Contacts of the helix formed by residues 210 - 226 (chain A) in PDB entry 3TQI
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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209A THR* 1.3 84.0 + - - +
211A LYS* 1.3 61.9 + - + +
212A HIS 3.2 2.3 - - - +
213A ILE* 3.6 20.1 - - - +
214A ILE* 2.8 35.0 + - + +
385A LYS* 4.1 42.6 - - + +
386A LEU* 4.2 13.8 - - + +
389A GLU* 4.2 23.3 - - + +
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Residues in contact with LYS 211 (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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209A THR* 3.7 13.4 - - + +
210A THR* 1.3 80.8 - - + +
212A HIS* 1.3 61.8 + - + +
214A ILE* 3.4 8.9 + - + +
215A GLU* 3.1 39.7 + - - +
389A GLU* 4.6 29.2 - - + -
199C ILE* 4.7 11.3 - - - +
200C HIS* 4.2 27.3 + - - +
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Residues in contact with HIS 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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5A ILE* 4.4 12.6 - - + +
207A ASN* 3.2 36.8 + - + +
209A THR* 3.1 31.3 + - + +
210A THR 3.2 1.4 - - - +
211A LYS* 1.3 78.0 - - + +
213A ILE* 1.3 59.2 + - - +
215A GLU* 3.9 18.4 - - - +
216A ASP* 3.0 29.6 + - - +
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Residues in contact with ILE 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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5A ILE* 5.1 2.0 - - + -
208A TRP* 3.4 57.4 - - + +
209A THR 4.5 2.9 - - - +
210A THR* 3.3 26.5 + - - +
212A HIS* 1.3 75.4 - - - +
214A ILE* 1.3 66.7 + - - +
216A ASP* 3.3 5.2 + - - +
217A SER* 2.9 27.4 + - - -
378A LEU* 4.0 21.8 - - + -
382A GLU* 4.5 5.4 - - + +
386A LEU* 4.0 27.6 - - + -
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Residues in contact with ILE 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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210A THR 2.8 25.4 + - - +
211A LYS* 3.7 8.5 - - + +
212A HIS 3.4 0.2 - - - -
213A ILE* 1.3 73.9 - - - +
215A GLU* 1.3 60.6 + - + +
217A SER* 3.7 5.1 - - - -
218A ILE* 3.0 48.2 + - + +
246A LEU* 4.5 5.0 - - + +
249A LYS* 5.5 1.6 - - + -
386A LEU* 3.9 20.2 - - + +
389A GLU* 4.0 34.3 - - + -
390A LEU* 4.0 31.4 - - + +
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Residues in contact with GLU 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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211A LYS* 3.1 21.8 + - - +
212A HIS* 3.9 22.1 - - - +
213A ILE 3.2 0.2 - - - -
214A ILE* 1.3 77.1 - - + +
216A ASP* 1.3 65.4 + - - +
218A ILE* 3.5 8.4 + - + +
219A ARG* 3.1 26.6 + - - +
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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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5A ILE* 3.0 34.0 - - + +
6A HIS* 3.7 17.4 + - - -
208A TRP* 6.3 0.7 - - - -
212A HIS 3.0 19.4 + - - +
213A ILE* 3.7 5.6 - - - +
215A GLU* 1.3 76.2 - - - +
217A SER* 1.3 58.2 + - - +
219A ARG* 3.5 5.3 + - - +
220A ASP* 3.0 29.8 + - - +
377A GLU* 5.5 0.5 - - - +
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Residues in contact with SER 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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213A ILE* 2.9 23.9 + - - -
214A ILE 3.7 3.6 - - - -
216A ASP* 1.3 77.3 + - - +
218A ILE* 1.3 60.9 + - - +
220A ASP* 3.3 7.2 + - - +
221A ILE* 2.9 35.5 + - - +
246A LEU* 3.4 31.3 - - - +
374A PRO* 3.7 22.2 + - - +
386A LEU* 5.7 0.2 - - - -
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Residues in contact with ILE 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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214A ILE* 3.0 38.0 + - + +
215A GLU* 3.9 7.9 - - + +
217A SER* 1.3 75.2 - - - +
219A ARG* 1.3 59.5 + - - +
221A ILE* 3.3 3.7 + - - +
222A GLN* 2.9 53.1 + - - +
246A LEU* 4.3 20.6 - - + +
249A LYS* 4.2 25.6 - - + +
250A ALA* 3.9 14.4 - - + -
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Residues in contact with ARG 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 GLU 3.1 16.1 + - - +
216A ASP* 3.7 6.7 - - - +
218A ILE* 1.3 79.0 - - - +
220A ASP* 1.3 57.1 + - - +
222A GLN* 3.3 20.4 + - + +
223A GLU* 3.0 54.9 + - + +
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Residues in contact with ASP 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* 3.0 21.0 + - - +
217A SER* 3.6 8.3 - - - +
218A ILE 3.2 0.2 - - - -
219A ARG* 1.3 74.3 - - - +
221A ILE* 1.3 67.0 + - + +
223A GLU* 3.3 12.0 + - - +
224A LYS* 2.8 63.1 + - - +
372A ILE* 4.7 3.6 - - - +
374A PRO* 6.1 0.9 - - - +
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Residues in contact with ILE 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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217A SER 2.9 21.9 + - - +
218A ILE 3.7 4.0 - - - +
220A ASP* 1.3 77.4 - - + +
222A GLN* 1.3 56.6 + - - +
224A LYS* 4.3 0.3 - - - +
225A VAL* 3.1 35.7 + - + +
230A VAL* 5.7 0.9 - - + -
246A LEU* 4.0 14.8 - - + +
247A VAL* 3.9 43.5 - - + +
250A ALA* 3.7 17.3 - - + -
251A ILE* 4.3 10.5 - - + -
372A ILE* 4.5 27.5 - - + +
374A PRO* 4.1 20.9 - - + -
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Residues in contact with GLN 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 ILE* 2.9 36.4 + - - +
219A ARG* 3.6 21.4 + - + +
220A ASP 3.1 0.2 - - - -
221A ILE* 1.3 78.0 - - - +
223A GLU* 1.3 58.8 + - + +
226A GLY* 3.1 28.9 + - - +
249A LYS 4.8 1.8 + - - -
250A ALA 3.0 31.9 + - - +
251A ILE* 4.7 6.5 - - + -
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Residues in contact with GLU 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 ARG* 3.0 46.3 + - + +
220A ASP* 3.3 12.0 + - - +
222A GLN* 1.3 77.0 - - + +
224A LYS* 1.3 63.2 + - + +
226A GLY* 4.5 2.4 + - - -
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Residues in contact with LYS 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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220A ASP* 2.8 46.6 + - - +
221A ILE 4.3 0.4 - - - +
223A GLU* 1.3 80.6 - - + +
225A VAL* 1.3 61.1 + - + +
330A TRP* 3.2 30.9 - - + -
371A LEU 6.0 0.4 - - - +
372A ILE* 3.5 30.1 - - + +
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Residues in contact with VAL 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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221A ILE* 3.1 23.0 + - + +
222A GLN 4.8 0.4 - - - +
224A LYS* 1.3 78.2 - - + +
226A GLY* 1.3 77.6 + - - +
227A LYS 3.3 0.3 + - - -
228A GLU* 3.1 38.9 - - - +
230A VAL* 3.2 31.4 - - + -
251A ILE* 3.8 21.5 - - + -
330A TRP* 3.5 31.8 + - + +
372A ILE* 5.8 4.0 - - + -
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Residues in contact with GLY 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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222A GLN* 3.1 19.3 + - - +
223A GLU 4.5 2.4 + - - -
224A LYS 3.6 1.4 - - - -
225A VAL* 1.3 82.3 - - - +
227A LYS* 1.3 58.3 + - - -
251A ILE* 4.5 3.3 - - - +
254A GLN* 3.1 17.0 + - - +
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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