Contacts of the helix formed by residues 181 - 195 (chain A) in PDB entry 4IBR
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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61A PRO 3.5 9.9 + - - -
62A GLU* 3.8 11.6 - - - +
63A GLU 3.4 21.5 - - - +
64A ARG* 3.9 10.1 - - + -
65A PHE* 5.0 0.2 - - - -
158A VAL* 3.5 20.5 - - + +
180A THR* 1.3 87.5 + - - +
182A PRO* 1.3 74.6 - - - +
183A VAL* 3.5 5.9 - - - +
184A ALA* 3.2 22.1 + - - +
185A MET* 3.1 20.8 + - - +
261A TYR* 4.8 1.3 - - - -
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Residues in contact with PRO 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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44A GLY* 4.0 23.8 - - - -
45A TYR 4.0 7.4 - - - +
46A ILE* 3.3 29.9 - - + +
60A ARG 3.5 14.8 - - - +
61A PRO* 3.2 15.7 - - + +
63A GLU 3.3 14.4 - - - +
65A PHE* 3.8 9.6 - - + -
181A THR* 1.3 82.5 - - - +
183A VAL* 1.3 61.6 + - - +
186A ALA* 3.1 18.9 + - - +
259A VAL* 3.9 18.0 - - + +
261A TYR* 4.4 5.8 - - + -
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Residues in contact with VAL 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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46A ILE* 3.7 27.8 - - + +
48A LEU* 5.6 1.1 - - + -
55A ILE* 4.2 15.0 - - + -
61A PRO* 3.0 29.2 + - + +
62A GLU* 4.1 15.9 - - + -
158A VAL* 6.5 0.4 - - + -
181A THR* 3.5 7.0 - - - +
182A PRO* 1.3 76.7 - - - +
184A ALA* 1.3 63.3 + - + +
186A ALA* 4.1 0.7 - - - +
187A THR* 2.6 43.3 + - - +
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Residues in contact with ALA 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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156A ASP* 4.1 6.7 - - - +
158A VAL* 3.7 29.4 - - + -
159A THR* 3.9 4.7 - - - +
180A THR* 3.8 10.1 - - - +
181A THR* 3.2 15.3 + - - +
183A VAL* 1.3 80.4 - - + +
185A MET* 1.3 61.9 + - - +
187A THR* 3.3 4.6 + - - -
188A THR* 2.8 36.0 + - - -
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Residues in contact with MET 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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67A MET* 3.8 17.9 - - + -
70A THR* 4.2 9.4 - - - +
74A LEU* 3.4 45.5 - - + -
159A THR* 4.7 1.1 - - + -
180A THR* 3.5 15.3 + - + +
181A THR 3.1 15.8 + - - +
182A PRO 4.1 2.2 - - - +
184A ALA* 1.3 77.7 - - - +
186A ALA* 1.3 53.0 + - - +
188A THR* 3.2 3.0 + - - -
189A LEU* 2.7 40.6 + - + +
245A ILE* 3.5 39.0 - - + -
259A VAL* 4.2 4.5 - - + -
261A TYR* 3.5 18.4 - - + +
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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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46A ILE* 3.5 14.6 - - + -
48A LEU* 3.7 19.5 - - + +
182A PRO 3.1 17.1 + - - +
183A VAL 4.1 2.0 - - - +
185A MET* 1.3 79.0 - - - +
187A THR* 1.3 57.2 + - - +
189A LEU* 3.5 3.3 + - - +
190A ARG* 2.9 30.1 + - - +
257A ILE* 3.9 13.1 - - + +
259A VAL* 3.4 22.0 - - + +
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Residues in contact with THR 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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48A LEU* 4.0 13.7 - - - +
183A VAL* 2.6 34.2 + - - +
184A ALA* 3.7 4.7 - - - -
186A ALA* 1.3 74.6 - - - +
188A THR* 1.3 59.3 + - - +
190A ARG* 3.4 3.6 + - - +
191A LYS* 3.0 52.1 + - + +
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Residues in contact with THR 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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74A LEU* 3.5 28.3 - - + -
151A LEU* 3.9 15.0 - - + -
154A MET* 3.7 23.6 - - + +
156A ASP* 2.5 35.8 + - - +
184A ALA 2.8 18.9 + - - -
185A MET* 3.6 5.4 - - - -
187A THR* 1.3 73.4 - - - +
189A LEU* 1.3 63.9 + - - +
191A LYS* 3.4 3.3 + - - -
192A LEU* 3.0 25.1 + - + +
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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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73A VAL* 3.9 28.5 - - + -
74A LEU* 5.1 2.0 - - + -
185A MET* 2.7 26.2 + - - +
186A ALA* 3.7 4.7 - - - +
188A THR* 1.3 74.1 - - - +
190A ARG* 1.3 59.0 + - - +
192A LEU* 3.2 8.6 + - + +
193A LEU* 2.9 50.7 + - + +
210A MET* 4.2 11.7 - - + -
245A ILE* 4.0 30.3 - - + -
246A ALA 4.2 14.6 - - - +
257A ILE* 4.3 19.1 - - + -
259A VAL* 5.3 0.9 - - + -
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Residues in contact with ARG 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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48A LEU* 4.2 11.2 - - + -
49A ASP 4.2 4.0 - - - -
50A LEU* 2.7 41.9 + - + +
51A ALA 3.1 18.2 + - - -
52A SER 3.2 12.7 + - - -
53A GLY* 3.4 26.0 - - - -
186A ALA 2.9 18.8 + - - +
187A THR* 3.7 6.1 - - - +
188A THR 3.2 0.2 - - - -
189A LEU* 1.3 74.7 - - - +
191A LYS* 1.3 63.6 + - - +
193A LEU* 4.5 2.2 - - - +
194A THR* 2.6 50.9 + - - +
257A ILE* 4.2 16.2 - - + -
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Residues in contact with LYS 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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154A MET* 3.0 45.0 + - + +
155A GLY* 3.9 16.8 + - - -
156A ASP* 4.7 1.2 - - - +
187A THR* 3.0 39.4 + - + +
188A THR* 3.7 6.9 + - - +
190A ARG* 1.3 79.5 - - - +
192A LEU* 1.3 63.1 + - - +
194A THR* 4.5 0.7 - - - -
195A GLY* 2.8 36.0 + - - +
197A LEU* 4.2 11.9 - - + +
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Residues in contact with LEU 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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73A VAL* 4.6 4.0 - - + +
74A LEU* 3.7 40.8 - - + +
77A GLY* 4.4 12.3 - - - -
150A PHE* 4.3 26.5 - - + -
151A LEU* 5.7 0.2 - - + -
154A MET* 4.2 12.8 - - + -
188A THR* 3.0 19.7 + - + +
189A LEU* 3.5 11.0 - - + +
191A LYS* 1.3 80.5 - - - +
193A LEU* 1.3 61.4 + - + +
195A GLY 4.6 1.9 + - - +
197A LEU* 4.3 9.9 - - + -
198A LEU* 3.8 24.3 - - + +
203A ARG* 3.7 15.6 - - - +
206A LEU* 4.0 19.5 - - + -
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A LEU* 5.7 0.9 - - + -
189A LEU* 2.9 39.0 + - + +
190A ARG* 4.2 1.3 - - - +
192A LEU* 1.3 78.2 - - - +
194A THR* 1.3 68.4 + - + +
203A ARG* 3.1 27.5 - - - +
206A LEU* 3.8 32.3 - - + -
207A ILE* 4.0 37.7 - - + +
210A MET* 4.6 6.3 - - - -
247A ALA* 4.0 26.9 - - + -
257A ILE* 4.5 6.3 - - + -
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Residues in contact with THR 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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50A LEU* 3.5 38.1 - - + +
190A ARG* 2.6 40.4 + - - +
191A LYS* 4.5 0.5 - - - -
193A LEU* 1.3 86.5 - - + +
195A GLY* 1.3 66.7 + - - +
196A GLU* 5.5 0.7 - - - +
203A ARG* 4.4 12.3 + - - +
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Residues in contact with GLY 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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191A LYS* 2.8 29.9 + - - +
192A LEU 4.8 0.7 - - - +
194A THR* 1.3 78.2 + - - +
196A GLU* 1.3 58.7 + - - -
197A LEU* 2.9 11.7 + - - -
198A LEU 3.6 4.0 + - - +
203A ARG* 3.2 21.6 + - - -
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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