Contacts of the helix formed by residues 145 - 166 (chain A) in PDB entry 3QNQ
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 GLY 145 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA* 3.6 6.3 - - - -
111A PHE* 4.3 2.9 - - - -
140A LEU* 3.7 18.7 + - - -
142A GLY 2.8 11.3 + - - -
143A SER 2.8 1.2 + - - -
144A GLN* 1.3 79.9 - - - +
146A LEU* 1.3 49.1 + - - -
147A PHE 2.5 5.6 + - - -
148A VAL* 2.4 40.2 + - - +
149A ALA 2.9 6.3 + - - -
213A HIS* 6.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.8 15.5 - - + -
32A THR* 6.5 0.2 - - + -
80A MET* 3.3 17.0 - - + -
81A ALA* 3.1 19.5 - - + +
84A ALA* 4.8 6.7 - - + -
143A SER* 3.4 17.9 + - - +
145A GLY* 1.3 73.6 - - - +
147A PHE* 1.3 66.3 + - + +
148A VAL 3.2 0.9 - - - -
149A ALA* 3.4 15.4 - - + +
150A MET* 3.3 28.9 + - - +
221A GLN* 4.7 0.4 - - - +
261A PRO* 3.4 39.0 - - + +
264A LEU* 3.1 34.8 - - + -
265A SER* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLY 2.5 6.6 + - - -
146A LEU* 1.3 77.7 - - - +
148A VAL* 1.3 58.3 + - + +
150A MET* 3.5 16.7 - - + +
151A ILE* 3.4 18.7 - - + +
216A VAL* 3.8 8.3 - - + +
220A LEU* 4.1 27.4 - - + -
221A GLN* 3.1 37.7 - - + +
224A LEU* 3.6 33.4 - - + -
261A PRO* 3.5 32.8 - - + -
262A ILE* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PHE* 3.1 29.8 - - + -
114A ALA* 6.0 1.3 - - + -
115A THR* 5.3 8.3 - - + -
144A GLN 4.7 4.9 - - - +
145A GLY* 2.4 27.1 + - - +
147A PHE* 1.3 76.3 - - + +
149A ALA* 1.3 62.7 + - - -
150A MET 3.0 1.8 - - - -
151A ILE* 3.1 7.8 + - + +
152A ILE* 2.8 34.1 + - + +
212A ILE* 4.8 10.1 - - + -
213A HIS* 4.5 17.3 - - + +
216A VAL* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA* 3.7 14.8 - - + +
84A ALA* 4.6 4.7 - - + +
85A VAL* 3.3 35.6 - - + +
88A ILE* 4.9 2.5 - - + -
111A PHE* 3.6 4.9 - - - -
145A GLY 2.9 4.6 + - - -
146A LEU* 3.4 25.8 - - + +
148A VAL* 1.3 77.7 - - - +
150A MET* 1.3 61.0 + - + +
152A ILE 4.0 0.2 - - - -
153A ALA* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 3.8 31.9 - - + -
29A LEU* 5.7 1.6 - - + -
88A ILE* 3.6 26.5 - - + -
146A LEU 3.3 8.5 + - - +
147A PHE* 3.5 54.1 - - + +
148A VAL 3.0 0.4 - - - -
149A ALA* 1.3 73.5 - - - +
151A ILE* 1.3 62.8 + - + +
152A ILE 2.8 10.8 + - - -
153A ALA* 3.0 1.8 + - - -
154A ILE* 2.9 32.1 + - + +
261A PRO* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PHE* 3.4 22.9 - - + +
148A VAL* 3.1 7.8 + - + +
150A MET* 1.3 76.5 - - + +
152A ILE* 1.3 61.4 + - + +
154A ILE* 4.8 6.1 - - - -
155A ILE* 3.1 44.6 + - + +
216A VAL* 4.2 16.2 - - + -
220A LEU* 4.0 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 5.3 0.9 - - + -
107A SER 3.9 9.0 - - - +
110A THR* 3.4 20.4 - - + -
111A PHE* 3.8 22.7 - - + +
114A ALA* 4.3 14.4 - - + -
148A VAL* 2.8 34.5 + - + +
149A ALA 4.2 1.8 - - - +
151A ILE* 1.3 80.0 - - + +
153A ALA* 1.3 60.5 + - - +
155A ILE* 4.8 4.7 - - + -
156A SER* 2.8 34.3 + - - -
197A VAL* 3.8 32.1 - - + -
200A ILE* 6.2 2.5 - - + -
212A ILE* 5.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 3.8 8.9 - - - +
88A ILE* 3.6 25.1 - - + -
89A ALA* 3.6 19.1 - - + +
92A LEU* 4.8 0.4 - - - -
107A SER* 3.5 12.6 - - - -
149A ALA 3.0 18.5 + - - +
150A MET 3.0 1.0 + - - +
152A ILE* 1.3 74.2 - - - +
154A ILE* 1.3 57.4 + - - +
157A THR* 2.7 41.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
21A HIS* 4.1 40.2 - - + +
24A ALA* 5.6 0.2 - - + -
25A ILE* 3.9 27.1 - - + -
88A ILE* 4.5 10.3 - - + -
92A LEU* 3.7 19.0 - - + +
150A MET* 2.9 26.9 + - + +
151A ILE* 4.6 4.7 - - - +
153A ALA* 1.3 74.0 - - - +
155A ILE* 1.3 59.5 + - + +
158A GLU* 2.7 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 3.1 36.0 + - + +
152A ILE* 4.8 5.4 - - + +
154A ILE* 1.3 83.0 - - + +
156A SER* 1.3 63.9 + - - +
158A GLU* 4.1 4.4 - - - +
159A ILE* 3.4 37.4 + - + +
197A VAL* 4.9 9.4 - - + -
200A ILE* 4.6 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 4.1 7.3 - - - +
107A SER* 3.5 14.6 + - - -
110A THR* 3.4 22.5 + - - -
152A ILE 2.8 23.5 + - - -
155A ILE* 1.3 77.9 - - - +
157A THR* 1.3 59.8 - - - +
159A ILE* 3.8 1.1 + - - -
160A TYR* 3.1 27.0 + - - +
193A VAL* 3.1 32.9 - - - +
197A VAL* 4.9 2.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
89A ALA* 3.3 35.2 + - - +
92A LEU* 3.8 36.3 - - + +
93A GLY* 4.0 5.8 - - - +
96A TYR* 5.0 5.2 - - + -
98A VAL* 5.5 0.4 - - + -
103A SER* 4.2 11.8 + - - +
107A SER* 3.5 1.9 + - - -
153A ALA 2.7 21.9 + - - -
154A ILE 4.0 1.3 - - - -
156A SER* 1.3 71.7 - - - +
158A GLU* 1.3 66.6 + - - +
160A TYR* 2.9 17.0 + - + +
161A ARG* 2.9 17.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 5.1 0.3 + - - -
21A HIS* 3.4 28.8 + - - -
92A LEU* 4.6 4.7 - - - +
96A TYR* 3.0 35.1 + - - -
154A ILE* 2.7 26.0 + - + +
155A ILE* 4.1 6.1 - - - +
157A THR* 1.3 74.8 - - - +
159A ILE* 1.3 63.6 + - + +
161A ARG* 3.1 33.1 + - - +
162A PHE* 3.2 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ILE* 3.4 25.8 + - + +
156A SER* 4.0 4.3 - - - +
157A THR 3.3 0.2 - - - -
158A GLU* 1.3 79.1 - - + +
160A TYR* 1.3 63.9 + - - +
162A PHE* 3.3 7.7 + - + +
163A LEU* 3.1 34.1 + - + +
192A ILE* 5.0 4.7 - - + -
193A VAL* 3.7 24.0 - - + +
196A VAL* 3.7 36.3 - - + -
197A VAL* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL* 4.4 13.2 - - + -
99A ASP* 3.9 24.7 - - - +
102A ALA* 3.5 22.6 - - + +
103A SER* 3.9 19.5 - - - -
106A LEU* 3.8 24.5 - - + -
156A SER 3.1 20.0 + - - +
157A THR* 2.9 10.9 + - + +
159A ILE* 1.3 79.1 - - - +
161A ARG* 1.3 65.6 + - - +
163A LEU* 3.2 5.2 + - - +
164A VAL* 3.1 37.7 + - + +
185A ALA 5.6 0.2 - - - -
186A ALA* 3.8 18.7 - - + +
189A PRO* 3.6 27.4 - - + -
190A GLY* 4.4 3.6 - - - -
193A VAL* 4.1 8.7 - - + -
443A ZDM 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 2.9 61.1 + - + -
98A VAL* 3.7 31.6 - - + -
157A THR* 2.9 14.8 + - + +
158A GLU* 3.1 30.2 + - - +
160A TYR* 1.3 72.4 - - - +
162A PHE* 1.3 95.4 + - - +
164A VAL* 3.7 1.7 - - - +
165A GLN* 2.8 53.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLU 3.2 9.3 + - - +
159A ILE* 3.3 13.2 - - + +
160A TYR 3.1 0.4 - - - -
161A ARG* 1.3 104.5 - - - +
163A LEU* 1.3 79.8 + - + +
165A GLN* 3.6 5.4 - - - +
166A LYS* 3.0 65.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 3.1 22.3 + - + +
160A TYR 3.2 6.7 + - - +
162A PHE* 1.3 92.7 - - + +
164A VAL* 1.3 61.6 + - - +
166A LYS* 3.3 6.1 + - - -
168A MET* 3.1 48.5 + - + +
189A PRO* 3.4 37.7 - - + +
192A ILE* 3.5 44.6 - - + -
193A VAL* 4.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL* 4.5 16.2 - - + -
99A ASP 6.1 0.4 - - - +
160A TYR* 3.1 44.6 + - + +
161A ARG* 3.2 7.4 + - - +
163A LEU* 1.3 75.2 - - - +
165A GLN* 1.3 63.6 + - + +
167A LYS* 3.1 14.2 + - - -
169A ILE* 4.4 17.2 - - + +
185A ALA 4.8 3.1 - - - +
189A PRO* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 4.1 22.6 + - - +
98A VAL* 5.1 6.1 - - + -
161A ARG* 2.8 56.1 + - + +
162A PHE* 3.6 4.1 - - - +
164A VAL* 1.3 75.6 - - + +
166A LYS* 1.3 58.3 + - + +
167A LYS* 2.8 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PHE* 3.0 62.1 + - + +
163A LEU* 3.3 6.0 + - - +
165A GLN* 1.3 74.0 - - + +
167A LYS* 1.3 66.9 + - - +
168A MET* 3.1 18.8 + - + +
----------------------------------------------------------
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