Contacts of the helix formed by residues 144 - 160 (chain A) in PDB entry 1O4X
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 GLU 144 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A MET* 1.3 75.1 - - - +
145A LYS* 1.3 68.9 + - + +
146A GLU* 3.3 28.8 + - - +
147A VAL* 3.3 31.8 + - + +
148A ILE* 3.3 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ILE* 4.3 9.4 - - + +
135A THR* 5.3 11.9 - - + +
138A ALA* 4.1 17.6 - - + +
143A MET 3.5 2.0 + - - -
144A GLU* 1.3 75.7 - - + +
146A GLU* 1.3 58.4 + - - +
148A ILE* 2.9 6.9 + - - +
149A ARG* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLU* 3.3 21.3 + - - +
145A LYS* 1.3 77.8 - - - +
147A VAL* 1.3 58.2 + - + +
149A ARG* 2.6 42.8 + - - +
150A VAL* 2.9 45.2 + - + +
318C T 5.3 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE* 4.5 25.3 - - + +
143A MET* 5.0 8.7 - - + -
144A GLU* 3.3 35.1 + - + +
145A LYS 3.2 0.2 - - - -
146A GLU* 1.3 77.7 - - + +
148A ILE* 1.3 64.5 + - + +
150A VAL* 3.5 2.6 + - - +
151A TRP* 3.0 25.8 + - - +
316C A 5.7 0.4 - - - +
317C A 3.9 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE* 5.9 0.4 - - + -
119A LEU* 4.0 28.7 - - + -
134A ILE* 3.9 24.5 - - + +
137A ILE* 4.6 8.5 - - + -
138A ALA* 4.1 13.9 - - + -
141A LEU* 4.8 6.7 - - + -
143A MET* 4.0 26.9 - - + -
144A GLU 3.5 12.6 - - - +
145A LYS 2.9 8.6 + - - +
147A VAL* 1.3 81.2 - - + +
149A ARG* 1.3 64.9 + - - +
151A TRP* 3.1 12.6 + - + +
152A PHE* 3.2 34.3 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
134A ILE* 3.9 31.6 - - + +
145A LYS 2.9 12.4 + - - +
146A GLU* 2.6 41.1 + - - +
148A ILE* 1.3 77.8 - - - +
150A VAL* 1.3 73.6 + - - +
152A PHE* 3.4 3.6 + - - +
153A CYS* 3.1 43.0 + - - -
318C T 5.1 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLU* 2.9 42.4 + - + +
147A VAL* 3.7 5.8 - - - +
149A ARG* 1.3 84.8 - - - +
151A TRP* 1.3 59.1 + - - +
153A CYS* 3.2 8.3 + - + +
154A ASN* 2.8 49.0 + - - +
316C A 4.6 0.7 - - + -
317C A 3.8 35.7 - - + +
318C T 4.3 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE* 3.7 19.5 - - + -
116A ARG* 4.4 21.5 - - + -
119A LEU* 3.4 47.8 + - + +
120A GLU* 3.6 29.6 - - + -
123A PHE* 5.4 0.2 - - - +
147A VAL 3.0 15.6 + - - +
148A ILE* 3.5 10.3 - - + +
150A VAL* 1.3 78.3 - - - +
152A PHE* 1.3 78.9 + + - +
154A ASN* 3.4 9.2 + - + +
155A ARG* 2.9 40.9 + - + +
158A LYS* 6.3 0.4 - - - -
315C T 4.5 10.3 - - - -
316C A 2.9 34.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 4.2 12.3 - - + -
122A SER* 3.4 28.3 - - - -
123A PHE* 3.8 23.8 - + + -
126A ASN 3.6 20.6 - - - -
127A GLN 3.6 9.2 - - - -
129A PRO* 3.6 33.0 - - + -
134A ILE* 5.0 4.5 - - + -
137A ILE* 4.4 8.1 - - + -
148A ILE* 3.2 34.4 + - + +
149A ARG* 3.8 7.9 - - - +
151A TRP* 1.3 92.1 - + - +
153A CYS* 1.3 66.7 + - - +
155A ARG* 3.6 2.7 - - - +
156A ARG* 2.9 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ARG* 3.1 49.2 + - - -
150A VAL* 3.2 10.7 + - + +
152A PHE* 1.3 77.7 - - - +
154A ASN* 1.3 63.1 + - - +
156A ARG* 3.3 25.7 + - - +
157A GLN* 3.1 38.7 + - - +
320D C 5.6 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 2.8 33.2 + - - +
151A TRP* 3.7 7.8 - - + +
153A CYS* 1.3 72.9 - - - +
155A ARG* 1.3 58.3 + - - +
157A GLN* 3.3 17.0 + - - +
158A LYS* 2.9 30.4 + - - +
161A ARG* 5.6 1.0 + - - -
316C A 3.5 28.0 + - + +
317C A 3.2 43.0 + - - +
318C T 4.7 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 3.4 28.2 + - - +
123A PHE* 3.3 44.1 - - + -
124A LEU* 6.4 0.4 - - - +
151A TRP* 2.9 31.4 + - + +
152A PHE* 3.6 9.6 - - - +
153A CYS 3.2 0.2 - - - -
154A ASN* 1.3 77.9 - - - +
156A ARG* 1.3 61.7 + - - +
158A LYS* 3.4 24.2 + - - +
159A GLU* 2.9 53.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 3.9 13.7 - - + -
127A GLN* 3.2 42.1 + - - +
128A LYS* 4.3 17.4 - - - +
129A PRO* 4.8 0.6 - - - +
152A PHE* 2.9 36.7 + - - +
153A CYS* 3.7 29.8 - - - +
155A ARG* 1.3 72.8 - - - +
157A GLN* 1.3 66.8 + - + +
159A GLU* 3.4 5.0 + - - +
160A LYS* 3.2 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A CYS* 3.1 27.4 + - - +
154A ASN* 3.5 20.0 + - - +
155A ARG 3.2 0.2 - - - -
156A ARG* 1.3 77.7 - - + +
158A LYS* 1.3 62.6 + - - +
160A LYS* 3.0 21.8 + - + +
161A ARG* 3.5 21.4 + - - +
317C A 4.7 0.5 + - - -
318C T 5.0 0.6 + - - -
320D C 3.5 36.8 - - + +
321D A 3.5 30.6 + - - +
322D T 3.8 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 6.0 0.4 + - - -
151A TRP* 6.3 0.6 - - - -
154A ASN 2.9 17.4 + - - +
155A ARG* 3.4 28.4 + - - +
157A GLN* 1.3 76.0 - - - +
159A GLU* 1.3 61.7 + - - +
161A ARG* 3.1 54.9 + - - +
163A ASN 5.6 1.7 - - - -
315C T 2.4 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 4.4 10.5 - - + -
127A GLN* 4.4 20.2 + - - +
155A ARG* 2.9 38.3 + - - +
156A ARG* 3.5 13.2 - - - +
158A LYS* 1.3 76.9 - - - +
160A LYS* 1.3 61.1 + - + +
161A ARG 3.2 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 3.2 23.1 - - - +
157A GLN* 3.0 13.5 + - + +
159A GLU* 1.3 77.6 - - + +
161A ARG* 1.3 63.4 + - - +
162A ILE* 3.8 1.0 + - - +
320D C 4.8 13.3 + - - -
----------------------------------------------------------
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