +
193K VAL* 4.2 16.2 - - + -
218K VAL* 5.8 0.2 - - - -
219K ASN 2.7 15.4 + - - +
220K ILE* 3.3 15.2 - - + +
221K VAL* 2.8 33.3 + - - +
232K ILE* 4.5 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 192 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164K GLN 2.7 10.6 + - - +
165K ILE* 3.5 23.1 - - + +
166K ILE* 3.0 27.3 + - - +
191K MET* 1.3 71.8 - - - +
193K VAL* 1.3 85.7 + - - +
194K ALA* 4.3 5.1 - - - +
195K GLU* 4.4 2.6 + - - +
221K VAL* 3.4 18.6 - - + +
223K GLY 3.1 23.2 + - - +
224K PHE 3.9 16.3 - - - -
225K GLY* 4.1 5.3 - - - +
228K ALA* 3.8 21.5 - - + -
229K GLY* 3.8 9.2 - - - +
232K ILE* 3.5 26.8 - - + +
----------------------------------------------------------
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