Contacts of the strand formed by residues 195 - 200 (chain B) in PDB entry 3HAD
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 HIS 195 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A THR* 3.8 25.7 + - + +
238A LEU* 3.8 23.5 - - + +
167B LYS* 2.6 16.8 + - + +
168B LEU* 3.5 10.9 - - - +
169B VAL* 3.1 19.9 + - - -
190B LYS* 6.3 0.9 - - - -
194B LYS* 1.3 73.6 - - - +
196B PRO* 1.3 78.4 + - + +
197B VAL* 5.0 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASP* 5.0 1.2 - - - +
169B VAL* 3.1 19.7 - - + +
171B VAL* 3.7 15.9 - - + -
186B VAL* 3.9 29.8 - - + +
189B SER* 3.6 17.5 - - - -
190B LYS* 4.0 16.8 - - + -
194B LYS 3.7 8.3 - - - +
195B HIS* 1.3 97.6 + - + +
197B VAL* 1.3 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASP* 3.6 34.1 - - + +
234A THR* 3.8 30.5 - - + -
235A ALA* 4.4 3.1 - - + -
168B LEU* 3.9 17.3 - - + -
169B VAL 2.9 14.9 + - - +
170B GLU* 3.6 18.6 - - + -
171B VAL* 2.8 28.3 + - - +
195B HIS* 4.6 2.0 - - + +
196B PRO* 1.3 80.0 - - - +
198B SER* 1.3 60.2 + - - +
206B ILE* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ALA* 3.5 19.1 - - - +
228A SER 4.9 0.3 + - - -
231A ASP* 2.8 21.1 + - - +
171B VAL 3.7 5.3 + - - -
173B LYS* 5.2 3.8 - - - +
182B PHE* 3.7 33.1 - - - -
197B VAL* 1.3 75.0 - - - +
199B CYS* 1.3 69.1 + - - +
206B ILE* 3.9 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 5.3 0.7 - - - -
226A ASP* 3.4 18.2 - - - -
227A ALA* 4.6 0.4 - - - -
170B GLU* 5.6 2.0 - - + -
171B VAL 3.6 4.1 + - - +
172B ILE* 3.6 18.3 - - + +
173B LYS* 3.5 21.7 + - - +
197B VAL 4.3 0.4 + - - -
198B SER* 1.3 80.4 + - - +
200B LYS* 1.3 85.0 + - - +
202B THR* 3.8 7.6 - - - -
205B PHE* 3.6 32.8 - - + -
206B ILE* 3.7 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ARG 5.6 1.6 + - - +
225A GLY* 3.7 23.0 + - - +
226A ASP* 3.2 20.0 + - - +
172B ILE* 3.9 5.7 - - - +
173B LYS 3.9 8.3 - - - +
199B CYS* 1.3 89.3 - - - +
201B ASP* 1.3 54.1 + - - +
202B THR* 2.5 41.2 + - + +
205B PHE* 4.0 1.2 - - - -
----------------------------------------------------------
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