Contacts of the helix formed by residues 177 - 191 (chain A) in PDB entry 3NIA
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 THR 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A MET 3.5 11.9 - - - -
57A ALA* 3.6 19.3 - - + +
58A GLN 3.4 15.7 - - - +
59A ARG* 4.1 10.1 - - + +
154A VAL* 3.8 17.9 - - + +
176A THR* 1.3 86.2 + - - +
178A PRO* 1.3 72.7 - - - +
179A ILE* 3.7 6.1 - - - +
180A ALA* 3.2 23.0 + - - +
181A MET* 3.0 20.4 + - - +
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Residues in contact with PRO 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLY* 3.7 24.0 - - - +
41A VAL 3.8 25.8 - - - +
42A ALA* 3.3 11.6 - - + +
55A ARG 3.7 14.1 - - - +
56A MET* 3.3 12.8 - - - +
58A GLN 3.1 16.8 - - - +
60A PHE* 3.9 11.7 - - + -
177A THR* 1.3 81.4 - - - +
179A ILE* 1.3 55.8 + - - +
182A ALA* 2.9 26.2 + - - +
254A ALA* 3.5 13.6 - - + +
256A TYR* 4.3 9.2 - - + -
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Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 3.5 11.4 - - + +
44A VAL* 3.6 28.9 - - + -
50A ILE* 4.0 14.4 - - + -
56A MET* 2.9 45.5 + - + +
57A ALA* 4.5 6.5 - - + -
177A THR* 3.7 6.3 - - - +
178A PRO* 1.3 77.3 - - - +
180A ALA* 1.3 66.3 + - + +
183A ARG* 3.1 55.2 + - - +
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASP* 3.7 15.4 - - - +
154A VAL* 3.6 32.3 - - + -
176A THR* 4.0 4.3 - - - +
177A THR* 3.2 18.4 + - - +
179A ILE* 1.3 85.3 - - + +
181A MET* 1.3 57.7 + - - +
183A ARG* 3.8 5.6 - - - +
184A THR* 3.0 29.5 + - - -
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Residues in contact with MET 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A MET* 3.5 32.3 - - - -
65A THR* 4.7 2.7 - - - +
66A PHE* 5.1 1.1 - - - -
69A PRO* 4.0 17.5 - - + -
147A PHE* 4.2 7.6 - - + -
152A ASP* 4.8 0.7 - - - -
155A SER* 3.9 6.1 - - - +
176A THR* 3.7 15.6 + - + +
177A THR 3.0 15.2 + - - +
178A PRO 4.0 1.6 - - - +
180A ALA* 1.3 73.3 - - - +
182A ALA* 1.3 60.8 + - - +
184A THR* 3.1 13.1 + - - -
185A VAL* 2.9 30.0 + - + +
241A ILE* 3.7 31.9 - - + -
254A ALA* 4.0 5.8 - - + -
256A TYR* 3.4 25.6 - - + +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 3.7 30.3 - - + +
44A VAL* 3.7 16.8 - - + +
178A PRO 2.9 18.9 + - - +
179A ILE 4.0 2.5 - - - +
181A MET* 1.3 76.0 - - - +
183A ARG* 1.3 57.1 + - - +
185A VAL* 3.2 8.9 + - - +
186A ALA* 3.0 24.1 + - - +
252A ALA* 3.5 11.1 - - - +
253A VAL 4.7 0.9 - - - -
254A ALA* 3.8 12.5 - - + +
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Residues in contact with ARG 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 4.1 5.4 - - + -
48A GLY* 2.7 35.5 + - - +
49A GLU* 4.5 4.2 + - - +
50A ILE* 3.5 26.8 - - - +
179A ILE* 3.1 45.3 + - + +
180A ALA* 3.8 5.2 - - - +
182A ALA* 1.3 76.0 - - - +
184A THR* 1.3 57.4 + - - +
186A ALA* 3.4 7.9 + - - +
187A LYS* 2.9 30.1 + - - +
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Residues in contact with THR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PRO* 4.4 9.2 - - + -
147A PHE* 4.3 12.1 - - + -
150A ILE* 3.7 22.9 + - + +
152A ASP* 2.7 37.2 + - - +
180A ALA 3.0 10.2 + - - -
181A MET* 3.4 24.5 - - - -
183A ARG* 1.3 73.4 - - - +
185A VAL* 1.3 66.7 + - - +
187A LYS* 3.2 7.1 + - - +
188A VAL* 3.0 28.7 + - + +
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE* 3.7 24.9 - - + -
69A PRO* 6.1 0.7 - - + -
181A MET* 2.9 22.3 + - + +
182A ALA* 3.5 9.4 - - - +
184A THR* 1.3 76.8 - - + +
186A ALA* 1.3 64.1 + - - +
188A VAL* 3.2 5.8 + - - -
189A LEU* 2.9 44.7 + - + +
241A ILE* 4.1 23.3 - - + -
242A GLY 3.4 26.2 - - - +
252A ALA* 3.7 10.1 - - + -
253A VAL 4.7 1.1 - - - +
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Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 3.9 5.6 - - + -
45A ASP 3.9 21.1 - - - +
46A PRO 3.9 11.4 - - - +
48A GLY* 4.6 4.7 - - - +
182A ALA 3.0 13.8 + - - +
183A ARG* 3.6 8.7 - - - +
184A THR 3.3 0.2 - - - -
185A VAL* 1.3 77.8 - - - +
187A LYS* 1.3 55.3 + - - +
190A TYR* 2.7 45.0 + - + +
191A GLY 3.0 5.2 + - - -
252A ALA* 3.7 10.1 - - + +
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Residues in contact with LYS 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ILE* 3.3 43.7 + - + +
151A GLY* 4.9 3.4 - - - -
183A ARG 2.9 17.4 + - - +
184A THR* 3.6 7.9 - - - +
186A ALA* 1.3 75.0 - - - +
188A VAL* 1.3 62.8 + - - +
191A GLY* 3.1 45.9 + - - +
193A ALA* 3.5 12.9 + - + -
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE* 4.0 21.8 - - + -
69A PRO* 5.7 2.9 - - + -
72A ALA* 3.8 32.1 - - + -
146A TYR* 4.3 5.8 - - + +
150A ILE* 4.0 20.4 - - + -
184A THR* 3.0 24.2 + - + +
185A VAL* 3.7 5.6 - - - +
187A LYS* 1.3 79.5 - - - +
189A LEU* 1.3 64.7 + - + +
192A GLY 5.1 0.3 + - - -
193A ALA* 3.9 10.6 + - + +
194A LEU* 4.0 21.5 + - + +
199A THR* 4.1 14.4 + - - +
202A ILE* 4.7 1.3 - - + -
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE* 3.9 18.4 - - + -
185A VAL* 2.9 28.6 + - + +
188A VAL* 1.3 82.0 - - + +
190A TYR* 1.3 77.9 + - + +
191A GLY 3.8 0.2 - - - -
192A GLY 5.2 0.7 - - - -
199A THR* 3.5 18.0 - - + +
202A ILE* 3.9 20.0 - - + -
203A GLU* 3.6 32.8 - - + +
206A LEU* 4.9 0.9 - - + -
243A PHE* 3.4 45.1 - - + -
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Residues in contact with TYR 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PRO* 3.7 42.6 - - + +
186A ALA* 2.7 26.7 + - + +
189A LEU* 1.3 93.4 - - + +
191A GLY* 1.3 56.4 + - - +
192A GLY 3.4 5.3 + - - -
203A GLU* 4.4 8.1 - - - -
243A PHE* 3.5 22.3 - + + +
244A PHE 4.3 0.7 + - - -
250A ASP* 3.6 35.8 - - + +
251A TYR 3.3 33.7 + - - -
252A ALA* 4.3 7.2 - - + -
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Residues in contact with GLY 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PRO 5.1 3.8 - - - -
186A ALA 3.0 10.2 + - - -
187A LYS* 3.1 29.3 + - - +
190A TYR* 1.3 77.8 - - - +
192A GLY* 1.3 61.6 + - - +
193A ALA 3.4 3.4 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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