Contacts of the strand formed by residues 191 - 196 (chain N) in PDB entry 6DZT
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 LEU 191 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162N MET* 3.7 30.1 - - + -
181N CYS* 4.2 5.8 - - + -
187N ILE* 3.8 12.6 - - + -
189N SER 3.0 4.0 + - - -
190N TYR* 1.3 75.6 - - - +
192N SER* 1.3 67.7 + - - +
193N TRP* 3.4 36.8 - - + +
206N ILE* 4.4 0.5 - - - +
207N TYR* 3.8 0.7 - - - -
208N TYR* 3.3 8.2 + - - +
209N ALA* 3.1 26.7 + - + -
229N PHE* 3.6 43.1 - - + -
246N CYS* 4.0 4.3 - - + -
247N LEU 3.4 16.8 - - - +
248N GLN* 4.0 0.4 - - - -
249N HIS* 4.3 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 192 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128N THR* 2.5 33.3 + - - -
191N LEU* 1.3 73.9 + - - +
193N TRP* 1.3 68.8 + - - +
194N TYR* 3.6 18.8 - - - -
206N ILE 3.3 11.6 + - - -
207N TYR* 4.3 1.7 - - - -
246N CYS* 3.3 8.3 - - - +
247N LEU* 2.8 31.1 + - - -
249N HIS* 3.2 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 193 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164N GLN* 3.7 17.7 - - - -
179N ILE* 4.0 18.2 - - + -
180N THR 4.1 4.9 - - - -
181N CYS* 3.6 33.2 - - + -
191N LEU* 3.4 20.1 - - + +
192N SER* 1.3 78.7 - - - +
194N TYR* 1.3 58.0 + - - +
204N THR* 3.8 1.4 - - - +
205N LEU* 2.8 34.2 + - + +
206N ILE* 2.9 44.4 + - + +
209N ALA* 5.3 4.3 + - - +
222N GLY* 5.3 0.7 - - - -
223N SER 5.5 0.4 + - - -
229N PHE* 4.7 2.0 - - - +
230N SER 4.0 17.3 + - - -
231N LEU* 3.7 49.8 - - + -
244N TYR* 4.5 2.9 - - + -
245N TYR 3.4 21.8 - - - -
246N CYS* 3.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 194 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67N LEU* 6.3 0.4 - - + -
128N THR* 2.5 26.4 + - - -
129N LEU* 3.2 29.1 + - + +
132N TRP* 3.6 21.3 - + - -
192N SER* 3.6 10.3 - - - -
193N TRP* 1.3 75.5 - - - +
195N GLN* 1.3 60.8 + - - +
202N PRO* 4.3 12.6 - - + -
203N LYS 3.3 7.9 - - - +
204N THR* 3.2 38.4 - - + -
205N LEU* 4.5 3.1 - - - -
244N TYR* 3.3 6.4 - - - +
245N TYR* 2.9 46.6 + - + +
247N LEU* 3.5 34.1 - - + +
256N PHE* 4.3 13.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 195 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194N TYR* 1.3 74.1 - - - +
196N GLN* 1.3 60.7 + - - +
197N LYS* 3.4 33.5 + - + +
201N SER 4.6 0.2 - - - +
202N PRO* 3.3 2.1 - - - +
203N LYS* 2.7 68.9 + - + +
205N LEU* 4.1 11.3 - - + +
220N PHE* 4.5 8.3 - - - -
239N ASP 4.6 5.7 + - - +
240N ASP* 4.8 0.3 - - - -
242N ALA* 4.0 8.7 - - + +
243N THR 3.4 5.2 - - - +
244N TYR* 3.0 42.5 + - + -
245N TYR* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 196 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61N GLN* 2.7 46.6 + - - +
117N TYR* 2.9 15.6 + - - -
195N GLN* 1.3 74.2 - - - +
197N LYS* 1.3 67.6 + - - +
198N PRO* 3.9 0.3 - - - +
199N TRP* 5.7 1.8 - - - +
200N LYS 3.1 22.8 + - - +
201N SER 4.8 0.2 - - - -
202N PRO* 3.9 21.7 - - + +
242N ALA* 3.3 4.5 - - - +
243N THR* 2.8 32.3 + - - +
245N TYR* 3.1 28.3 + - + -
----------------------------------------------------------
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