Contacts of the helix formed by residues 210 - 226 (chain A) in PDB entry 4IB4
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A THR* 6.5 0.9 - - + -
208A VAL* 3.7 16.3 + - + +
209A LEU* 1.3 73.1 - - - +
211A LYS* 1.4 55.1 - - - +
212A GLU* 4.0 6.7 + - - +
213A ARG* 3.3 25.6 + - - +
214A PHE* 2.8 39.3 + - - +
2001A ERM 3.7 2.7 - - - -
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Residues in contact with LYS 211 (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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210A THR* 1.4 72.0 - - - +
212A GLU* 1.4 58.0 + - - +
215A GLY* 3.1 24.4 + - - +
347A LEU* 3.3 25.6 + - + +
348A VAL* 3.4 30.6 + - + -
350A CYS 4.0 9.3 + - - -
351A ASP* 4.4 12.1 - - - +
355A GLN* 3.7 21.0 + - - +
2001A ERM 3.7 27.7 - - + -
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Residues in contact with GLU 212 (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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210A THR* 3.3 7.7 + - - +
211A LYS* 1.4 80.4 - - - +
213A ARG* 1.3 59.5 + - + +
215A GLY 4.8 0.7 + - - -
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Residues in contact with ARG 213 (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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193A LYS* 2.8 62.3 + - - +
194A GLY 3.1 29.4 + - - -
195A ILE* 3.9 1.0 - - - +
196A GLU* 3.4 39.8 - - - +
210A THR* 3.3 18.1 + - - +
212A GLU* 1.3 80.7 - - + +
214A PHE* 1.4 73.3 + - + +
215A GLY 3.7 0.9 - - - -
2009A OLA 3.9 2.3 - - - +
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Residues in contact with PHE 214 (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 PRO 4.0 2.2 - - - -
190A VAL* 4.0 21.1 - - + -
193A LYS* 3.6 28.3 - - + -
194A GLY 3.3 29.4 - - - -
195A ILE* 5.0 4.0 - - + -
209A LEU* 3.7 39.3 - - + -
210A THR 2.8 24.3 + - - +
213A ARG* 1.4 91.2 - - + +
215A GLY* 1.3 52.9 + - - +
216A ASP 3.4 2.7 - - - -
217A PHE* 3.1 26.1 + + + -
218A MET* 2.8 51.5 + - + +
2001A ERM 4.8 0.4 - - - -
2009A OLA 4.7 0.7 - - - -
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Residues in contact with GLY 215 (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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210A THR 3.8 0.6 + - - -
211A LYS* 3.1 27.3 + - - -
212A GLU 4.7 0.8 + - - -
213A ARG 3.7 1.6 - - - -
214A PHE* 1.3 76.8 - - - +
216A ASP* 1.3 60.9 - - - +
218A MET* 3.4 5.0 + - - +
219A LEU* 3.1 17.3 + - - +
348A VAL* 3.5 29.9 - - - +
2001A ERM 4.9 0.2 - - - -
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Residues in contact with ASP 216 (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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214A PHE 3.4 0.2 - - - -
215A GLY* 1.3 71.7 - - - +
217A PHE* 1.4 61.3 + - - +
219A LEU* 3.2 8.0 + - - +
220A PHE* 2.9 58.5 + - + +
348A VAL* 6.0 0.3 - - - +
2009A OLA 3.6 27.2 + - + +
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Residues in contact with PHE 217 (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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136A VAL* 4.2 9.6 - - + -
186A ILE 3.1 27.4 - - - -
189A PRO* 3.7 28.7 - - + -
190A VAL* 3.7 24.2 - - + -
209A LEU* 4.2 3.4 - - + -
214A PHE* 3.1 29.9 + + + +
216A ASP* 1.4 76.6 - - - +
218A MET* 1.3 73.5 + - + +
221A GLY* 2.8 37.5 + - - -
2001A ERM 3.8 28.2 - + - -
2009A OLA 3.6 35.5 + - + +
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Residues in contact with MET 218 (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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209A LEU* 3.5 34.3 - - + -
214A PHE* 2.8 19.4 + - + +
215A GLY 3.4 6.7 - - - +
217A PHE* 1.3 91.2 - - + +
219A LEU* 1.3 57.9 + - - +
222A SER* 2.7 31.0 + - - -
344A ASN* 3.0 35.7 + - - +
345A ILE* 4.7 0.6 - - - +
348A VAL* 3.8 11.9 - - + -
2001A ERM 3.7 66.1 - - + +
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Residues in contact with LEU 219 (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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215A GLY 3.1 11.3 + - - +
216A ASP* 3.2 14.1 + - - +
218A MET* 1.3 78.0 - - - +
220A PHE* 1.3 83.5 + - + +
222A SER* 3.5 3.5 + - - -
223A LEU* 3.3 42.4 + - + +
345A ILE* 4.5 16.8 - - + +
348A VAL* 3.7 25.4 - - + -
349A LEU* 3.8 32.1 - - + -
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Residues in contact with PHE 220 (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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216A ASP* 2.9 51.6 + - + +
219A LEU* 1.3 87.9 - - + +
221A GLY* 1.3 58.8 + - - +
222A SER 3.3 0.2 - - - -
223A LEU* 3.4 21.5 + - + +
224A ALA* 3.0 30.1 + - - +
2009A OLA 4.5 23.5 - - + +
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Residues in contact with GLY 221 (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 ILE* 4.1 8.7 - - - +
217A PHE* 2.8 27.4 + - - -
220A PHE* 1.3 73.1 - - - +
222A SER* 1.4 50.8 + - - +
224A ALA* 3.4 1.9 + - - +
225A ALA* 2.8 38.5 + - - +
2001A ERM 3.9 14.9 - - - -
2009A OLA 4.5 12.6 - - - +
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Residues in contact with SER 222 (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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218A MET 2.7 24.4 + - - -
219A LEU 3.7 4.9 - - - -
220A PHE 3.3 0.4 - - - -
221A GLY* 1.4 74.3 - - - +
223A LEU* 1.4 58.1 + - - +
226A PHE* 3.0 25.5 + - - +
227A PHE* 3.2 14.2 + - - -
341A PHE* 3.3 28.0 - - - -
344A ASN* 2.8 18.9 + - - +
345A ILE* 3.8 19.5 - - - +
2001A ERM 4.2 2.4 - - - -
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Residues in contact with LEU 223 (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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219A LEU* 3.3 29.5 + - + +
220A PHE* 3.7 32.8 - - + +
221A GLY 3.3 0.4 - - - -
222A SER* 1.4 75.5 - - - +
224A ALA* 1.3 53.3 + - - +
227A PHE* 3.5 24.9 + - + -
228A THR* 2.7 42.9 + - - +
345A ILE* 5.3 5.6 - - + -
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Residues in contact with ALA 224 (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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144A TRP* 3.3 29.1 + - - -
186A ILE* 3.6 22.4 - - + +
220A PHE 3.0 16.7 + - - +
221A GLY 3.9 2.7 - - - +
223A LEU* 1.3 77.9 - - - +
225A ALA* 1.3 59.1 + - - +
228A THR* 3.8 7.6 - - - -
229A PRO* 3.6 3.7 - - - +
2009A OLA 4.1 18.4 - - + -
2011A PEG 4.3 10.3 + - - +
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Residues in contact with ALA 225 (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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140A THR* 3.6 17.4 - - + +
143A ILE* 3.4 18.7 - - + +
144A TRP* 3.8 9.9 + - - +
186A ILE* 4.0 6.1 - - + -
221A GLY 2.8 21.8 + - - +
222A SER 4.7 0.4 - - - +
224A ALA* 1.3 73.8 - - - +
226A PHE* 1.3 58.9 - - - +
229A PRO* 3.3 14.9 - - - +
341A PHE* 4.9 3.8 - - + -
2001A ERM 3.4 27.8 - - + +
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Residues in contact with PHE 226 (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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143A ILE* 4.4 9.5 - - + +
222A SER 3.0 12.7 + - - +
225A ALA* 1.3 78.6 - - - +
227A PHE* 1.3 92.7 + + - +
228A THR 3.3 1.8 - - - -
229A PRO* 3.4 4.6 - - - +
230A LEU* 3.1 45.7 + - + +
334A LEU* 3.4 48.2 - - + +
337A TRP* 3.7 15.0 - + + -
338A CYS* 3.7 22.7 - - - -
341A PHE* 3.5 40.8 - + + -
342A ILE* 6.1 0.4 - - + -
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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