Contacts of the helix formed by residues 147 - 158 (chain A) in PDB entry 3P8P
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 ASN 147 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASN 3.2 21.9 + - - -
124A ALA* 3.6 2.6 - - - -
125A THR* 3.0 34.1 + - - +
142A LEU* 3.4 14.4 - - - +
143A SER 5.7 0.2 - - - +
146A THR* 1.3 75.2 - - - +
148A GLN* 1.3 71.8 + - + +
149A ARG* 3.4 4.9 + - - -
150A GLY* 3.0 25.3 + - - -
151A ALA 3.2 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 3.7 28.5 - - - +
147A ASN* 1.3 74.6 - - + +
149A ARG* 1.3 68.4 + - + +
150A GLY 2.8 1.4 + - - -
151A ALA* 2.9 6.1 + - - +
152A GLU* 2.7 49.4 + - - +
165A THR* 4.6 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASP* 3.4 23.1 + - - +
123A ASN* 4.0 13.9 - - + +
124A ALA* 3.4 21.3 - - + -
147A ASN* 3.4 6.1 + - - +
148A GLN* 1.3 79.7 - - + +
150A GLY* 1.3 53.5 + - - +
152A GLU* 2.9 36.8 + - - +
153A ILE* 2.7 68.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A MET* 3.8 8.2 - - - +
124A ALA* 4.0 4.4 - - - +
125A THR 3.7 16.6 - - - -
126A LEU* 3.7 17.8 - - - +
146A THR* 4.6 0.2 - - - -
147A ASN* 3.0 14.6 + - - -
148A GLN 2.8 2.8 + - - -
149A ARG* 1.3 79.2 - - - +
151A ALA* 1.3 62.3 + - - +
153A ILE* 3.1 2.6 + - - +
154A LEU* 2.9 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 4.3 2.0 - - - +
140A VAL* 3.9 24.0 - - + -
142A LEU* 4.6 2.0 - - + -
146A THR* 4.5 1.6 - - - +
147A ASN 3.2 7.5 + - - +
148A GLN* 2.9 10.7 + - - +
150A GLY* 1.3 70.2 - - - -
152A GLU* 1.3 54.0 + - + +
154A LEU* 3.1 7.7 + - - +
155A ALA* 2.7 38.3 + - - +
163A VAL* 4.4 4.2 - - + +
165A THR* 3.4 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLN* 2.7 53.0 + - + +
149A ARG* 2.9 41.0 + - - +
151A ALA* 1.3 73.6 - - - +
153A ILE* 1.3 61.6 + - - +
155A ALA* 3.5 6.6 + - - +
156A ASP* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 5.0 5.8 - - + -
117A VAL* 5.7 3.6 - - + -
118A GLU 5.7 1.6 - - - +
119A MET* 4.1 28.9 - - + -
120A LYS 5.4 0.4 - - - +
121A ASP* 3.9 24.7 - - + +
124A ALA* 3.9 10.5 - - + -
149A ARG* 2.7 51.7 + - - +
150A GLY 3.7 3.1 - - - +
152A GLU* 1.3 69.1 - - - +
154A LEU* 1.3 56.5 + - - +
156A ASP* 3.1 10.0 + - + +
157A THR* 2.7 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 4.8 5.8 - - + -
89A LEU* 3.7 24.8 - - + +
126A LEU* 3.5 24.2 - - + -
131A VAL* 3.9 25.4 - - + -
138A PHE* 4.2 11.7 - - + -
140A VAL* 4.3 4.9 - - + -
150A GLY 2.9 16.6 + - - +
151A ALA* 3.6 4.5 - - - +
153A ILE* 1.3 78.2 - - - +
155A ALA* 1.3 63.3 + - - +
157A THR* 3.1 6.7 + - - -
158A PHE* 3.1 42.3 + - + +
163A VAL* 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ALA 2.7 21.5 + - - +
152A GLU* 3.7 8.1 - - - +
154A LEU* 1.3 72.9 - - - +
156A ASP* 1.3 62.1 + - - +
158A PHE 3.5 19.1 - - - +
159A LYS* 3.6 5.5 + - - +
161A TYR 4.8 1.4 - - - +
163A VAL* 3.6 32.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLU 3.2 10.2 + - - +
153A ILE* 3.1 13.8 + - + +
154A LEU 3.1 0.4 - - - -
155A ALA* 1.3 80.5 - - - +
157A THR* 1.3 62.2 + - - +
159A LYS* 3.4 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A THR* 4.2 9.6 + - + +
89A LEU* 4.1 11.7 - - + +
117A VAL* 3.8 43.0 - - + +
153A ILE* 2.7 25.3 + - - +
154A LEU* 3.1 10.1 + - - -
156A ASP* 1.3 78.5 - - - +
158A PHE* 1.3 86.6 + - + +
159A LYS* 3.6 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 3.8 25.6 - - + -
84A CYS* 3.3 29.4 - - + -
87A THR* 3.7 28.0 - - - -
89A LEU* 3.9 20.0 - - + -
138A PHE* 3.6 38.1 - + + -
154A LEU* 3.1 38.2 + - + +
155A ALA 3.5 6.1 - - - +
157A THR* 1.3 88.1 - - + +
159A LYS* 1.3 57.2 + - - +
160A ASP* 2.9 14.6 + - - +
161A TYR* 2.9 26.8 + - + +
163A VAL* 4.9 0.8 - - + +
----------------------------------------------------------
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