Contacts of the strand formed by residues 189 - 193 (chain E) in PDB entry 3MQ6
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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E SER* 3.4 37.7 - - - +
110E MET* 3.9 18.2 - - + -
147E VAL* 3.8 17.9 - - + -
148E LEU 3.4 15.5 - - - +
149E ASN* 4.8 0.9 - - - +
150E LEU* 4.4 1.8 - - - -
187E PRO* 3.1 7.5 - - - +
188E ASP* 1.3 81.4 - - - +
190E ALA* 1.3 65.5 + - - +
191E VAL* 3.7 28.5 - - + -
238E ALA* 3.3 4.0 - - - -
239E VAL* 2.8 40.3 + - + +
241E PHE* 4.0 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 190 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E LEU* 2.9 38.1 + - + +
150E LEU* 4.2 12.5 - - + +
159E LEU* 4.0 27.1 - - + -
187E PRO* 5.2 4.3 - - + -
189E LEU* 1.3 78.6 - - - +
191E VAL* 1.3 59.2 + - - +
192E VAL* 4.3 8.1 - - + -
235E ILE* 5.0 8.3 - - + -
237E LEU 3.3 7.6 - - - +
238E ALA* 4.5 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E MET* 3.8 18.8 - - + -
145E VAL* 4.0 25.6 - - + -
146E ALA 3.3 11.0 - - - +
147E VAL* 4.4 6.3 - - + -
189E LEU* 3.7 19.3 - - + -
190E ALA* 1.3 72.1 - - - +
192E VAL* 1.3 58.3 + - - +
235E ILE* 4.0 0.3 - - - +
236E SER* 2.7 38.9 + - - -
237E LEU* 2.8 33.0 + - + +
326E PHE* 3.9 20.4 - - + -
329E PHE* 5.9 0.4 - - + -
330E LEU* 4.7 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E VAL* 3.2 5.4 - - - -
146E ALA* 2.7 42.0 + - + +
148E LEU* 4.1 11.0 - - + -
159E LEU* 4.4 7.2 - - + -
190E ALA* 3.9 15.9 + - + -
191E VAL* 1.3 80.2 - - - +
193E VAL* 1.3 64.7 + - - +
226E LEU* 3.4 32.5 - - + -
230E VAL* 3.8 26.0 - - + -
234E GLU 3.2 11.2 - - - +
235E ILE* 4.1 17.5 - - + -
236E SER* 4.0 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E ARG 3.8 19.5 - - - +
144E GLN 3.6 13.0 - - - +
145E VAL* 4.3 1.6 - - - +
192E VAL* 1.3 75.8 - - - +
194E LEU* 1.3 77.8 + - - +
195E PRO* 3.1 9.5 - - - +
199E GLN* 4.7 1.8 - - - +
230E VAL* 5.2 1.9 - - - +
233E GLY 5.2 1.1 - - - +
234E GLU* 2.9 48.6 + - + +
236E SER* 3.6 15.7 + - - +
334E MET* 4.1 17.9 - - + -
337E VAL* 4.5 13.5 - - + -
----------------------------------------------------------
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