Contacts of the helix formed by residues 238 - 250 (chain A) in PDB entry 1TAD
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 ARG 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ALA* 5.5 1.6 - - - +
38A GLY 3.9 8.7 + - - -
39A GLU* 2.8 45.8 + - - +
143A GLN* 2.6 30.5 + - - -
225A ALA* 3.6 26.9 - - + +
228A MET* 2.7 44.7 + - - +
229A VAL 2.9 27.0 + - - +
230A LEU* 3.8 22.0 - - + +
231A VAL* 3.7 9.4 - - - +
236A VAL 3.6 0.6 + - - -
237A ASN* 1.3 71.0 - - - +
239A MET* 1.3 58.4 + - - +
241A GLU* 3.2 4.2 + - - +
242A SER* 2.9 27.3 + - - -
266A LYS* 5.6 3.0 - - - +
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Residues in contact with MET 239 (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 ALA 3.5 25.1 - - - +
223A LEU* 3.5 19.7 - - - +
225A ALA* 3.7 4.9 + - - -
226A TYR* 3.8 21.3 - - + +
237A ASN* 3.0 10.6 + - - +
238A ARG* 1.3 75.4 - - - +
240A HIS* 1.3 61.7 + - - +
242A SER* 3.6 5.1 - - - -
243A LEU* 2.9 29.5 + - + +
264A LEU* 5.8 0.4 - - + -
282A CYS* 3.7 9.6 - - - -
283A PHE* 3.8 32.1 - - + -
299A ILE* 3.7 29.8 - - + -
303A PHE* 4.2 19.1 - - + -
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Residues in contact with HIS 240 (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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236A VAL* 5.0 4.9 - - + -
237A ASN* 3.2 32.0 + - + +
239A MET* 1.3 76.8 - - - +
241A GLU* 1.3 63.6 + - - +
243A LEU* 3.3 14.4 + - - +
244A HIS* 3.0 43.7 + + + +
281A ILE 5.2 1.4 + - - -
282A CYS* 3.1 48.1 + - - -
283A PHE* 4.8 5.2 - + - -
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Residues in contact with GLU 241 (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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37A ALA* 4.7 4.9 - - + -
201A ARG* 2.9 35.7 + - - +
204A ARG* 2.8 41.3 + - - +
230A LEU* 3.5 34.3 - - + +
236A VAL* 4.0 5.9 - - + +
237A ASN 3.2 6.6 + - - +
238A ARG 3.3 9.4 - - - +
240A HIS* 1.3 79.1 - - - +
242A SER* 1.3 63.4 + - - +
244A HIS* 3.2 12.9 + - - +
245A LEU* 2.9 22.3 + - - +
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Residues in contact with SER 242 (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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37A ALA* 4.8 13.8 + - - +
219A PHE* 3.7 9.7 - - - -
220A ILE 4.7 0.5 + - - -
221A ALA* 3.4 29.8 - - - +
222A ALA 5.7 1.8 - - - -
225A ALA* 6.4 0.9 - - - -
238A ARG 2.9 15.6 + - - -
239A MET* 3.3 8.9 + - - -
241A GLU* 1.3 76.6 - - - +
243A LEU* 1.3 52.5 + - - +
245A LEU* 3.3 6.7 + - - +
246A PHE* 2.8 35.5 + - - +
303A PHE* 3.5 9.5 - - - -
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Residues in contact with LEU 243 (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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239A MET* 2.9 27.7 + - + +
240A HIS* 3.5 12.8 - - - +
242A SER* 1.3 76.6 - - - +
244A HIS* 1.3 62.5 + - + +
246A PHE* 3.4 0.7 + - - +
247A ASN* 2.9 23.6 + - - +
283A PHE* 3.6 33.7 - - + -
302A GLN* 3.8 26.5 - - + +
303A PHE* 3.7 41.5 - - + -
306A LEU* 3.1 20.3 - - + +
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Residues in contact with HIS 244 (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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236A VAL* 6.3 0.6 - - + +
240A HIS* 3.0 30.9 + - + +
241A GLU* 3.2 13.6 + - - +
243A LEU* 1.3 78.6 - - + +
245A LEU* 1.3 66.3 + - - +
247A ASN* 3.3 8.8 + - + +
248A SER* 3.1 22.5 + - - -
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Residues in contact with LEU 245 (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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36A GLY 3.8 1.8 - - - -
37A ALA* 3.7 32.3 - - + +
204A ARG* 3.8 41.5 - - + +
207A TRP* 3.7 30.7 - - + -
219A PHE* 3.9 12.6 - - + -
241A GLU 2.9 16.4 + - - +
242A SER 3.6 4.3 - - - +
244A HIS* 1.3 77.1 - - - +
246A PHE* 1.3 62.4 + - - +
248A SER* 2.8 26.5 + - - +
249A ILE* 3.0 16.9 + - + +
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Residues in contact with PHE 246 (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 PHE* 3.6 47.9 - + + -
242A SER 2.8 21.0 + - - +
243A LEU 3.7 4.0 - - - +
245A LEU* 1.3 71.8 - - - +
247A ASN* 1.3 53.3 + - - +
249A ILE* 4.5 1.8 - - + -
250A CYS* 2.6 57.7 + - + +
260A ILE* 4.4 14.6 - - + -
262A LEU* 4.4 15.0 - - + -
303A PHE* 3.1 51.4 - + + -
304A LEU* 4.3 2.5 - - + -
306A LEU* 4.1 6.5 - - + -
315A ILE* 3.8 31.2 - - + -
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Residues in contact with ASN 247 (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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243A LEU 2.9 14.3 + - - +
244A HIS* 3.4 14.1 - - + +
245A LEU 3.2 0.2 - - - -
246A PHE* 1.3 76.8 - - - +
248A SER* 1.3 58.5 + - - +
250A CYS* 4.4 0.9 - - - -
251A ASN* 2.7 59.5 + - - +
306A LEU* 3.6 34.9 + - + +
308A MET* 4.5 6.1 - - - -
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Residues in contact with SER 248 (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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244A HIS 3.1 12.3 + - - -
245A LEU* 2.8 30.1 + - - +
247A ASN* 1.3 77.1 - - - +
249A ILE* 1.3 65.3 + - - +
251A ASN* 3.7 2.5 + - - -
252A HIS* 3.3 30.1 + - - -
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Residues in contact with ILE 249 (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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35A LEU* 4.1 10.8 - - + -
207A TRP* 3.9 34.8 - - + -
211A PHE* 4.0 20.9 - - + -
217A ILE* 4.1 30.3 - - + -
219A PHE* 4.3 13.0 - - + -
245A LEU* 3.0 21.3 + - + +
246A PHE* 3.8 6.5 - - + +
248A SER* 1.3 80.2 - - - +
250A CYS* 1.3 66.9 + - - +
252A HIS* 3.1 24.1 + - + +
255A PHE* 3.6 9.6 - - + +
260A ILE* 4.6 4.4 - - + +
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Residues in contact with CYS 250 (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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246A PHE* 2.6 40.6 + - + +
247A ASN* 3.9 4.9 - - - +
249A ILE* 1.3 75.6 - - - +
251A ASN* 1.3 58.8 + - - +
252A HIS 3.3 4.4 + - - +
255A PHE* 5.4 2.1 - - - +
260A ILE* 4.2 19.1 - - - +
306A LEU 4.5 0.4 - - - -
307A ASN* 3.4 48.2 - - - +
309A ARG* 4.6 5.2 + - - +
315A ILE* 3.4 20.6 - - - -
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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