Contacts of the helix formed by residues 181 - 196 (chain A) in PDB entry 1IN7
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 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A PHE 5.4 1.6 - - - +
180A TYR* 1.3 76.1 - - - +
182A VAL* 1.3 65.2 + - - +
183A LYS* 3.5 8.2 + - - +
184A GLU* 3.0 42.7 + - - +
185A LEU* 3.0 24.0 + - - +
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Residues in contact with VAL 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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181A THR* 1.3 73.1 - - - +
183A LYS* 1.3 57.6 - - - +
185A LEU* 3.3 5.6 + - + -
186A LYS* 2.9 26.3 + - - +
206A GLU* 3.6 28.9 - - - +
209A ALA* 3.4 24.2 - - + +
210A LYS* 4.0 33.2 - - + +
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Residues in contact with LYS 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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181A THR* 3.2 8.5 + - - +
182A VAL* 1.3 80.6 - - - +
184A GLU* 1.3 63.6 + - + +
186A LYS* 3.3 21.8 + - - +
187A GLU* 3.1 44.2 + - + +
206A GLU* 5.5 0.7 - - - -
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Residues in contact with GLU 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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28A ILE* 3.8 4.7 - - + +
29A GLY* 3.6 25.9 - - - -
30A GLN* 4.1 5.1 + - - -
31A GLU* 5.0 7.4 - - - +
180A TYR* 3.4 25.1 - - + +
181A THR* 3.0 49.1 + - - +
183A LYS* 1.3 74.1 - - + +
185A LEU* 1.3 66.6 + - - +
187A GLU* 3.1 19.5 + - - +
188A ILE* 3.0 27.1 + - - +
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Residues in contact with LEU 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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180A TYR* 3.8 21.1 - - + +
181A THR 3.0 23.5 + - - +
182A VAL* 3.3 6.0 + - + +
184A GLU* 1.3 75.4 - - - +
186A LYS* 1.3 57.2 + - - +
188A ILE* 3.1 8.4 + - + +
189A ILE* 2.9 37.9 + - + +
209A ALA* 3.8 27.1 - - + +
212A SER* 4.1 4.3 - - - -
214A GLY* 3.5 28.9 - - - +
215A THR 3.7 8.5 - - - +
216A PRO* 3.7 34.1 - - + -
219A ALA* 4.4 5.6 - - + +
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Residues in contact with LYS 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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182A VAL 2.9 17.6 + - - +
183A LYS* 3.6 21.6 - - - +
184A GLU 3.2 0.2 - - - -
185A LEU* 1.3 75.8 - - - +
187A GLU* 1.3 60.2 + - - +
189A ILE* 3.2 6.7 + - - +
190A LYS* 2.9 38.9 + - - +
202A ASP* 2.8 36.9 + - - +
205A ALA* 3.5 17.7 - - + -
206A GLU* 3.2 39.7 + - - +
209A ALA* 3.6 12.3 - - + +
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Residues in contact with GLU 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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28A ILE* 3.1 35.7 - - + +
183A LYS* 3.1 34.9 + - + +
184A GLU* 3.1 13.7 + - - +
186A LYS* 1.3 80.3 - - + +
188A ILE* 1.3 60.0 + - - +
190A LYS* 3.5 9.3 + - + +
191A ARG* 3.1 24.1 + - - +
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Residues in contact with ILE 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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28A ILE* 3.8 18.2 - - + -
180A TYR* 4.1 13.7 - - + -
184A GLU 3.0 20.3 + - - +
185A LEU* 3.1 12.3 + - + +
187A GLU* 1.3 75.0 - - - +
189A ILE* 1.3 57.4 + - - +
191A ARG* 3.4 6.9 + - - +
192A ALA* 2.9 27.2 + - - +
216A PRO* 3.9 30.3 - - + +
219A ALA* 5.2 2.9 - - + -
220A ILE* 4.0 24.5 - - + -
600A ADP 3.7 43.1 - - + +
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Residues in contact with ILE 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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185A LEU 2.9 20.4 + - - +
186A LYS* 3.4 6.1 - - - +
187A GLU 3.2 0.2 - - - -
188A ILE* 1.3 74.5 - - - +
190A LYS* 1.3 61.0 + - - +
192A ALA* 3.1 4.5 + - - +
193A ALA* 2.8 28.2 + - - +
200A ILE* 4.2 24.0 - - + -
205A ALA* 3.7 12.1 - - + +
208A ILE* 3.6 15.0 - - + -
209A ALA* 3.3 37.9 - - + +
219A ALA* 3.8 22.2 - - + +
220A ILE* 6.0 0.2 - - - -
223A THR* 3.3 28.7 - - + +
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Residues in contact with LYS 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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186A LYS* 2.9 37.7 + - - +
187A GLU* 3.5 7.8 + - - +
189A ILE* 1.3 75.1 - - - +
191A ARG* 1.3 57.8 + - - +
193A ALA* 3.4 7.1 + - - +
194A SER* 3.0 30.0 + - - -
200A ILE* 4.5 12.7 - - + +
201A GLU 5.5 0.4 - - - -
202A ASP* 2.9 38.9 + - - +
205A ALA* 4.0 15.7 - - + -
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Residues in contact with ARG 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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18A PHE 5.3 1.2 + - - -
19A LEU* 3.5 23.2 + - - +
20A ARG 4.5 3.0 + - - -
21A PRO* 4.1 15.9 - - - +
26A GLU* 3.9 39.1 + - - +
28A ILE* 4.1 20.9 - - + -
187A GLU 3.1 18.4 + - - +
188A ILE* 3.5 7.4 + - - +
190A LYS* 1.3 75.1 - - - +
192A ALA* 1.3 64.7 + - - +
194A SER* 3.5 6.6 + - - -
195A LEU* 3.2 48.9 + - + +
220A ILE* 6.2 0.6 - - - +
600A ADP 4.2 13.8 - - - -
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Residues in contact with ALA 192 (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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19A LEU* 4.0 22.0 - - + -
188A ILE 2.9 17.4 + - - +
189A ILE* 3.7 5.6 - - - +
191A ARG* 1.3 75.4 - - - +
193A ALA* 1.3 66.5 + - - +
195A LEU* 3.3 2.6 + - - +
196A MET* 3.1 33.1 + - + +
220A ILE* 4.4 25.6 - - + -
223A THR* 4.7 9.6 - - + -
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Residues in contact with ALA 193 (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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189A ILE 2.8 17.0 + - - +
190A LYS 3.6 4.9 - - - +
192A ALA* 1.3 77.2 - - - +
194A SER* 1.3 61.7 + - - +
196A MET* 3.1 9.9 + - - -
198A VAL* 3.0 52.6 + - + +
200A ILE* 3.8 23.8 - - + -
223A THR* 4.3 10.4 - - + +
238A ILE* 5.4 0.9 - - + -
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Residues in contact with SER 194 (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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190A LYS 3.0 17.9 + - - -
191A ARG* 3.7 6.7 - - - -
193A ALA* 1.3 76.9 - - - +
195A LEU* 1.3 64.9 + - - +
197A ASP* 3.2 16.8 + - - +
198A VAL 3.9 5.6 + - - +
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Residues in contact with LEU 195 (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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18A PHE* 4.0 28.1 - - + +
19A LEU* 3.5 32.8 - - + -
191A ARG* 3.2 45.6 + - + +
192A ALA 3.8 0.4 - - - +
193A ALA 3.3 0.2 - - - -
194A SER* 1.3 79.4 - - - +
196A MET* 1.3 58.6 + - - +
197A ASP* 3.2 10.2 + - - +
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Residues in contact with MET 196 (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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18A PHE* 4.0 22.0 - - + -
19A LEU* 4.5 4.5 - - + -
192A ALA* 3.1 22.4 + - + +
193A ALA* 3.1 5.7 + - - +
195A LEU* 1.3 76.5 - - - +
197A ASP* 1.3 72.5 + - - +
198A VAL* 3.4 2.5 - - + -
220A ILE 5.2 0.2 - - - +
223A THR* 3.7 35.9 - - + +
224A LYS* 3.5 34.3 - - + -
227A ARG* 3.2 46.6 + - - +
601A ACT 3.9 9.9 - - - +
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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