Contacts of the strand formed by residues 149 - 151 (chain C) in PDB entry 6CU0
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 149 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LEU* 3.7 22.4 - - + -
147C LEU* 4.2 10.1 - - + -
148C GLU* 1.3 76.7 - - - +
150C ARG* 1.3 59.0 + - - +
161C VAL* 3.9 19.7 - - + -
183C VAL* 3.6 25.6 - - + -
185C LEU* 3.6 21.3 - - + -
195C SER* 3.4 6.9 - - - -
196C ALA* 2.9 28.5 + - + +
226C TRP* 3.8 16.4 - - + -
227C GLN 3.4 10.5 - - - +
228C LEU* 3.6 28.0 - - + -
229C THR* 3.2 8.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LEU* 1.3 74.3 - - - +
151C ARG* 1.3 67.2 + - - +
152C VAL* 3.4 9.4 + - + +
194C ASN 4.2 7.6 - - - +
195C SER* 4.5 1.1 - - - +
226C TRP* 3.3 5.9 - - - -
227C GLN* 2.8 37.0 + - + +
228C LEU 5.5 0.2 - - - -
229C THR* 3.4 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C ARG* 1.3 73.1 - - - +
152C VAL* 1.3 61.9 + - - +
153C VAL 3.7 14.8 - - - +
154C ALA* 4.4 4.5 - - - +
155C GLY 4.1 12.8 - - - +
156C GLU 2.8 40.1 + - - +
157C GLY 2.8 19.8 + - - -
186C PRO* 2.8 30.5 + - - +
187C PRO 4.6 0.2 + - - -
188C ALA* 3.6 22.4 - - - +
192C ALA* 5.2 0.2 - - - +
193C ARG 5.0 3.0 - - - +
194C ASN* 2.7 48.7 + - - +
225C ALA 3.5 7.4 - - - +
226C TRP* 3.2 38.0 - - + +
----------------------------------------------------------
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