Contacts of the strand formed by residues 189 - 195 (chain B) in PDB entry 4XXD
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 TYR 189 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 3.9 31.9 - - + -
149B TRP* 4.3 4.9 - + + -
150B ASN* 3.7 8.1 - - - -
154B LEU* 3.7 26.2 - - + -
179B VAL* 3.4 38.5 - - + +
180B PRO* 5.0 0.2 - - - +
183B SER* 3.6 18.0 - - - -
184B LEU* 3.6 24.5 - - + -
187B GLN* 3.6 39.0 - - + +
188B THR* 1.3 72.0 - - - +
190B ILE* 1.3 59.0 + - - +
205B LYS* 3.5 4.2 - - - +
206B VAL* 2.8 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TRP* 3.6 6.1 - - - -
150B ASN* 2.8 45.9 + - - +
188B THR* 3.9 20.6 - - + -
189B TYR* 1.3 79.8 - - - +
191B CYS* 1.3 67.2 + - - +
192B ASN* 4.3 7.6 + - - +
203B ASP* 4.0 15.5 - - + -
204B LYS 3.4 20.9 - - - +
205B LYS* 4.0 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B VAL* 4.5 0.4 - - - -
135B CYS* 2.8 42.2 - - - -
147B VAL* 4.1 7.0 - - + -
148B SER 3.3 11.4 - - - +
149B TRP* 3.6 27.4 - - + -
190B ILE* 1.3 73.6 - - - +
192B ASN* 1.3 60.8 + - - +
193B VAL* 4.0 16.4 - - - -
202B VAL 3.8 1.0 - - - +
203B ASP* 3.3 4.9 - - - -
204B LYS* 3.1 39.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B THR* 3.5 3.3 + - - +
147B VAL* 3.4 3.7 - - - -
148B SER* 2.7 52.5 + - - +
150B ASN* 3.6 2.9 + - - +
151B SER* 2.8 42.5 + - - +
190B ILE* 4.4 8.7 + - - +
191B CYS* 1.3 75.3 - - - +
193B VAL* 1.4 60.1 + - - +
194B ASN* 5.2 1.3 - - - +
202B VAL 3.8 3.6 - - - -
203B ASP* 2.7 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PRO* 4.6 8.7 - - + -
116B VAL* 3.9 37.5 - - + -
137B VAL* 3.8 31.9 - - + -
145B VAL* 4.7 5.6 - - + -
146B THR 3.4 3.1 - - - +
147B VAL* 3.8 21.3 - - + -
191B CYS* 4.0 14.6 - - - -
192B ASN* 1.4 72.8 - - - +
194B ASN* 1.3 63.9 + - - +
195B HIS 4.3 0.2 - - - -
200B THR 4.1 0.5 - - - +
201B LYS* 3.6 5.7 - - - +
202B VAL* 2.8 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PRO 4.4 0.2 - - - +
145B VAL* 3.3 6.6 - - - -
146B THR* 2.8 55.8 + - + +
192B ASN 4.0 1.5 + - - +
193B VAL* 1.3 73.1 - - - +
195B HIS* 1.3 60.0 + - - +
196B LYS* 3.2 40.0 + - - +
200B THR 3.9 3.7 + - - +
201B LYS* 3.4 41.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LYS 3.4 24.2 + - - -
114B PRO* 3.7 20.2 - - + +
140B TYR* 3.7 4.9 - + + -
141B PHE 3.8 8.5 - - - -
142B PRO 2.7 26.0 + - - -
144B PRO 3.2 25.4 - - - -
145B VAL* 3.4 20.0 - - + -
193B VAL 4.3 0.4 - - - -
194B ASN* 1.3 71.7 + - - +
196B LYS* 1.3 63.9 + - - +
197B PRO* 3.4 10.0 - - + +
198B SER* 2.6 37.5 + - - +
199B ASN 3.2 16.6 + - - -
200B THR* 2.9 22.4 + - - +
----------------------------------------------------------
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