Contacts of the strand formed by residues 196 - 201 (chain A) in PDB entry 5V5W
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 THR 196 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 3.7 34.9 + - + +
157A CYS 3.2 10.5 - - - +
158A THR* 3.2 20.3 - - + +
167A PHE* 4.0 4.9 - - - -
188A GLU* 3.8 22.7 - - - +
189A PRO* 3.8 12.6 - - + -
192A THR* 3.5 21.9 - - - +
193A GLN 4.6 0.3 + - - -
194A GLY 2.7 21.2 + - - -
195A GLU* 1.3 71.4 - - - +
197A LYS* 1.3 72.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A CYS 2.8 34.8 + - - -
167A PHE* 3.3 50.2 - - + -
169A TRP* 3.4 16.4 - - - +
186A ILE* 3.8 27.8 - - + -
187A TYR* 3.8 14.4 - - - +
188A GLU* 4.3 18.3 + - - +
196A THR* 1.3 77.7 + - - +
198A VAL* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PHE* 4.2 17.5 - - + -
155A LEU 3.2 7.9 - - - +
156A ARG* 3.9 21.1 - - + -
169A TRP* 4.4 1.8 - - - -
185A ASP 3.7 0.9 - - - +
186A ILE* 3.3 8.3 - - - +
187A TYR* 2.8 66.0 + - + +
189A PRO* 3.5 35.4 - - + -
197A LYS* 1.3 74.6 - - - +
199A LEU* 1.3 71.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A VAL 3.4 3.5 - - - +
154A PHE* 3.4 0.7 - - - -
155A LEU* 2.7 47.0 + - + +
169A TRP* 3.7 38.8 - - + -
175A THR* 4.8 3.4 - - - +
184A VAL* 3.6 21.3 - - + -
185A ASP 3.6 1.1 - - - +
186A ILE* 3.5 28.3 - - + -
198A VAL* 1.3 74.1 - - - +
200A LYS* 1.3 59.0 + - - +
201A LEU* 3.3 38.4 - - + -
212A TYR* 4.7 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A THR* 5.1 2.9 - - - -
153A VAL 3.3 5.8 - - - +
154A PHE* 3.4 37.2 - - + -
183A GLY 3.7 6.1 - - - +
184A VAL* 3.9 2.9 - - - -
185A ASP* 2.8 61.3 + - + +
187A TYR* 3.9 19.4 - - + +
198A VAL 4.0 0.4 - - - -
199A LEU* 1.3 72.0 - - - +
201A LEU* 1.3 69.5 + - - +
202A LYS* 3.8 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LYS 4.2 0.5 - - - +
152A THR* 3.3 3.5 - - - -
153A VAL* 2.8 47.3 + - + +
155A LEU* 4.2 11.4 - - + -
171A ARG* 5.2 3.8 - - - +
183A GLY 4.5 0.7 - - - +
184A VAL* 4.4 20.4 - - + -
199A LEU* 3.3 29.4 - - + -
200A LYS* 1.3 75.1 - - - +
202A LYS* 1.3 64.1 + - - +
203A ASN 3.8 9.1 - - - +
204A LEU* 4.9 5.0 - - + +
212A TYR* 3.5 45.1 - - + +
233A LEU* 4.4 11.7 - - + -
----------------------------------------------------------
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