Contacts of the helix formed by residues 153 - 166 (chain F) in PDB entry 2A69
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 PRO 153 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F ALA* 5.5 0.4 - - + -
151F LEU* 3.4 7.4 - - + -
152F ASP* 1.3 96.1 - - + +
154F LYS* 1.3 85.4 + - + +
155F THR 3.3 0.9 - - - -
156F VAL* 3.1 20.0 - - + +
157F GLU* 3.3 17.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F LEU* 3.9 19.3 - - + +
153F PRO* 1.3 87.0 - - + +
155F THR* 1.3 66.1 + - - +
157F GLU* 3.5 5.9 + - - +
158F GLU* 2.8 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 155 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F GLU 4.7 1.8 + - - +
150F THR* 3.1 27.0 - - - +
151F LEU* 2.8 48.5 + - - +
153F PRO 3.1 1.4 + - - -
154F LYS* 1.3 80.7 - - - +
156F VAL* 1.3 64.1 + - - +
158F GLU* 3.0 22.9 + - - +
159F ILE* 3.3 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F GLU 5.9 0.2 - - - -
130F VAL* 3.7 11.8 - - + +
133F ALA* 4.6 13.0 - - + -
134F LYS* 5.6 6.5 - - - -
142F ARG* 3.8 23.1 - - - +
150F THR* 3.6 17.0 - - - +
151F LEU 4.0 1.3 - - - +
152F ASP 3.3 18.6 - - - +
153F PRO* 3.1 19.3 - - + +
155F THR* 1.3 76.0 - - - +
157F GLU* 1.3 62.3 + - + +
159F ILE* 3.1 20.7 - - + +
160F ASP* 2.6 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 157 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F LYS* 3.1 33.6 + - - +
153F PRO* 3.5 21.3 - - + +
154F LYS* 3.6 6.7 - - - +
155F THR 3.1 0.4 - - - -
156F VAL* 1.3 81.6 - - + +
158F GLU* 1.3 66.4 + - - +
160F ASP* 2.8 21.7 + - - +
161F GLN* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 158 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F LEU* 4.6 4.3 - - - +
154F LYS* 2.8 47.5 + - + +
155F THR* 3.0 15.5 + - - +
157F GLU* 1.3 74.1 - - - +
159F ILE* 1.3 65.3 + - + +
161F GLN* 3.3 27.2 + - - +
162F LYS* 3.4 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F LEU* 4.1 25.8 - - + -
126F LEU* 5.2 6.7 - - + +
127F ILE* 5.6 3.8 - - + -
130F VAL* 3.4 39.0 - - + -
155F THR* 3.3 31.2 - - + +
156F VAL* 3.1 17.0 - - + +
157F GLU 3.1 0.2 - - - -
158F GLU* 1.3 81.0 - - + +
160F ASP* 1.3 58.6 + - - +
161F GLN 3.4 0.2 + - - -
162F LYS* 3.6 10.8 + - - +
163F LEU* 3.3 25.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 160 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F VAL* 3.2 18.3 - - - +
134F LYS* 3.3 39.4 - - - +
156F VAL* 2.6 31.0 + - - +
157F GLU* 2.8 14.9 + - - +
159F ILE* 1.3 74.1 - - - +
161F GLN* 1.3 64.5 + - - +
163F LEU* 3.2 17.3 - - - +
164F LYS* 3.1 23.2 + - - +
174F LEU* 5.1 1.4 - - - +
178F ARG* 4.0 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 161 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157F GLU* 3.0 22.7 + - - +
158F GLU* 3.4 16.6 - - - +
159F ILE 3.2 0.2 - - - -
160F ASP* 1.3 75.1 - - - +
162F LYS* 1.3 61.7 + - + +
164F LYS* 3.1 20.8 + - - +
165F SER* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 162 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F THR* 4.3 27.1 - - + -
122F LEU* 4.9 18.1 - - + +
158F GLU* 3.4 22.8 + - - +
159F ILE* 4.0 7.4 - - - +
160F ASP 3.4 0.2 - - - -
161F GLN* 1.3 76.3 - - + +
163F LEU* 1.3 60.6 + - - +
165F SER* 3.4 10.8 + - - -
166F LEU* 3.2 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F LEU* 3.9 32.8 - - + -
120F THR* 5.7 3.4 - - - +
127F ILE* 5.1 8.1 - - + -
130F VAL* 4.6 10.5 - - + -
131F VAL* 5.4 6.1 - - + -
159F ILE* 3.3 23.8 - - + +
160F ASP* 3.2 28.2 + - - +
161F GLN 3.1 0.2 - - - -
162F LYS* 1.3 78.2 - - + +
164F LYS* 1.3 64.3 + - - +
166F LEU* 3.3 24.5 - - + +
171F LYS* 3.6 3.8 - - - +
174F LEU* 3.4 48.2 - - + +
178F ARG* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 164 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419D ASP 3.8 11.9 - - - +
420D VAL* 3.0 48.4 + - + +
421D LEU 4.8 0.9 - - - +
160F ASP 3.1 12.7 + - - +
161F GLN* 3.1 24.8 + - + +
163F LEU* 1.3 73.1 - - - +
165F SER* 1.3 65.5 + - - +
166F LEU 3.0 13.4 + - - +
171F LYS* 3.5 29.5 - - - +
174F LEU* 4.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 165 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F GLN* 2.9 16.7 + - - +
162F LYS* 3.5 13.1 - - - -
164F LYS* 1.3 72.3 - - - +
166F LEU* 1.3 65.6 + - - +
167F PRO* 2.8 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F LEU* 3.5 25.8 - - + -
119F ILE* 4.4 18.4 - - + +
120F THR* 4.8 11.4 - - + +
162F LYS 3.2 17.9 + - - +
163F LEU* 3.3 26.2 - - + +
164F LYS 3.0 7.0 + - - +
165F SER* 1.3 72.5 - - - +
167F PRO* 1.3 73.8 - - - +
170F HIS* 3.3 50.3 - - + +
171F LYS* 3.0 16.2 - - - +
174F LEU* 4.7 0.9 - - + -
----------------------------------------------------------
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