Contacts of the helix formed by residues 239 - 254 (chain A) in PDB entry 3TMP
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 MET 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ALA* 3.5 9.6 - - + -
234A TYR* 3.6 54.1 - - + -
236A ASP* 3.2 11.4 + - + +
237A GLN 3.0 1.8 - - - -
238A ASP* 1.3 90.0 + - - +
240A HIS* 1.3 62.8 + - - +
241A GLU 3.2 2.9 - - - -
242A VAL* 3.1 33.4 + - + +
243A VAL* 3.1 21.3 + - - +
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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
----------------------------------------------------------
221A ASP* 5.0 1.3 - - - -
223A ALA* 3.5 21.9 - - + +
226A PHE* 3.7 29.7 - - + +
227A ARG* 3.3 43.6 + - + +
230A ALA* 3.6 0.4 - - - +
237A GLN 3.1 23.8 + - - +
238A ASP* 3.2 10.0 - - - -
239A MET* 1.3 78.6 - - - +
241A GLU* 1.3 87.1 + - + +
243A VAL* 3.4 0.4 + - - -
244A ARG* 2.9 32.0 + - - +
276A ASN* 4.5 12.4 + - + -
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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
----------------------------------------------------------
238A ASP 4.6 7.7 + - - +
239A MET* 3.2 0.8 - - - +
240A HIS* 1.3 106.8 + - + +
242A VAL* 1.3 59.7 + - + +
244A ARG* 3.9 1.7 - - - +
245A LYS* 3.0 30.1 + - - +
276A ASN* 3.6 31.2 + - - +
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Residues in contact with VAL 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TYR* 4.3 9.6 - - + +
239A MET* 3.1 39.9 + - + +
241A GLU* 1.3 77.8 - - + +
243A VAL* 1.3 59.4 + - - +
245A LYS* 3.4 8.8 + - + +
246A HIS* 2.9 58.0 + - + +
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Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A PHE* 4.1 10.5 - - + +
229A VAL* 3.8 15.3 - - + -
230A ALA* 3.7 25.6 - - + +
233A VAL* 5.4 0.2 - - + -
234A TYR* 3.8 13.7 - - + -
239A MET 3.1 14.5 + - - +
240A HIS 3.8 6.3 - - - +
241A GLU 3.4 0.2 - - - -
242A VAL* 1.3 72.1 - - - +
244A ARG* 1.3 61.0 + - - +
246A HIS* 3.3 1.8 + - - +
247A CYS* 2.9 32.1 + - - +
288A MET* 3.5 28.0 - - - -
292A TYR* 3.5 26.5 + - + +
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Residues in contact with ARG 244 (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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223A ALA* 3.5 13.3 - - - +
226A PHE* 3.4 46.3 - - + -
240A HIS* 2.9 20.0 + - - +
241A GLU* 3.9 4.3 - - - +
243A VAL* 1.3 77.0 - - - +
245A LYS* 1.3 58.2 + - - +
247A CYS* 3.4 1.4 + - - +
248A MET* 2.9 44.1 + - + +
273A LYS* 2.8 35.0 + - - +
274A ARG* 3.3 25.6 - - - +
275A LYS 3.0 13.9 + - - -
276A ASN* 3.0 36.4 + - - +
278A CYS* 2.9 30.9 + - - +
279A HIS 5.2 0.2 - - - -
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Residues in contact with LYS 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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241A GLU 3.0 18.6 + - - +
242A VAL* 3.7 7.9 - - + +
244A ARG* 1.3 79.1 - - - +
246A HIS* 1.3 78.5 + - + +
248A MET* 3.4 0.9 + - - -
249A ASP* 3.0 46.5 + - - +
274A ARG* 3.8 17.5 + - - +
62F GLN* 4.4 7.5 - - - +
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Residues in contact with HIS 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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234A TYR* 3.9 16.0 + - - -
242A VAL* 2.9 43.6 + - + +
243A VAL* 3.8 4.0 - - - +
245A LYS* 1.3 98.7 + - + +
247A CYS* 1.3 58.0 + - - +
249A ASP* 3.3 7.5 + - - +
250A TYR* 2.9 24.6 + - - +
291A MET* 3.3 24.9 - - + +
292A TYR* 4.4 6.5 + - - -
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Residues in contact with CYS 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A PHE* 4.2 3.6 - - + -
243A VAL 2.9 17.3 + - - +
244A ARG 3.6 4.5 - - - +
246A HIS* 1.3 77.5 - - - +
248A MET* 1.3 76.3 + - - +
250A TYR* 3.4 3.4 + - - +
251A LEU* 3.0 34.0 + - - +
284A GLU* 3.8 28.5 - - - -
287A ALA* 4.3 4.8 - - - +
288A MET* 3.8 28.5 - - + -
291A MET* 3.7 10.7 - - + -
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Residues in contact with MET 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A PHE* 3.8 16.4 - - + -
244A ARG* 2.9 21.1 + - + +
246A HIS 3.3 0.2 - - - -
247A CYS* 1.3 87.5 - - - +
249A ASP* 1.3 62.8 + - - +
251A LEU* 3.3 19.9 + - - +
252A MET* 3.0 27.7 + - - +
270A ILE* 3.8 10.8 - - + +
273A LYS* 3.6 38.8 - - + +
274A ARG* 3.7 42.6 - - + +
284A GLU* 3.6 27.6 - - + -
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Residues in contact with ASP 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LYS* 3.0 42.2 + - - +
246A HIS* 3.7 9.1 - - + +
248A MET* 1.3 75.0 - - - +
250A TYR* 1.3 58.2 + - - +
252A MET* 3.3 6.2 + - - +
253A LYS* 3.0 29.1 + - - +
274A ARG* 2.9 30.7 + - - +
60F ASN* 3.6 8.0 + - - -
62F GLN* 3.2 37.3 + - - +
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Residues in contact with TYR 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 HIS 2.9 17.9 + - - +
247A CYS* 3.6 4.3 - - - +
248A MET 3.2 0.2 - - - -
249A ASP* 1.3 78.4 - - - +
251A LEU* 1.3 60.4 + - - +
253A LYS* 3.3 14.1 + - + +
254A ASN* 3.0 64.2 + - - +
258A PHE* 4.1 8.5 - + - -
287A ALA* 3.8 27.4 - - + +
290A GLU* 2.7 41.0 + - + +
291A MET* 3.8 33.4 - - + -
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Residues in contact with LEU 251 (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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247A CYS* 3.0 30.8 + - - +
248A MET* 3.7 14.8 - - - +
249A ASP 3.3 0.2 - - - -
250A TYR* 1.3 78.3 - - - +
252A MET* 1.3 56.7 + - - +
254A ASN 3.2 3.5 + - - -
255A ALA* 3.0 28.1 + - - -
258A PHE* 3.4 39.4 - - + -
266A PHE* 3.4 9.4 - - + -
269A TYR* 4.9 0.2 - - + -
270A ILE* 3.7 28.0 - - + -
283A ILE* 3.7 22.2 - - + -
284A GLU* 4.1 7.0 - - + +
287A ALA* 3.6 21.3 - - + -
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Residues in contact with MET 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A MET 3.0 16.9 + - - +
249A ASP* 3.6 9.9 - - - +
251A LEU* 1.3 76.3 - - - +
253A LYS* 1.3 60.8 + - - +
255A ALA* 3.3 16.5 + - - +
266A PHE* 4.0 13.5 - - - -
267A THR* 4.0 22.7 - - + +
270A ILE* 3.8 35.4 - - + -
274A ARG* 4.1 11.2 - - - +
45F PHE* 3.7 46.9 - - + -
46F ALA* 3.8 16.2 - - + +
59F TYR 5.3 2.9 - - - +
60F ASN* 5.9 2.2 - - + +
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Residues in contact with LYS 253 (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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249A ASP 3.0 17.4 + - - +
250A TYR* 3.8 13.7 - - + +
252A MET* 1.3 75.7 - - - +
254A ASN* 1.3 72.2 + - - +
255A ALA 3.5 1.2 + - - -
45F PHE* 5.4 2.5 - - - -
62F GLN* 5.8 4.3 - - + +
63F LYS* 4.3 12.7 + - - +
64F GLU* 3.4 44.9 + - - +
65F SER* 4.9 14.6 - - - +
66F THR* 5.1 11.7 + - - +
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Residues in contact with ASN 254 (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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250A TYR* 3.0 58.2 + - - +
251A LEU 3.2 4.3 - - - -
252A MET 3.1 0.2 - - - -
253A LYS* 1.3 91.3 + - - +
255A ALA* 1.3 62.4 + - - +
256A ASP* 3.2 4.0 - - - -
257A TYR* 3.1 11.8 + - + +
258A PHE* 3.1 38.1 + - + -
290A GLU* 5.2 1.0 + - - -
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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
------------------------------------------------------------
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