Contacts of the helix formed by residues 147 - 159 (chain L) in PDB entry 2X17
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 SER 147 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495 GLN* 3.2 21.8 + - - -
144L ALA* 4.0 17.2 - - - +
145L LYS 3.4 5.0 + - - -
146L ASP* 1.3 78.3 - - - +
148L PRO* 1.3 63.0 - - - +
149L GLN* 3.1 17.5 + - - -
150L ILE* 3.4 28.8 + - - +
151L LEU* 3.5 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 148 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146L ASP 4.0 6.5 - - - +
147L SER* 1.3 83.3 - - - +
149L GLN* 1.3 76.1 + - - +
150L ILE 3.4 0.2 - - - -
151L LEU* 3.7 11.0 - - + +
152L PHE* 3.0 28.6 + - - +
143Y PHE* 3.8 31.4 - - + +
147Y SER* 6.3 0.4 - - - -
150Y ILE* 3.9 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 149 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495 GLN* 3.9 24.2 + - + +
149J GLN* 6.3 0.7 - - + -
146L ASP 5.3 0.2 - - - +
147L SER* 3.1 18.1 + - - +
148L PRO* 1.3 98.2 - - - +
150L ILE* 1.3 58.9 + - - +
152L PHE* 3.5 5.2 + - - +
153L MET* 3.2 33.5 + - + +
147Y SER* 3.5 20.2 + - - -
149Y GLN* 3.9 34.2 + - + -
150Y ILE* 3.9 16.1 - - + +
153Y MET* 3.9 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1485 PRO* 3.9 15.0 - - + +
1495 GLN* 3.9 38.6 - - + +
1525 PHE* 4.1 31.4 - - + -
140L LYS* 4.9 2.5 - - + +
143L PHE* 4.5 7.4 - - + +
144L ALA* 3.6 26.7 - - + -
147L SER* 3.4 24.8 + - - +
148L PRO 3.4 0.2 - - - -
149L GLN* 1.3 75.5 - - - +
151L LEU* 1.3 59.3 + - - +
152L PHE 3.3 0.4 - - - -
153L MET* 3.7 10.5 - - + -
154L LEU* 2.9 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L LEU* 4.4 20.2 - - + +
39L PHE* 4.0 14.1 - - + -
83L PRO* 4.3 21.1 - - + -
141L LEU* 3.8 28.3 - - + -
144L ALA* 4.8 5.1 - - + +
147L SER 3.5 13.5 + - - +
148L PRO* 3.5 10.2 + - + +
149L GLN 3.3 0.4 - - - -
150L ILE* 1.3 78.3 - - - +
152L PHE* 1.3 60.9 + - - +
154L LEU* 3.6 6.6 + - - +
155L ASP* 3.2 22.3 + - - +
143Y PHE* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L LEU* 5.6 2.7 - - + -
148L PRO 3.0 17.5 + - - +
149L GLN* 3.6 7.4 - - - +
150L ILE 3.3 0.2 - - - -
151L LEU* 1.3 77.1 - - - +
153L MET* 1.3 63.4 + - - +
155L ASP* 3.4 18.0 + - + +
156L LYS* 3.5 14.9 + - + +
140Y LYS* 4.7 16.6 - - + -
143Y PHE* 5.0 12.1 - + + -
150Y ILE* 4.1 18.8 - - + -
153Y MET* 3.7 46.4 - - + -
154Y LEU* 4.2 22.2 - - + -
157Y GLU* 3.3 37.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 153 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495 GLN* 4.2 14.4 - - + +
1525 PHE* 3.7 33.9 - - + -
1535 MET* 3.7 17.7 - - + +
11745 AG 2.7 28.5 - - - -
149L GLN* 3.2 24.0 + - + +
150L ILE* 3.8 17.7 - - + +
151L LEU 3.3 0.2 - - - -
152L PHE* 1.3 77.4 - - + +
154L LEU* 1.3 61.6 + - - +
156L LYS* 3.5 6.8 + - - +
157L GLU* 3.3 26.8 + - - +
153Y MET* 3.9 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1525 PHE* 4.7 10.3 - - + -
39L PHE* 3.9 10.3 - - + -
137L ILE* 4.5 15.3 - - + -
140L LYS* 3.9 56.1 - - + +
141L LEU* 4.1 20.6 - - + -
144L ALA* 5.4 1.6 - - + -
150L ILE* 2.9 26.1 + - + +
151L LEU* 3.8 6.5 - - - +
152L PHE 3.4 0.2 - - - -
153L MET* 1.3 73.7 - - - +
155L ASP* 1.3 65.0 + - - +
157L GLU* 3.4 12.9 + - + +
158L LEU* 3.1 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 155 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L GLY 4.7 1.9 - - - +
36L LEU* 3.3 24.0 - - + +
37L GLU* 3.7 6.9 + - - +
38L GLY* 2.9 50.1 + - - -
39L PHE* 3.2 24.6 + - + -
151L LEU 3.2 15.4 + - - +
152L PHE* 3.5 15.5 - - + +
153L MET 3.3 0.2 - - - -
154L LEU* 1.3 77.5 - - - +
156L LYS* 1.3 59.8 + - - +
158L LEU* 3.6 0.4 + - - -
159L SER* 3.2 8.7 + - - -
140Y LYS* 5.6 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 156 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1565 LYS* 5.6 6.4 - - - +
152L PHE* 3.5 11.8 + - + +
153L MET* 3.9 9.4 - - - +
154L LEU 3.3 0.4 - - - -
155L ASP* 1.3 80.8 - - - +
157L GLU* 1.3 61.1 + - + +
159L SER* 2.6 25.8 + - - +
160L ALA* 4.1 2.8 + - - +
156Y LYS* 5.3 11.1 - - - +
157Y GLU* 4.7 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 157 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1525 PHE* 3.7 31.2 - - + -
1565 LYS* 3.9 33.8 - - - +
140L LYS* 4.2 15.9 + - - -
153L MET 3.3 13.7 + - - +
154L LEU* 3.4 11.3 + - + +
156L LYS* 1.3 78.0 - - + +
158L LEU* 1.3 65.3 + - + +
159L SER 3.7 0.2 + - - -
160L ALA* 3.8 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L GLY 3.4 19.6 - - - +
39L PHE* 3.6 46.0 - - + -
42L TRP* 3.6 30.8 - - + +
87L PHE* 4.9 1.3 - - + -
137L ILE* 3.9 30.5 - - + -
154L LEU* 3.1 23.4 + - + +
157L GLU* 1.3 77.4 - - + +
159L SER* 1.3 59.4 + - - +
160L ALA 3.1 6.6 + - - -
161L ARG* 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 159 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L GLU 5.4 0.4 - - - -
38L GLY* 3.8 15.7 - - - -
41L ASN* 5.3 7.7 + - - -
155L ASP 3.2 14.7 + - - -
156L LYS* 2.6 28.8 + - - +
158L LEU* 1.3 75.6 - - - +
160L ALA* 1.3 63.9 + - - +
161L ARG 3.2 8.5 + - - +
162L ALA* 4.7 5.2 - - - +
----------------------------------------------------------
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