Contacts of the helix formed by residues 145 - 167 (chain C) in PDB entry 2NP5
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 145 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A HIS* 4.3 9.7 + - - -
182A ILE* 3.3 29.5 - - + +
143C THR 3.6 1.0 + - - -
144C PRO* 1.3 74.4 - - + +
146C ALA* 1.3 66.5 + - - +
147C GLU 3.2 3.0 + - - -
148C THR* 3.3 21.4 + - + -
149C ARG* 2.8 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C SER* 4.4 1.6 - - - +
138C LEU* 3.6 25.3 - - + +
139C ILE* 3.5 32.8 - - + +
143C THR* 3.5 16.7 + - - +
144C PRO 3.1 5.9 + - - -
145C GLU* 1.3 75.3 - - - +
147C GLU* 1.3 59.0 + - - +
149C ARG* 3.3 1.2 + - - -
150C ALA* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ARG* 5.2 1.4 + - - +
135C SER* 3.5 27.2 + - - +
139C ILE* 4.4 17.2 - - + +
145C GLU 3.2 0.8 + - - -
146C ALA* 1.3 80.4 - - - +
148C THR* 1.3 63.7 + - - +
150C ALA* 3.3 4.0 + - - +
151C ALA* 3.0 23.4 + - - +
132D THR* 4.7 6.9 - - - +
136D ALA* 3.6 27.5 - - - +
139D ILE* 5.0 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 6.0 3.4 - - + +
178A HIS* 3.9 21.0 + - + +
179A ALA* 4.9 5.8 - - + -
182A ILE* 3.8 37.7 - - + -
145C GLU* 3.3 21.9 + - - -
147C GLU* 1.3 79.9 - - - +
149C ARG* 1.3 61.6 + - - +
151C ALA* 3.3 8.7 + - + +
152C LEU* 3.0 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE* 4.7 7.5 - - + +
186A MSE 3.9 36.2 - - + +
189A GLN* 5.7 4.4 - - - +
138C LEU* 4.3 4.5 - - + -
143C THR* 3.7 7.9 - - - +
144C PRO* 3.2 34.4 + - - +
145C GLU* 2.8 24.3 + - + +
146C ALA 3.8 3.8 - - - +
148C THR* 1.3 78.2 - - - +
150C ALA* 1.3 56.1 + - - +
152C LEU* 3.2 8.2 + - - +
153C LEU* 2.8 30.5 + - - +
186C MSE 4.0 2.2 + - - -
187C ILE* 2.9 44.2 + - + +
189C GLN* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ARG* 4.0 6.3 - - + +
134C LEU* 3.8 15.4 - - + +
135C SER* 3.3 43.1 - - - +
138C LEU* 3.7 10.2 - - + +
146C ALA 2.8 17.2 + - - +
147C GLU 3.5 1.6 - - - +
149C ARG* 1.3 73.4 - - - +
151C ALA* 1.3 62.4 + - - +
153C LEU* 3.3 5.4 + - - +
154C LEU* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 6.0 2.0 - - + -
175A TYR* 3.5 24.5 - - - +
179A ALA* 6.5 0.4 - - + -
131C ARG* 3.8 28.3 - - - +
147C GLU 3.0 13.6 + - - +
148C THR* 3.4 12.8 - - + +
150C ALA* 1.3 75.3 - - - +
152C LEU* 1.3 58.7 + - + +
154C LEU* 3.5 2.5 + - - +
155C ALA* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A THR* 3.6 29.8 - - + -
160A LEU* 4.6 4.9 - - + -
179A ALA* 3.6 37.9 - - + +
182A ILE* 3.4 33.2 - - + -
183A GLN* 3.7 6.7 - - + +
186A MSE 3.6 21.1 - - + -
148C THR* 3.0 21.4 + - + +
149C ARG* 3.6 7.4 - - - +
150C ALA 3.2 0.2 - - - -
151C ALA* 1.3 75.7 - - + +
153C LEU* 1.3 64.3 + - - +
155C ALA* 3.8 1.5 - - + +
156C THR* 2.8 32.8 + - - +
183C GLN* 5.3 1.6 - - - +
187C ILE* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 4.2 15.5 - - + -
89C MSE 3.9 31.2 - - + -
134C LEU* 4.2 19.7 - - + -
138C LEU* 5.6 2.2 - - + -
149C ARG 2.8 15.3 + - - +
150C ALA* 3.6 7.4 - - - +
152C LEU* 1.3 74.4 - - - +
154C LEU* 1.3 57.1 + - - +
156C THR* 3.8 3.2 - - - -
157C VAL* 2.9 41.5 + - + +
180C LEU* 4.2 9.0 - - + -
183C GLN* 3.9 15.0 - - + -
184C ILE* 4.2 12.8 - - + -
187C ILE* 3.4 36.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASP* 5.8 0.7 - - - +
89C MSE 4.3 8.1 - - - -
92C LEU* 3.7 29.8 - - + -
127C LEU* 3.8 45.1 - - + +
130C ILE* 3.9 32.5 - - + -
131C ARG* 4.0 13.2 - - + +
134C LEU* 4.1 5.2 - - + -
150C ALA 3.1 12.8 + - - +
151C ALA* 3.8 5.2 - - - +
153C LEU* 1.3 80.2 - - - +
155C ALA* 1.3 56.3 + - - +
157C VAL* 3.3 1.0 + - - -
158C ASP* 2.9 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ALA 4.6 0.7 - - - -
156A THR* 4.5 2.0 - - + +
159A GLY* 3.2 12.2 - - - -
160A LEU* 3.9 39.0 - - + +
163A ASP* 4.4 11.7 - - - +
151C ALA 2.9 19.1 + - - +
152C LEU* 3.8 7.2 - - + +
154C LEU* 1.3 74.3 - - - +
156C THR* 1.3 58.6 + - - +
158C ASP* 3.3 6.2 + - - +
159C GLY 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 3.7 44.9 - - + +
155A ALA* 3.6 5.1 - - + +
156A THR* 2.7 29.4 + - - +
183A GLN* 3.9 5.0 + - - -
152C LEU 2.8 25.9 + - - -
153C LEU 3.8 2.9 - - - -
155C ALA* 1.3 76.7 - - - +
157C VAL* 1.3 55.8 + - + +
159C GLY 3.3 0.9 + - - -
160C LEU* 2.8 35.5 + - + +
183C GLN* 3.7 18.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C MSE 3.7 26.9 - - + +
92C LEU* 3.6 35.0 - - + -
93C LEU* 3.6 13.8 - - + +
153C LEU* 2.9 24.3 + - + +
154C LEU 3.8 3.8 - - - +
156C THR* 1.3 77.3 - - + +
158C ASP* 1.3 62.8 + - - +
160C LEU* 3.2 11.0 + - + +
161C ALA* 3.0 22.5 + - - +
180C LEU* 3.8 29.2 - - + -
183C GLN* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY* 4.3 7.2 - - - -
162A LEU* 4.5 9.5 - - + +
163A ASP* 3.5 10.0 - - - +
92C LEU* 4.0 13.1 - - - +
123C ARG* 3.0 29.0 + - - +
127C LEU* 3.6 16.4 - - - +
154C LEU* 2.9 30.3 + - - +
155C ALA* 3.5 7.2 - - - +
157C VAL* 1.3 75.6 - - - +
159C GLY* 1.3 55.4 + - - +
161C ALA* 3.4 7.3 + - - +
162C LEU* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ALA* 3.3 26.7 - - - -
158A ASP* 4.2 4.5 - - - -
159A GLY* 3.5 12.9 - - - -
155C ALA 2.9 14.6 + - - -
158C ASP* 1.3 70.2 - - - +
160C LEU* 1.3 59.6 + - - +
162C LEU* 3.2 4.5 + - - +
163C ASP* 2.8 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ALA* 4.6 7.9 - - + +
152A LEU* 3.9 22.2 - - + -
155A ALA* 3.7 18.5 - - + +
93C LEU* 3.8 20.6 - - + -
156C THR* 2.8 24.7 + - + +
157C VAL* 3.2 12.1 + - + +
159C GLY* 1.3 71.4 - - - +
161C ALA* 1.3 58.5 + - - +
163C ASP* 3.5 3.3 + - - +
164C ALA* 2.9 31.6 + - - +
171C TYR* 3.9 30.4 - - + -
175C TYR* 5.7 0.2 - - + -
176C LEU* 4.2 10.5 - - + +
179C ALA* 4.1 18.8 - - + -
180C LEU* 4.7 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 3.4 26.2 - - + +
93C LEU* 3.9 1.3 - - + +
94C PRO* 3.9 17.0 - - + -
103C ALA* 4.4 10.8 - - + +
107C ALA* 6.1 1.1 - - + -
157C VAL 3.0 15.0 + - - +
158C ASP* 3.6 8.3 - - - +
160C LEU* 1.3 75.9 - - - +
162C LEU* 1.3 62.6 + - - +
164C ALA* 3.3 1.4 + - - +
165C ILE* 3.1 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA* 4.6 9.9 - - + +
110A ALA* 3.9 25.3 - - + +
111A VAL* 3.9 28.5 - - + -
123A ARG* 4.2 10.5 + - - +
158A ASP* 4.4 14.4 - - + +
162A LEU* 4.2 34.3 - - + -
107C ALA* 3.9 14.8 - - + +
158C ASP 3.0 17.2 + - - +
159C GLY* 3.2 4.7 + - - +
161C ALA* 1.3 76.1 - - - +
163C ASP* 1.3 63.7 + - - +
164C ALA 3.2 0.7 + - - -
165C ILE* 3.2 25.3 + - + +
166C GLY* 3.5 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ARG* 2.7 24.7 + - - +
127A LEU* 3.9 13.0 - - + +
151A ALA 4.8 0.7 - - - +
154A LEU* 4.2 2.1 - - - +
155A ALA* 3.5 23.9 + - - +
158A ASP* 2.5 31.1 - - - +
159C GLY 2.8 24.1 + - - +
160C LEU* 3.6 5.1 - - - +
162C LEU* 1.3 72.6 - - - +
164C ALA* 1.3 55.5 + - - +
166C GLY* 3.6 0.7 + - - -
167C SER* 3.1 31.4 + - - -
171C TYR* 3.7 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C PRO* 3.6 26.5 - - + -
160C LEU 2.9 18.1 + - - +
161C ALA 3.7 0.7 - - - +
162C LEU 3.2 0.2 - - - -
163C ASP* 1.3 75.1 - - - +
165C ILE* 1.3 67.9 + - - +
168C PRO* 3.1 27.7 - - - +
171C TYR* 3.6 30.5 - - + +
176C LEU* 4.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA 4.6 2.9 - - - +
111A VAL* 4.6 7.9 - - - -
113A ALA 4.6 0.3 - - - +
114A ALA* 3.7 31.8 - - + +
94C PRO* 4.3 11.9 - - + -
100C SER* 4.3 9.6 - - - +
103C ALA* 4.0 22.9 - - + +
104C HIS* 4.0 23.8 - - + +
107C ALA* 3.9 28.5 - - + -
161C ALA 3.1 18.8 + - - +
162C LEU* 3.2 23.8 - - + +
164C ALA* 1.3 77.7 - - - +
166C GLY* 1.3 59.6 + - - +
168C PRO* 3.7 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA 4.0 6.1 - - - -
113A ALA* 3.7 25.6 - - - +
120A ALA* 3.3 32.0 - - - +
123A ARG* 4.3 6.2 - - - +
162C LEU 3.5 5.7 + - - -
163C ASP 4.0 1.8 - - - -
164C ALA 3.2 0.2 - - - -
165C ILE* 1.3 83.1 - - - +
167C SER* 1.3 65.1 + - - +
168C PRO* 3.7 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ALA* 5.1 0.4 - - - -
123A ARG* 3.5 2.1 - - - +
124A ARG* 3.3 40.4 + - - -
127A LEU* 3.5 17.0 - - - +
163C ASP 3.1 12.7 + - - -
164C ALA 3.2 4.0 - - - -
166C GLY* 1.3 81.4 + - - +
168C PRO* 1.3 66.9 - - - +
169C ALA 3.3 2.7 - - - -
170C LEU* 3.2 18.7 + - - -
171C TYR* 3.2 13.7 - - - -
----------------------------------------------------------
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