Contacts of the helix formed by residues 146 - 166 (chain A) in PDB entry 1HJX
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 ASP 146 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A SER* 5.1 1.7 + - - -
104A GLN* 5.7 0.5 - - - +
107A SER* 2.7 31.6 + - - -
139A TRP* 3.5 26.2 + - + -
142A PRO* 3.8 4.3 - - + -
143A GLY* 3.0 29.8 + - - +
145A ARG* 1.3 96.6 - - - +
147A LYS* 1.3 64.2 + - - +
148A GLN 3.3 2.7 - - - -
149A HIS* 3.2 15.9 + - - -
150A PHE* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLY 3.8 3.8 + - - -
145A ARG 3.6 3.4 - - - +
146A ASP* 1.3 77.2 - - - +
148A GLN* 1.3 81.5 + - - +
150A PHE* 3.5 3.5 + - - +
151A THR* 3.2 24.6 + - - -
186A ASP 2.8 22.9 + - - -
187A SER 3.4 26.0 - - - +
188A SER 3.4 20.3 - - - +
189A TYR 3.6 9.6 - - - +
190A ASP* 3.9 17.6 + - + +
1389A GOL 2.6 36.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
145A ARG* 5.2 7.7 + - - +
146A ASP 3.3 0.6 - - - -
147A LYS* 1.3 98.2 - - - +
149A HIS* 1.3 66.4 + - + +
151A THR* 3.2 8.4 + - - -
152A THR* 2.9 34.4 + - - +
190A ASP* 5.7 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A SER 5.1 0.4 + - - +
110A ALA* 4.2 21.3 - - + +
111A SER* 3.2 41.6 + - - -
116A ARG* 5.3 3.8 - - - -
139A TRP* 4.8 2.9 - - + -
145A ARG 3.8 13.9 + - - -
146A ASP* 3.2 24.7 + - - +
148A GLN* 1.3 82.2 - - + +
150A PHE* 1.3 57.9 + - - +
152A THR* 3.3 8.5 + - - +
153A LEU* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 5.0 10.8 - - + -
139A TRP* 3.5 46.6 - + + -
142A PRO* 3.9 11.9 - - + -
146A ASP 2.9 16.6 + - - +
147A LYS 3.7 5.2 - - - +
149A HIS* 1.3 78.6 - - - +
151A THR* 1.3 63.9 + - - +
153A LEU* 3.6 8.7 - - + +
154A ILE* 3.0 52.0 + - + +
176A ALA* 4.7 6.7 - - + -
177A ALA 5.6 0.7 - - - -
178A LEU* 3.8 16.6 - - + -
188A SER 4.2 4.7 - - - +
189A TYR* 3.6 35.9 - + - -
190A ASP 5.7 0.4 - - - -
194A ILE* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LYS* 3.2 13.6 + - - +
148A GLN* 3.5 12.2 - - - -
150A PHE* 1.3 79.7 - - - +
152A THR* 1.3 59.1 + - - +
154A ILE* 3.3 3.1 + - - +
155A LYS* 3.0 33.0 + - + +
190A ASP* 3.7 21.5 + - - +
193A LYS* 4.0 32.3 - - + -
194A ILE* 3.8 17.6 - - + +
196A GLN* 6.1 0.2 - - - +
197A HIS* 5.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 3.6 27.8 - - - +
148A GLN* 2.9 20.3 + - - +
149A HIS* 3.5 9.8 - - - -
151A THR* 1.3 75.4 - - - +
153A LEU* 1.3 60.4 + - - +
155A LYS* 3.3 6.7 + - - +
156A GLU* 2.9 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 4.1 26.7 - - + -
110A ALA* 4.4 16.8 - - + -
116A ARG* 4.1 28.0 - - + +
119A PHE* 4.0 26.2 - - + -
120A ILE* 4.1 7.9 - - + -
137A LEU* 4.5 20.0 - - + -
139A TRP* 4.4 11.0 - - + -
149A HIS 2.8 20.7 + - - +
150A PHE* 3.6 10.3 - - + +
152A THR* 1.3 72.0 - - - +
154A ILE* 1.3 60.0 + - - +
156A GLU* 4.0 1.4 - - - +
157A MET* 2.9 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 3.6 24.0 - - + -
150A PHE* 3.0 55.9 + - + +
151A THR 3.7 3.8 - - - +
153A LEU* 1.3 78.9 - - + +
155A LYS* 1.3 63.8 + - - +
157A MET* 3.3 5.3 + - - +
158A LYS* 2.9 23.9 + - - +
174A LEU* 3.9 3.7 - - + +
176A ALA* 4.9 0.7 - - + -
194A ILE* 3.8 25.6 - - + +
197A HIS* 3.7 22.0 - - + -
198A LEU* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A THR* 3.0 21.3 + - + +
152A THR* 3.8 7.9 - - - +
154A ILE* 1.3 77.4 - - - +
156A GLU* 1.3 62.8 + - + +
158A LYS* 3.4 2.6 + - - +
159A ALA* 3.0 27.9 + - + +
196A GLN* 6.1 0.2 - - - +
197A HIS* 3.7 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 2.6 47.3 + - - +
117A ARG* 5.5 1.4 + - - -
120A ILE* 3.4 17.9 - - + +
152A THR* 2.9 27.2 + - + +
155A LYS* 1.3 78.0 - - + +
157A MET* 1.3 65.6 + - - +
159A ALA* 3.2 8.1 + - + +
160A GLU* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 3.5 31.9 - - + -
120A ILE* 3.4 40.5 - - + +
123A VAL* 4.0 15.3 - - + -
135A LEU* 4.1 6.5 - - + -
137A LEU* 5.0 5.2 - - + -
153A LEU* 2.9 22.5 + - + +
154A ILE* 3.8 3.4 - - - +
156A GLU* 1.3 76.1 - - - +
158A LYS* 1.3 64.0 + - - +
160A GLU* 3.2 3.1 + - - +
161A PHE* 3.1 56.5 + - + -
174A LEU* 3.9 21.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
154A ILE 2.9 17.5 + - - +
155A LYS 3.7 3.8 - - - +
157A MET* 1.3 76.9 - - - +
159A ALA* 1.3 64.0 + - - +
161A PHE* 3.1 10.8 + - + -
162A ILE* 3.0 38.6 + - + +
171A GLN* 3.7 22.7 - - - -
172A LEU 5.4 1.1 - - - -
174A LEU* 4.0 13.5 - - + +
196A GLN 5.4 0.8 + - - -
197A HIS* 2.8 52.8 + - + +
198A LEU 4.6 0.4 - - - -
199A ASP* 3.5 30.8 + - - +
253A LYS* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LYS* 3.0 15.6 + - + +
156A GLU* 3.2 12.1 + - - +
158A LYS* 1.3 76.8 - - - +
160A GLU* 1.3 62.3 + - - +
162A ILE* 3.3 14.0 + - - +
163A LYS* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ARG* 2.7 37.5 + - - -
120A ILE* 3.5 32.8 - - + +
121A LYS* 4.6 9.1 - - - +
124A PRO* 3.9 22.2 - - + +
156A GLU 3.0 6.4 + - - +
157A MET 3.5 5.4 - - - +
158A LYS 3.2 0.2 - - - -
159A ALA* 1.3 74.7 - - - +
161A PHE* 1.3 61.3 + - + +
163A LYS* 3.3 23.7 + - - +
164A GLU* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A VAL* 3.8 26.0 - - + -
124A PRO* 3.9 17.5 - - + -
127A LEU* 4.3 4.0 - - + -
135A LEU* 3.9 9.6 - - + -
157A MET* 3.1 36.5 + - + -
158A LYS* 3.1 13.5 + - + +
160A GLU* 1.3 80.1 - - + +
162A ILE* 1.3 64.1 + - - +
164A GLU* 3.5 6.4 + - - +
165A ALA* 3.2 24.3 + - - +
171A GLN* 3.9 7.8 - - + +
172A LEU* 3.3 42.7 + - + +
173A LEU 3.3 21.5 - - - -
174A LEU* 4.0 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LYS* 3.0 35.3 + - + +
159A ALA* 3.6 11.0 - - - +
160A GLU 3.2 0.2 - - - -
161A PHE* 1.3 77.0 - - - +
163A LYS* 1.3 57.6 + - - +
165A ALA* 3.3 3.1 + - - +
166A GLN* 2.9 30.4 + - + +
171A GLN* 3.4 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ARG* 4.2 19.8 - - - +
159A ALA 3.0 16.2 + - - +
160A GLU* 3.6 24.5 + - - +
161A PHE 3.3 0.2 - - - -
162A ILE* 1.3 77.5 - - - +
164A GLU* 1.3 59.5 + - - +
166A GLN* 2.8 52.4 + - - +
167A PRO* 3.8 1.0 - - - +
1385A SO4 5.1 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 3.7 28.5 - - + -
128A ARG* 2.8 51.4 + - - +
160A GLU* 2.9 20.1 + - - +
161A PHE* 3.8 5.6 - - - +
163A LYS* 1.3 78.0 - - - +
165A ALA* 1.3 63.5 + - - +
167A PRO* 3.5 9.7 - - - +
169A LYS* 2.9 30.5 + - - +
172A LEU* 4.0 5.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE 3.2 16.9 + - - +
162A ILE 4.1 2.2 - - - +
164A GLU* 1.3 83.7 - - - +
166A GLN* 1.3 65.4 + - - +
167A PRO* 2.8 7.4 - - - -
168A GLY* 3.2 1.6 + - - -
169A LYS* 3.0 36.6 + - + +
171A GLN* 3.7 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ILE* 2.9 15.5 + - + +
163A LYS* 2.8 42.0 + - - +
165A ALA* 1.3 74.6 - - - +
167A PRO* 1.3 82.9 - - + +
168A GLY 3.0 6.4 + - - -
----------------------------------------------------------
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