Contacts of the helix formed by residues 239 - 254 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230G ALA* 3.6 5.8 - - + +
234G TYR* 4.0 34.8 - - + +
236G ASP* 3.0 28.8 + - + +
238G ASP* 1.3 93.0 - - + +
240G HIS* 1.3 62.3 + - - +
241G GLU* 3.2 4.6 + - - -
242G VAL* 3.2 34.7 + - + +
243G VAL* 3.4 5.0 + - - +
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Residues in contact with HIS 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221G ASP* 5.2 1.3 - - - -
223G ALA* 3.5 22.3 - - + +
226G PHE* 3.7 9.0 - - + +
227G ARG* 3.6 55.9 + - + +
230G ALA* 3.6 8.9 - - - +
237G GLN 3.2 23.1 + - - +
238G ASP* 3.1 11.3 + - - -
239G MET* 1.3 78.6 - - - +
241G GLU* 1.3 82.8 + - + +
243G VAL* 3.3 2.7 + - - +
244G ARG* 2.9 31.8 + - - +
276G ASN* 4.4 12.6 + - + -
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Residues in contact with GLU 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238G ASP 4.7 3.5 + - - +
239G MET 3.2 1.0 + - - -
240G HIS* 1.3 98.8 - - + +
242G VAL* 1.3 68.2 + - + +
244G ARG* 3.4 5.9 + - - +
245G LYS* 3.0 24.6 + - - +
276G ASN* 3.0 33.7 + - - +
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Residues in contact with VAL 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234G TYR* 4.2 18.4 - - + +
239G MET* 3.3 32.1 - - + +
241G GLU* 1.3 79.6 - - + +
243G VAL* 1.3 62.9 + - - +
245G LYS* 3.5 5.1 + - - +
246G HIS* 3.1 49.3 + - + +
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Residues in contact with VAL 243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G PHE* 4.0 11.7 - - + +
229G VAL* 3.6 15.5 - - + +
230G ALA* 3.8 28.3 - - + +
234G TYR* 3.7 20.4 - - + -
239G MET 3.4 1.7 + - - +
240G HIS 3.3 7.7 + - - +
242G VAL* 1.3 79.8 - - - +
244G ARG* 1.3 58.3 + - - +
246G HIS* 3.4 2.8 + - - +
247G CYS* 2.9 28.2 + - - +
288G MET* 3.5 28.0 - - - -
291G MET* 4.4 0.9 - - - +
292G TYR* 3.3 26.2 - - - +
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Residues in contact with ARG 244 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222G GLY 3.5 7.1 + - - -
223G ALA* 3.5 7.5 - - - +
226G PHE* 3.3 46.8 - - + +
240G HIS* 2.9 17.8 + - - +
241G GLU* 3.8 5.2 - - - +
243G VAL* 1.3 78.5 - - - +
245G LYS* 1.3 63.5 + - - +
247G CYS* 3.3 1.7 + - - +
248G MET* 3.0 37.4 + - + +
273G LYS* 3.0 26.5 + - - +
274G ARG* 3.5 24.2 - - - +
275G LYS 3.1 14.3 + - - -
276G ASN* 2.9 34.6 + - - +
278G CYS* 2.7 31.3 + - - +
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Residues in contact with LYS 245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241G GLU 3.0 17.8 + - - +
242G VAL* 3.9 5.4 - - - +
244G ARG* 1.3 77.9 - - - +
246G HIS* 1.3 67.9 + - + +
248G MET* 3.4 1.4 + - - -
249G ASP* 2.8 59.7 + - - +
274G ARG* 3.9 14.6 + - - +
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Residues in contact with HIS 246 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234G TYR* 4.0 14.8 + - - -
242G VAL* 3.1 40.8 + - + +
243G VAL* 3.7 4.0 - - - +
245G LYS* 1.3 82.7 + - + +
247G CYS* 1.3 60.8 + - - +
249G ASP* 3.4 13.4 + - + +
250G TYR* 2.9 25.3 + - - +
291G MET* 3.3 26.9 - - + +
292G TYR* 4.7 5.7 + - - -
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Residues in contact with CYS 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226G PHE* 4.2 3.4 - - + -
243G VAL 2.9 18.7 + - - +
244G ARG 3.5 5.4 - - - +
246G HIS* 1.3 76.5 - - - +
248G MET* 1.3 70.7 + - + +
250G TYR* 3.2 4.6 + - - +
251G LEU* 2.9 33.0 + - - +
284G GLU* 3.8 44.2 - - - -
287G ALA* 4.2 4.8 - - - +
288G MET* 3.8 18.8 - - + -
291G MET* 3.5 11.7 - - - -
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Residues in contact with MET 248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G PHE* 3.7 17.7 - - + -
244G ARG* 3.0 24.6 + - + +
246G HIS 3.3 0.2 - - - -
247G CYS* 1.3 80.7 - - - +
249G ASP* 1.3 66.1 + - - +
251G LEU* 3.4 21.0 + - - +
252G MET* 3.0 28.4 + - - +
270G ILE* 3.9 10.4 - - + +
273G LYS* 3.5 39.0 - - + +
274G ARG* 3.7 42.4 - - + +
284G GLU* 3.6 25.4 - - + -
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Residues in contact with ASP 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245G LYS* 2.8 51.3 + - - +
246G HIS* 3.6 11.3 - - + +
248G MET* 1.3 75.3 - - - +
250G TYR* 1.3 58.2 + - - +
252G MET* 3.3 6.0 + - - +
253G LYS* 3.0 28.9 + - - +
274G ARG* 2.9 30.4 + - - +
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Residues in contact with TYR 250 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246G HIS 2.9 17.9 + - - +
247G CYS* 3.2 4.2 + - - +
249G ASP* 1.3 74.0 - - - +
251G LEU* 1.3 67.7 + - - +
253G LYS* 3.2 19.9 + - - -
254G ASN* 3.0 56.0 + - - +
258G PHE* 4.1 11.2 - + - -
287G ALA* 3.7 27.4 - - + -
290G GLU* 2.7 41.8 + - + +
291G MET* 3.6 33.2 - - + -
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Residues in contact with LEU 251 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247G CYS* 2.9 26.3 + - - +
248G MET* 3.7 16.8 - - - +
249G ASP 3.4 0.2 - - - -
250G TYR* 1.3 77.7 - - - +
252G MET* 1.3 62.5 + - - +
254G ASN 3.1 3.7 + - - +
255G ALA* 2.9 23.7 + - - -
258G PHE* 3.3 44.0 - - + -
266G PHE* 3.5 7.8 - - + -
270G ILE* 3.7 25.4 - - + -
283G ILE* 3.7 16.2 - - + -
284G GLU* 4.0 19.1 - - + +
287G ALA* 3.7 15.7 - - + -
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Residues in contact with MET 252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248G MET 3.0 20.1 + - - +
249G ASP* 3.6 7.0 - - - +
250G TYR 3.3 0.2 - - - -
251G LEU* 1.3 76.5 - - - +
253G LYS* 1.3 60.4 + - - +
254G ASN 3.4 0.7 + - - -
255G ALA* 3.5 16.5 + - + +
266G PHE* 4.0 14.4 - - + -
267G THR* 3.9 26.7 - - + +
270G ILE* 3.7 37.0 - - + -
274G ARG* 4.0 10.5 - - - +
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Residues in contact with LYS 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249G ASP 3.0 15.3 + - - +
250G TYR* 3.2 23.8 + - + +
252G MET* 1.3 75.4 - - - +
254G ASN* 1.3 85.6 + - - +
255G ALA 3.5 1.4 + - - -
256G ASP 5.4 0.2 + - - -
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Residues in contact with ASN 254 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250G TYR* 3.0 48.0 + - - +
251G LEU 3.2 4.3 - - - -
253G LYS* 1.3 107.2 + - - +
255G ALA* 1.3 61.5 + - - +
256G ASP* 3.2 3.8 - - - -
257G TYR* 3.1 10.1 + - + +
258G PHE* 3.1 38.4 + - + -
290G GLU* 5.2 0.6 - - - +
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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