Contacts of the strand formed by residues 189 - 193 (chain B) in PDB entry 1V1A
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 189 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 4.0 11.0 - - + -
159B ARG* 4.2 9.9 - - - +
160B VAL 3.0 3.4 + - - -
161B SER* 3.5 17.0 - - - +
162B LEU 2.6 32.1 + - - -
187B VAL* 3.0 10.1 - - - +
188B ASP* 1.3 80.8 - - - +
190B LEU* 1.3 64.6 + - - +
191B PHE* 3.4 37.9 - - + -
215B GLU* 3.3 33.7 - - + +
217B VAL* 4.2 5.4 - - + -
257B TYR* 4.0 19.5 - - + -
258B LEU* 3.7 12.8 - - + -
261B ALA* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 3.2 31.0 - - + +
164B VAL* 3.7 27.4 - - + -
180B LEU* 5.6 4.5 - - + -
184B LEU* 4.9 8.7 - - + -
187B VAL* 4.1 9.2 - - + -
189B LEU* 1.3 77.9 - - - +
191B PHE* 1.3 65.9 + - - +
192B LEU* 4.5 8.3 - - + -
211B LEU* 4.2 32.3 - - + +
213B ALA* 4.4 4.5 - - + +
215B GLU 3.0 7.1 + - - -
216B VAL* 3.4 28.1 - - + +
217B VAL 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B HIS* 4.2 6.5 - + - -
161B SER* 2.9 26.0 - - - -
162B LEU 2.6 31.2 + - - +
163B ASP* 3.3 19.3 - - + +
164B VAL* 2.8 35.3 + - - +
189B LEU* 3.4 26.2 - - + -
190B LEU* 1.3 72.1 - - - +
192B LEU* 1.3 58.6 + - - +
217B VAL* 3.5 19.7 - - + -
219B LYS* 4.2 7.0 - - - +
253B PHE* 4.4 12.1 - + - -
254B ALA* 3.6 40.4 - - + -
257B TYR* 3.7 25.4 - + + -
258B LEU* 4.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ASP* 5.0 0.2 - - - -
164B VAL* 4.0 15.3 - - + -
190B LEU* 4.5 10.1 - - + +
191B PHE* 1.3 76.4 - - - +
193B SER* 1.3 74.0 + - - +
196B GLU* 3.5 26.0 - - + +
197B ALA* 3.5 25.6 - - + +
200B LEU* 6.1 0.7 - - + -
201B PHE* 6.4 0.9 - - + -
207B ALA* 4.6 10.1 - - + -
208B LEU* 4.8 13.7 - - + -
211B LEU* 4.8 14.8 - - + -
216B VAL* 5.4 3.8 - - + -
217B VAL 3.0 8.6 + - - +
218B LEU* 3.2 18.1 - - + +
219B LYS* 2.7 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LEU* 1.3 80.2 - - - +
194B GLU* 1.3 64.1 + - - +
195B GLU* 3.8 11.0 + - - +
196B GLU* 2.8 45.0 + - - +
197B ALA 3.1 15.8 + - - -
218B LEU* 3.7 2.2 - - - -
219B LYS* 3.3 17.4 - - - +
1303B ADP 4.3 25.6 - - - -
----------------------------------------------------------
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