Contacts of the helix formed by residues 145 - 153 (chain C) in PDB entry 3REO
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 TYR 145 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LYS* 6.0 0.3 + - - -
141C GLU* 3.6 30.6 + - - -
142C PRO 2.8 8.8 + - - +
144C PHE* 1.3 85.4 - - + +
146C LEU* 1.3 66.1 + - - +
147C LYS 3.3 1.6 - - - -
148C ASP* 3.3 25.1 + - - +
149C ALA* 3.1 23.0 + - - +
156C PRO* 3.7 19.2 - - + +
159C LYS* 3.7 27.9 + - + +
160C ALA* 3.8 30.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA* 4.6 4.3 - - - -
40A ALA* 3.5 24.7 - - + -
79A MET* 4.7 2.7 - - + -
83A VAL* 4.2 19.7 - - + -
142C PRO 3.5 2.5 + - - +
143C TRP* 3.4 48.3 + - + +
144C PHE 3.5 0.2 - - - -
145C TYR* 1.3 75.1 - - - +
147C LYS* 1.3 68.0 + - - +
149C ALA* 3.1 2.8 + - - -
150C ILE* 3.0 39.0 + - + +
156C PRO* 3.8 23.1 - - + -
324C LEU* 4.3 22.0 - - + -
325C ALA* 5.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 4.4 7.3 - - + +
43A GLU* 3.8 52.0 + - + +
44A LEU* 4.0 29.0 - - + +
143C TRP 5.1 0.2 + - - -
144C PHE 5.2 3.5 + - - +
145C TYR 3.3 0.4 - - - -
146C LEU* 1.3 78.5 - - - +
148C ASP* 1.3 71.7 + - - +
150C ILE* 3.2 2.1 + - - +
151C LEU* 3.0 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C PHE 4.6 3.0 - - - +
145C TYR* 3.3 34.0 + - - +
146C LEU 3.2 0.2 - - - -
147C LYS* 1.3 90.6 - - - +
149C ALA* 1.3 52.9 + - - +
151C LEU* 4.8 2.6 - - - +
152C GLU* 2.6 51.3 + - + +
159C LYS* 3.9 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 3.2 4.2 + - - -
79A MET* 3.7 9.7 - - + +
145C TYR 3.1 6.4 + - - +
146C LEU 3.1 4.7 + - - +
148C ASP* 1.3 72.6 - - - +
150C ILE* 1.3 65.8 + - - +
153C GLY* 2.9 32.8 + - - -
154C GLY 3.7 15.5 - - - +
156C PRO* 3.6 40.6 - - + -
159C LYS* 3.6 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 5.3 0.9 - - + -
44A LEU* 3.6 37.7 - - + -
69A LEU* 4.4 10.3 - - + -
71A THR* 3.7 2.3 + - - -
73A ASN* 3.0 24.1 + - - +
76A ALA* 3.7 25.9 - - + +
79A MET* 3.6 31.4 - - + -
80A LEU* 4.5 12.3 - - + -
83A VAL* 4.5 13.9 - - + -
146C LEU* 3.0 35.2 + - + +
147C LYS 3.6 6.1 - - - +
149C ALA* 1.3 78.1 - - - +
151C LEU* 1.3 59.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
44A LEU* 3.5 31.4 - - + -
69A LEU* 4.0 17.5 - - + -
70A PRO* 3.9 24.6 - - + +
71A THR* 2.9 40.3 + - + -
72A THR* 4.5 3.5 + - - +
73A ASN* 4.1 2.3 + - - +
147C LYS* 3.0 38.4 + - + +
148C ASP* 4.1 2.9 - - - +
150C ILE* 1.3 79.6 - - - +
152C GLU* 1.3 79.7 + - + +
153C GLY 3.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PRO 4.9 3.8 - - - +
73A ASN* 4.8 2.2 - - - -
148C ASP* 2.6 32.8 + - + +
151C LEU* 1.3 96.9 - - + +
153C GLY* 1.4 61.6 + - - +
159C LYS* 4.6 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 3.4 22.5 - - - +
149C ALA* 2.9 18.7 + - - -
151C LEU 3.5 1.8 - - - -
152C GLU* 1.4 77.0 - - - +
154C GLY* 1.3 61.0 + - - -
159C LYS* 2.9 28.6 + - - -
----------------------------------------------------------
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