Contacts of the helix formed by residues 170 - 194 (chain A) in PDB entry 4NJP
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 170 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A VAL 3.1 6.6 + - - +
166A GLU* 3.4 23.0 + - - -
167A LYS 5.5 0.2 - - - -
169A LEU* 1.3 77.3 - - - +
171A SER* 1.3 64.6 + - - -
172A GLY 3.4 2.0 - - - -
173A LYS* 3.4 7.2 + - - +
174A LEU 3.4 14.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 3.9 11.4 - - - +
96A VAL* 3.9 12.1 - - - +
166A GLU* 2.8 33.8 + - - +
170A GLY* 1.3 68.7 - - - -
172A GLY* 1.3 60.4 + - - +
174A LEU* 3.2 4.8 + - - +
175A ILE* 2.9 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLY* 3.4 0.8 - - - -
171A SER* 1.3 78.1 - - - +
173A LYS* 1.3 57.1 + - - +
175A ILE* 3.4 13.1 + - - +
176A VAL* 3.0 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A VAL* 3.8 20.6 - - + -
169A LEU* 4.1 20.9 - - + +
170A GLY 3.4 17.1 + - - +
171A SER 3.3 0.2 - - - -
172A GLY* 1.3 72.2 - - - +
174A LEU* 1.3 65.8 + - - +
176A VAL* 3.2 5.9 + - - +
177A ILE* 2.9 38.3 + - + +
210A TYR* 3.7 12.5 + - + +
214A ARG* 4.2 6.9 - - - +
264A MET* 5.0 6.3 - - + -
268A ASP* 2.6 40.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
96A VAL* 3.8 20.6 - - + -
97A THR* 3.7 16.2 - - - +
158A TRP* 3.9 19.7 - - + -
162A GLY* 3.4 39.7 - - - +
165A VAL* 4.5 11.7 - - + -
166A GLU* 4.0 9.2 - - + -
170A GLY 3.4 7.6 + - - +
171A SER* 3.2 9.8 + - - +
173A LYS* 1.3 79.7 - - - +
175A ILE* 1.3 59.9 + - - +
177A ILE* 3.3 3.4 + - + +
178A THR* 2.7 40.2 + - - +
207A LEU* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A VAL* 3.8 27.1 - - + -
171A SER* 2.9 28.9 + - - +
172A GLY* 3.4 12.1 - - - +
174A LEU* 1.3 77.5 - - - +
176A VAL* 1.3 61.8 + - + +
178A THR* 3.6 4.5 - - - -
179A LEU* 3.0 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLY 3.0 22.3 + - - +
173A LYS* 3.9 4.9 - - - +
175A ILE* 1.3 80.1 - - + +
177A ILE* 1.3 67.9 + - - +
179A LEU* 3.3 7.2 + - + +
180A ILE* 3.0 46.8 + - + +
264A MET* 3.6 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A VAL* 4.1 13.2 - - + -
173A LYS* 2.9 38.5 + - + +
174A LEU* 3.8 4.7 - - - +
176A VAL* 1.3 76.1 - - - +
178A THR* 1.3 54.0 + - - +
180A ILE* 4.2 0.9 - - - +
181A SER* 2.6 39.4 + - - +
203A VAL* 5.2 0.7 - - + +
206A ALA* 4.0 26.7 - - + +
207A LEU* 4.3 22.7 - - + -
210A TYR* 4.1 25.8 - - + -
260A VAL* 4.5 1.5 - - + +
261A GLY* 5.2 3.4 - - - -
264A MET* 3.4 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A VAL* 6.0 1.6 - - + -
100A MET* 3.7 28.9 - - + -
142A ALA* 6.5 0.4 - - + -
158A TRP* 3.5 24.3 - - + -
174A LEU* 2.7 24.1 + - - +
175A ILE* 3.6 6.5 - - - +
177A ILE* 1.3 75.6 - - - +
179A LEU* 1.3 66.5 + - + +
181A SER* 3.2 5.0 + - - -
182A ALA* 2.9 35.9 + - + +
203A VAL* 3.8 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PHE* 3.8 30.1 - - + -
175A ILE* 3.0 43.2 + - + +
176A VAL* 3.9 7.6 - - + +
178A THR* 1.3 81.6 - - + +
180A ILE* 1.3 65.8 + - + +
182A ALA* 3.8 4.1 - - - +
183A LEU* 3.2 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A VAL* 3.0 40.7 + - + +
177A ILE* 4.2 0.7 - - - +
179A LEU* 1.3 76.5 - - + +
181A SER* 1.3 59.2 + - - +
183A LEU* 3.4 7.5 + - + +
184A LEU* 3.0 30.7 + - + +
260A VAL* 3.8 25.8 - - + -
264A MET* 4.5 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE 2.6 26.5 + - - -
178A THR* 3.2 4.3 + - - -
180A ILE* 1.3 75.8 - - - +
182A ALA* 1.3 57.9 + - - +
184A LEU* 4.8 0.2 - - - -
185A SER* 2.7 37.8 + - - -
202A GLY 4.1 3.4 - - - -
203A VAL* 3.4 23.2 - - - +
206A ALA* 3.4 26.8 - - - +
257A GLY* 4.6 3.7 - - - -
260A VAL* 4.1 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TYR 4.6 0.2 - - - -
139A PHE* 4.9 11.7 - - + +
141A HIS* 3.1 27.4 + - + +
142A ALA* 4.6 10.8 - - + -
178A THR* 2.9 23.3 + - + +
179A LEU* 3.8 5.8 - - - +
181A SER* 1.3 78.3 + - - +
183A LEU* 1.3 56.5 + - - +
185A SER* 3.9 3.8 - - - -
186A GLY 3.0 21.1 + - - -
203A VAL* 3.8 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TRP* 4.0 8.4 - - + -
138A TYR* 3.6 39.5 - - + +
139A PHE* 3.4 31.0 - - + -
179A LEU* 3.2 24.2 + - + +
180A ILE* 3.9 6.5 - - + +
182A ALA* 1.3 75.3 - - - +
184A LEU* 1.3 62.9 + - - +
186A GLY* 3.4 1.2 + - - -
187A TYR* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ILE* 3.0 20.5 + - + +
181A SER 4.1 1.6 - - - +
183A LEU* 1.3 74.7 - - - +
185A SER* 1.3 65.8 + - - +
187A TYR* 3.0 23.2 + - + +
188A VAL* 3.0 32.9 + - + +
256A ALA* 3.5 35.4 - - + +
259A ALA* 5.6 2.2 - - + -
260A VAL* 3.6 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A HIS* 5.0 1.7 - - - -
181A SER 2.7 25.2 + - - -
182A ALA* 3.5 5.5 + - - -
184A LEU* 1.3 76.7 - - - +
186A GLY* 1.3 64.8 + - - +
189A GLN* 2.9 27.4 + - - +
202A GLY* 3.8 20.2 - - - -
249A MET* 3.2 18.9 - - - +
253A ALA* 3.3 27.3 - - - +
256A ALA* 4.2 4.7 - - - +
257A GLY 4.4 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TRP* 3.7 8.5 - - - -
141A HIS* 3.9 4.7 - - - -
182A ALA 3.0 21.0 + - - -
183A LEU 3.7 1.1 - - - -
185A SER* 1.3 79.1 + - - +
187A TYR* 1.3 57.0 + - - +
190A GLN* 2.8 30.8 + - - +
197A PHE* 3.4 29.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TRP* 3.8 18.2 - + + -
183A LEU 2.9 17.8 + - - +
184A LEU* 3.0 15.2 + - + +
186A GLY* 1.3 77.8 - - - +
188A VAL* 1.3 68.8 + - + +
190A GLN* 2.8 44.8 + - - +
191A LYS* 2.9 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU* 3.2 27.1 - - + +
185A SER 3.9 2.7 - - - +
187A TYR* 1.3 84.1 - - + +
189A GLN* 1.3 67.6 + - - +
191A LYS* 3.2 6.2 + - - +
192A PHE* 3.0 49.7 + - + -
252A GLY 3.6 6.1 - - - +
253A ALA* 3.6 24.5 - - - +
256A ALA* 3.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A SER 2.9 18.9 + - - +
186A GLY 3.6 4.7 - - - +
188A VAL* 1.3 78.0 - - - +
190A GLN* 1.3 56.8 + - - +
192A PHE* 3.4 2.6 + - - -
193A SER* 2.9 60.7 + - - -
194A GLY 3.8 0.9 + - - -
196A TRP 5.7 0.2 + - - -
197A PHE* 3.4 36.8 - - + +
248A SER 4.0 10.5 + - - -
249A MET* 3.5 14.5 - - + -
250A ALA* 2.8 37.5 + - - +
253A ALA* 3.3 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TRP* 3.0 37.5 + - + +
186A GLY 2.8 18.4 - - - +
187A TYR* 2.8 47.5 + - - +
189A GLN* 1.3 77.5 - - - +
191A LYS* 1.3 71.5 + - - +
194A GLY* 2.9 37.6 + - - +
195A PRO* 5.2 2.7 - - + -
197A PHE* 4.0 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 2.9 44.1 + - + +
188A VAL* 3.4 10.1 - - - +
190A GLN* 1.3 87.7 - - - +
192A PHE* 1.3 76.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A VAL* 3.0 45.7 + - + +
189A GLN* 4.3 1.8 - - - +
191A LYS* 1.3 90.9 - - + +
193A SER* 1.4 66.6 + - - +
250A ALA* 6.2 4.5 - - + -
252A GLY* 4.7 12.8 - - - -
253A ALA 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLN* 2.9 33.1 + - - -
191A LYS 3.4 0.4 - - - -
192A PHE* 1.4 86.3 + - - +
194A GLY* 1.3 63.7 + - - +
196A TRP* 5.0 5.2 + - - +
250A ALA* 4.8 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLN* 3.9 1.6 + - - +
190A GLN* 2.9 33.3 + - - -
191A LYS 5.0 0.2 + - - -
193A SER* 1.3 78.4 - - - +
195A PRO* 1.3 69.7 - - - +
196A TRP* 3.2 10.8 + - - +
197A PHE* 3.6 8.1 - - - +
----------------------------------------------------------
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