Contacts of the helix formed by residues 161 - 180 (chain A) in PDB entry 3NC0
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 161 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A SER 4.7 1.1 - - - -
159A THR 4.1 2.0 + - - -
160A SER* 1.3 69.5 + - - +
162A SER* 1.3 62.3 + - - +
164A CYS* 3.1 7.4 + - - +
165A GLN* 2.8 28.9 + - - +
216A SER* 3.8 4.5 + - - -
217A GLN 5.1 0.9 + - - -
218A ASN* 2.9 41.5 + - - +
221A LEU* 3.4 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER 4.5 15.1 - - - +
115A SER* 4.9 11.4 - - - -
116A ASP 6.1 0.4 - - - -
160A SER* 3.5 8.1 + - - -
161A GLU* 1.3 75.1 - - - +
163A LEU* 1.3 59.2 + - - +
164A CYS 2.8 10.4 + - - -
165A GLN* 3.1 17.3 + - - +
166A ASN* 3.3 15.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
111A ILE* 3.7 35.9 - - + -
114A SER* 5.1 6.3 + - - -
115A SER* 3.5 24.4 + - - +
156A ALA* 3.7 29.6 - - + +
157A SER* 3.7 3.6 + - - -
160A SER* 3.2 25.4 + - - +
161A GLU 3.4 0.2 - - - -
162A SER* 1.3 77.3 - - - +
164A CYS* 1.3 52.3 + - - +
166A ASN* 5.3 2.9 - - - -
167A ASN* 2.6 48.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A SER* 3.2 33.7 - - - +
160A SER 3.1 12.8 + - - +
161A GLU* 3.1 12.3 - - - +
162A SER 2.8 2.0 + - - -
163A LEU* 1.3 79.2 - - - +
165A GLN* 1.3 65.8 + - - +
166A ASN 3.3 1.1 - - - -
167A ASN* 3.0 4.9 + - - +
168A MET* 2.9 28.1 + - - +
208A LEU* 4.9 5.2 - - - -
212A VAL* 4.6 13.9 - - - -
221A LEU* 3.5 25.4 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
124A LYS* 5.8 1.4 + - - -
161A GLU* 2.8 15.0 + - - +
162A SER* 3.1 8.4 + - - +
164A CYS* 1.3 74.5 - - - +
166A ASN* 1.3 63.8 + - - +
168A MET* 3.1 19.9 + - - +
169A VAL* 3.5 9.6 + - + +
218A ASN* 3.6 15.6 - - - +
220A PRO* 3.4 21.8 - - - +
221A LEU* 3.4 41.8 - - + +
224A ALA* 4.7 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 3.8 5.2 - - - +
114A SER* 3.0 31.6 + - - +
127A ILE* 3.6 15.0 - - - +
131A ASN* 2.9 43.7 - - - +
162A SER 3.3 10.3 + - - +
163A LEU* 5.2 1.8 - - - -
164A CYS 3.3 0.4 - - - -
165A GLN* 1.3 80.9 - - - +
167A ASN* 1.3 59.9 + - - +
169A VAL* 2.8 29.7 + - - +
170A ILE* 2.9 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 5.9 0.8 - - - +
153A ILE* 3.4 26.8 - - + +
157A SER* 3.2 18.2 + - - +
163A LEU* 2.6 41.1 + - - +
164A CYS 3.0 9.9 + - - +
166A ASN* 1.3 74.8 + - - +
168A MET* 1.3 59.7 + - + +
169A VAL 2.9 5.2 - - - -
170A ILE* 2.9 43.7 + - + +
171A LEU* 2.9 23.9 + - + +
208A LEU* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A SER* 5.9 0.2 - - - +
164A CYS* 2.9 23.7 + - - +
165A GLN* 3.1 11.6 + - - +
167A ASN* 1.3 76.4 - - + +
169A VAL* 1.3 59.6 + - - +
171A LEU* 3.5 27.4 - - + -
172A LYS* 3.6 5.4 + - - +
208A LEU* 4.5 17.3 - - + -
209A CYS* 4.0 19.7 - - - -
212A VAL* 5.1 3.6 - - - -
221A LEU* 4.3 9.9 - - + -
224A ALA* 3.9 17.4 - - + +
225A THR* 3.1 40.2 - - - +
228A THR* 3.1 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLY* 5.9 2.5 - - - -
131A ASN* 4.4 15.9 - - + +
165A GLN* 3.8 11.9 - - + +
166A ASN* 2.8 21.6 + - - +
168A MET* 1.3 79.3 - - - +
170A ILE* 1.3 63.1 + - - +
171A LEU 3.2 1.3 - - - -
172A LYS* 3.3 22.1 + - - +
173A LEU* 3.2 36.5 + - + +
224A ALA* 4.8 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 4.9 4.9 - - + -
131A ASN* 3.5 22.2 - - + +
134A LEU* 4.0 30.7 - - + -
135A VAL* 3.7 14.8 - - + +
138A LEU* 4.7 2.9 - - + -
149A PHE* 4.5 16.8 - - + -
153A ILE* 5.6 5.4 - - + -
166A ASN* 2.9 24.0 + - - +
167A ASN* 2.9 36.2 + - + +
169A VAL* 1.3 79.0 - - - +
171A LEU* 1.3 60.2 + - + +
173A LEU* 3.6 6.9 + - - -
174A LEU* 3.1 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE* 5.3 1.1 - - + -
150A ILE* 4.5 4.3 - - + -
153A ILE* 3.9 25.1 - - + -
167A ASN* 2.9 17.5 + - + +
168A MET* 3.5 25.6 - - + -
170A ILE* 1.3 76.8 - - + +
172A LYS* 1.3 60.0 + - - +
174A LEU* 3.2 14.5 + - + +
175A SER* 2.9 31.5 + - - -
198A MET* 5.0 4.3 - - + +
205A ILE* 3.5 49.8 - - + -
208A LEU* 5.3 5.2 - - + -
228A THR* 4.2 9.6 - - - +
232A PHE* 4.2 11.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A MET 3.6 13.7 + - - +
169A VAL* 3.3 29.3 + - - +
171A LEU* 1.3 78.3 - - - +
173A LEU* 1.3 70.6 + - - +
175A SER* 3.5 6.1 + - - -
176A GLU* 3.1 39.6 + - - +
227A GLU* 4.2 28.9 - - + +
228A THR* 3.7 15.2 + - - +
231A ARG* 3.6 32.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLY* 4.3 6.1 - - - +
131A ASN* 3.8 32.5 - - + +
132A MET* 3.9 32.5 - - - +
135A VAL* 3.7 14.8 - - + -
169A VAL* 3.2 23.8 + - + +
170A ILE* 3.8 0.9 - - - +
172A LYS* 1.3 84.4 - - - +
174A LEU* 1.3 67.8 + - - +
176A GLU* 3.2 18.6 + - - +
177A GLU* 2.9 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 3.8 25.3 - - + +
138A LEU* 4.1 33.2 - - + -
139A LYS* 5.1 4.5 - - + +
142A TRP* 5.0 13.5 - - + -
149A PHE* 4.5 12.6 - - + -
150A ILE* 5.2 2.0 - - + -
170A ILE* 3.1 16.2 + - + +
171A LEU* 3.2 14.8 + - + +
173A LEU* 1.3 78.7 - - - +
175A SER* 1.3 62.3 + - - +
177A GLU* 3.9 0.6 - - + -
178A VAL* 3.1 44.1 + - + +
194A LEU* 6.2 0.7 - - + -
198A MET* 3.6 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU 2.9 17.1 + - - -
172A LYS* 3.7 6.1 - - - -
174A LEU* 1.3 75.8 - - - +
176A GLU* 1.3 58.9 + - - +
179A PHE* 2.9 34.7 + - - +
180A ASP* 4.2 1.8 + - - +
198A MET* 4.1 10.5 - - - +
231A ARG* 3.4 16.1 + - - -
232A PHE* 3.6 19.7 - - - -
235A TRP* 3.0 26.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LYS* 3.1 28.7 + - - +
173A LEU* 3.6 21.6 - - - +
175A SER* 1.3 75.5 - - - +
177A GLU* 1.3 58.3 + - + +
180A ASP* 2.8 26.9 + - - +
181A PHE* 2.8 55.5 + - + -
231A ARG* 3.4 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A MET* 3.7 35.4 - - + +
135A VAL* 3.8 10.5 - - + -
136A GLN* 6.1 1.6 - - - -
139A LYS* 3.1 34.6 + - + +
173A LEU* 2.9 19.6 + - - +
174A LEU 4.0 3.6 - - - +
175A SER 3.3 0.2 - - - -
176A GLU* 1.3 79.8 - - + +
178A VAL* 1.3 62.3 + - + +
181A PHE* 4.1 12.5 - - - +
182A SER* 3.7 10.7 + - - -
185A GLN* 3.7 12.9 + - - -
186A ILE* 3.7 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LYS* 5.5 4.3 - - + -
142A TRP* 5.8 0.2 - - + -
174A LEU* 3.1 36.7 + - + +
177A GLU* 1.3 84.5 - - + +
179A PHE* 1.3 83.0 + - + +
180A ASP 3.8 0.2 - - - -
182A SER* 3.4 20.5 + - - -
186A ILE* 5.0 2.2 - - + -
191A ALA* 4.6 6.0 - - - +
194A LEU* 3.9 42.0 - - + -
195A LYS* 4.0 11.9 - - - +
198A MET* 4.2 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A SER* 2.9 17.3 + - - +
178A VAL* 1.3 98.7 - - + +
180A ASP* 1.3 69.0 + - - +
181A PHE 3.8 0.2 - - - -
182A SER* 4.8 4.9 + - - -
195A LYS* 3.3 51.6 - - + -
198A MET* 3.7 15.5 - - + -
234A ASN* 5.9 0.4 - - + -
235A TRP* 3.4 74.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A SER* 4.2 3.5 + - - +
176A GLU* 2.8 34.7 + - - +
179A PHE* 1.3 87.6 - - - +
181A PHE* 1.3 81.3 + - + +
182A SER 3.7 1.3 - - - -
231A ARG* 4.5 11.3 - - - +
234A ASN* 3.6 30.7 - - - +
235A TRP* 6.2 0.2 - - - -
----------------------------------------------------------
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