Contacts of the helix formed by residues 147 - 152 (chain C) in PDB entry 5U0A
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 GLY 147 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C THR* 3.1 9.5 + - - -
146C SER* 1.3 79.4 - - - +
148C VAL* 1.3 67.3 + - - -
149C ASN* 3.2 3.6 - - - -
150C LYS* 3.2 6.6 + - - +
151C LEU 3.3 8.1 + - - -
170C ASP* 5.8 3.1 - - - -
173C PRO* 6.5 0.4 - - - -
293C ASP* 4.7 5.8 - - - -
294C ALA* 2.7 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C GLY* 1.3 73.5 - - - -
149C ASN* 1.3 74.5 + - - +
151C LEU* 2.9 6.1 + - + +
152C ALA* 2.8 32.8 + - - +
173C PRO* 4.1 20.6 - - + +
174C HIS 4.6 5.6 - - - +
175C PRO* 5.2 0.9 - - + -
176C LEU* 4.2 24.5 - - + -
291C VAL* 3.7 27.6 - - + +
292C VAL 3.3 33.5 + - - +
293C ASP* 4.1 2.0 - - - +
294C ALA* 4.0 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C GLY* 3.2 1.7 - - - -
148C VAL* 1.3 86.9 - - - +
150C LYS* 1.3 59.8 + - - +
152C ALA 3.5 7.1 - - - +
155C ARG* 3.4 36.8 + - + +
156C THR 3.1 23.6 + - - +
157C ALA* 4.3 1.8 + - - +
168C HIS* 3.9 29.6 - - - +
170C ASP* 3.7 33.1 + - - +
173C PRO* 3.5 27.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C SER* 3.3 38.2 + - - +
147C GLY 3.2 3.8 + - - +
148C VAL 3.2 0.4 - - - -
149C ASN* 1.3 78.3 - - - +
151C LEU* 1.3 62.1 + - - +
152C ALA 4.7 0.6 - - - +
157C ALA* 3.9 26.2 - - + +
158C GLY 5.3 0.4 - - - +
188C THR* 5.4 0.9 - - - +
193C PRO* 3.7 29.5 - - - +
197C CYS* 5.1 14.3 - - - +
198C THR* 5.8 3.1 - - + -
278C HIS* 5.7 0.2 - - - -
296C VAL* 4.6 15.2 - - + +
56M T 4.1 22.2 - - - -
57M T 4.2 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C GLY 3.3 10.6 + - - +
148C VAL* 2.9 10.3 + - + +
150C LYS* 1.3 80.0 - - - +
152C ALA* 1.3 68.5 + - + +
153C TRP* 3.6 4.5 + - - -
176C LEU* 6.2 2.9 - - + -
181C ALA* 5.0 7.0 - - + +
184C HIS* 4.3 17.0 - - + +
185C LEU* 4.3 8.7 - - + +
188C THR* 3.2 56.0 - - + +
280C VAL* 3.7 25.1 - - + -
282C LEU* 5.4 9.4 - - + -
291C VAL* 5.6 4.0 - - + -
294C ALA* 3.9 20.4 - - + -
296C VAL* 4.0 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C VAL 2.8 17.3 + - - +
149C ASN 3.5 5.4 - - - +
150C LYS 4.7 1.0 - - - +
151C LEU* 1.3 77.1 - - + +
153C TRP* 1.3 61.5 + - - +
155C ARG* 3.2 42.1 + - + +
176C LEU* 4.0 11.7 - - + -
184C HIS* 3.6 33.2 - - + +
----------------------------------------------------------
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