Contacts of the helix formed by residues 214 - 223 (chain A) in PDB entry 4TQ1
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 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A LEU 4.3 6.3 - - - +
213A HIS* 1.3 78.9 - - - +
215A LEU* 1.3 65.7 + - - +
216A GLY* 3.3 4.3 + - - -
217A ASP* 2.8 35.6 + - - +
218A LEU* 3.1 20.6 + - - +
247A LEU 3.2 11.9 + - - -
248A GLU* 3.5 24.9 - - + +
249A THR 3.3 8.5 - - - +
250A PRO* 4.7 2.7 - - + -
251A LEU* 4.3 6.3 - - - +
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Residues in contact with LEU 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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214A THR* 1.3 73.0 - - - +
216A GLY* 1.3 62.0 + - - +
218A LEU* 3.2 13.9 + - + +
219A LEU* 3.0 40.6 + - + +
238A VAL* 4.5 17.7 - - + -
240A ILE* 4.6 6.5 - - + -
245A PRO* 3.9 25.4 - - + +
246A MET 3.8 18.4 - - - +
247A LEU* 3.6 12.1 - - + +
249A THR 2.9 15.8 + - - +
251A LEU* 4.4 6.4 - - + +
254A LEU* 4.0 17.3 - - + -
267A ILE* 4.4 23.3 - - + -
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Residues in contact with GLY 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 THR* 3.7 2.0 - - - -
215A LEU* 1.3 76.6 - - - +
217A ASP* 1.3 56.7 + - - +
219A LEU* 3.3 4.4 + - - +
220A LYS* 2.8 45.7 + - - +
227A ILE* 4.6 1.2 - - - +
247A LEU* 2.8 40.8 + - - +
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Residues in contact with ASP 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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203A PHE* 4.0 5.3 - - + -
212A LEU 4.3 1.4 - - - +
213A HIS* 3.3 28.9 - - + -
214A THR* 2.8 40.1 + - - +
216A GLY* 1.3 76.8 - - - +
218A LEU* 1.3 63.4 + - - +
220A LYS* 3.4 15.0 + - - +
221A GLU* 3.1 24.3 + - - +
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Residues in contact with LEU 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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187A PHE* 3.7 40.6 - - + -
189A ILE* 4.5 4.7 - - + -
203A PHE* 3.6 41.2 - - + -
214A THR 3.1 9.3 + - - +
215A LEU* 3.5 14.4 - - + +
217A ASP* 1.3 80.4 - - - +
219A LEU* 1.3 59.3 + - + +
221A GLU* 3.2 2.9 + - - +
222A VAL* 2.9 39.7 + - + +
251A LEU* 4.1 23.6 - - + -
267A ILE* 4.1 23.1 - - + -
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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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189A ILE* 3.9 26.2 - - + -
215A LEU* 3.0 28.2 + - + +
216A GLY 3.9 3.1 - - - +
218A LEU* 1.3 74.8 - - + +
220A LYS* 1.3 63.3 + - - +
222A VAL* 4.7 0.2 - - - -
223A CYS* 2.8 46.9 + - + +
224A PRO* 4.4 0.7 - - - -
226A ALA* 4.6 4.5 - - + -
227A ILE* 4.0 17.5 - - + -
238A VAL* 3.8 32.1 - - + -
247A LEU* 4.0 23.6 - - + -
267A ILE* 5.3 1.3 - - + -
269A ILE* 4.2 17.7 - - + -
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Residues in contact with LYS 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 GLY* 2.8 32.4 + - - +
217A ASP* 3.6 15.5 - - - +
218A LEU 3.3 0.2 - - - -
219A LEU* 1.3 76.4 - - - +
221A GLU* 1.3 60.9 + - - +
224A PRO* 3.5 21.0 - - - +
227A ILE* 4.2 24.9 - - + +
232A GLY* 3.4 30.2 + - - -
247A LEU* 5.0 1.4 - - - +
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Residues in contact with GLU 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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203A PHE* 3.9 21.1 - - + -
217A ASP 3.1 16.4 + - - +
218A LEU 3.7 3.1 - - - +
220A LYS* 1.3 79.9 - - - +
222A VAL* 1.3 72.7 + - + +
224A PRO* 4.4 4.0 - - - +
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Residues in contact with VAL 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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187A PHE* 4.0 6.5 - - + -
189A ILE* 3.6 27.4 - - + -
199A ILE* 3.6 27.2 - - + +
201A LYS* 3.9 30.1 - - + +
202A LEU 5.7 0.2 - - - +
203A PHE* 4.6 4.5 - - + -
218A LEU* 2.9 38.3 + - + +
221A GLU* 1.3 92.7 - - + +
223A CYS* 1.3 61.1 - - - +
224A PRO* 3.6 5.6 - - - +
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Residues in contact with CYS 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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189A ILE* 4.3 14.1 - - + -
191A GLN* 4.0 17.3 - - - -
199A ILE* 3.9 21.3 - - + -
219A LEU* 2.8 30.0 + - + +
222A VAL* 1.3 81.6 - - - +
224A PRO* 1.3 64.0 - - - +
225A SER* 3.1 21.3 - - - -
226A ALA* 3.0 29.0 + - - +
227A ILE 4.3 0.2 + - - -
269A ILE* 4.5 4.5 - - - -
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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