Contacts of the helix formed by residues 281 - 292 (chain C) 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 ASN 281 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176C ASN* 5.9 0.8 - - - +
177C SEP 2.9 34.2 + - - +
180C GLU* 2.9 27.1 + - - +
225C LEU* 3.8 4.0 - - - +
269C TYR* 5.0 1.3 - - - +
280C GLY* 1.3 74.3 - - - -
282C HIS* 1.3 79.4 + - - +
283C ILE* 3.3 4.5 - - + +
284C GLU* 3.0 23.0 + - - +
285C MET* 3.1 18.9 + - - +
42D ARG* 5.3 2.1 - - - +
70D VAL* 6.1 1.3 - - - -
71D LEU 3.8 3.7 - - - +
73D LEU 2.9 31.1 + - - -
74D ARG* 2.9 13.0 + - - +
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Residues in contact with HIS 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C ASN* 1.3 79.8 + - - +
283C ILE* 1.3 64.5 + - - +
285C MET* 3.0 10.8 + - - -
286C GLN* 3.0 23.5 + - + +
314C PHE* 3.4 38.2 - + - -
7D THR* 6.4 0.4 - - - -
8D LEU* 3.7 32.8 - - + +
69D LEU 4.8 2.0 - - - -
70D VAL* 3.8 11.8 - - + +
71D LEU* 2.8 61.0 + - + +
73D LEU* 3.9 12.2 - - + +
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Residues in contact with ILE 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C ASN* 4.4 10.5 - - - +
251C LEU* 3.7 24.9 - - + +
258C PHE* 4.3 7.7 - - + +
261C TYR* 3.6 36.8 - - + +
262C VAL* 4.0 15.7 - - + -
266C PHE* 5.7 0.2 - - + -
269C TYR* 3.5 23.6 - - + +
281C ASN* 3.2 2.8 + - + +
282C HIS* 1.3 78.0 - - - +
284C GLU* 1.3 72.2 - - - +
286C GLN* 3.6 2.9 + - - +
287C ALA* 3.1 22.0 + - - +
8D LEU* 3.7 20.9 - - + -
70D VAL* 4.5 7.9 - - + -
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Residues in contact with GLU 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C LEU* 4.4 3.1 - - + -
226C PHE* 3.9 18.6 - - + -
247C CYS* 3.7 15.2 - - - -
248C MET* 3.7 26.5 - - + -
251C LEU* 3.9 3.9 - - + +
269C TYR* 2.3 37.9 + - - -
273C LYS* 2.8 29.8 + - + +
281C ASN* 3.0 23.2 + - - +
283C ILE* 1.3 87.3 - - - +
285C MET* 1.3 58.1 + - - +
287C ALA* 3.4 2.6 + - - +
288C MET* 2.9 34.4 + - - +
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Residues in contact with MET 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C LEU* 3.7 26.5 - - + -
281C ASN 3.1 20.8 + - - +
282C HIS* 3.0 6.3 + - - +
284C GLU* 1.3 74.8 - - - +
286C GLN* 1.3 60.2 + - - +
288C MET* 3.4 10.3 + - + +
289C ALA* 3.0 28.8 + - - +
296C VAL* 3.9 20.1 - - + +
298C VAL* 3.3 33.4 - - + -
314C PHE* 4.0 22.2 - - + -
327C VAL* 4.1 2.7 - - + -
335C TYR* 3.7 33.7 - - + +
73D LEU* 4.2 8.1 - - - -
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Residues in contact with GLN 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C PHE* 3.9 12.8 - - + -
282C HIS* 3.0 14.7 + - + +
283C ILE 3.8 7.2 - - - +
285C MET* 1.3 73.3 - - - +
287C ALA* 1.3 66.0 + - - +
289C ALA* 3.3 3.4 + - - +
290C GLU* 2.7 62.4 + - - +
314C PHE* 3.6 24.4 - - - +
315C HIS 3.1 24.3 + - - -
8D LEU* 3.4 39.1 + - + +
9D THR* 3.6 16.1 - - - +
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Residues in contact with ALA 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C CYS* 4.2 7.9 - - - +
250C TYR* 3.9 14.9 - - + -
251C LEU* 3.6 30.7 - - + -
258C PHE* 4.1 10.5 - - + -
283C ILE 3.1 18.3 + - - +
284C GLU 3.5 5.8 - - - +
286C GLN* 1.3 76.6 - - - +
288C MET* 1.3 58.2 + - - +
290C GLU* 3.4 3.0 + - - +
291C MET* 2.8 32.0 + - - +
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Residues in contact with MET 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C LEU* 3.9 26.5 - - + -
226C PHE* 4.0 16.8 - - + -
229C VAL* 3.7 27.8 - - + -
243C VAL* 3.5 28.7 - - - -
247C CYS* 3.9 11.7 - - + -
284C GLU 2.9 28.5 + - - +
285C MET* 3.9 9.6 - - + +
287C ALA* 1.3 70.0 - - - +
289C ALA* 1.3 66.8 + - - +
291C MET* 3.9 17.0 - - + -
292C TYR* 2.9 41.0 + - + +
296C VAL* 4.8 6.5 - - + -
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Residues in contact with ALA 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C MET 3.0 16.9 + - - +
286C GLN 3.6 4.9 - - - +
288C MET* 1.3 75.3 - - - +
290C GLU* 1.3 58.6 + - - +
292C TYR* 5.3 0.2 - - - -
293C ASN* 3.0 23.4 + - - -
294C ARG 3.1 30.7 + - - +
296C VAL* 3.8 12.0 - - + +
314C PHE* 3.5 28.5 - - + +
315C HIS* 4.1 5.8 - - - +
316C GLY 4.7 4.2 + - - -
325C ILE* 5.4 0.2 - - - -
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Residues in contact with GLU 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C TYR* 2.8 34.3 + - + +
254C ASN* 5.5 0.5 - - - -
257C TYR* 4.6 6.3 - - - -
258C PHE* 3.7 16.6 - - - -
286C GLN* 2.7 45.4 + - - +
287C ALA 3.6 3.6 - - - +
289C ALA* 1.3 73.9 - - - +
291C MET* 1.3 64.5 + - - +
293C ASN* 3.3 21.3 + - - +
316C GLY* 3.6 23.0 - - - -
317C ILE* 5.5 3.2 - - - +
8D LEU 4.4 2.9 - - - +
9D THR 5.2 2.8 - - - +
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Residues in contact with MET 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C VAL 4.8 0.7 - - - +
246C HIS* 3.2 42.4 - - + +
247C CYS* 3.8 21.8 - - - +
250C TYR* 3.7 27.5 - - + -
287C ALA 2.8 16.5 + - - +
288C MET* 3.9 25.1 - - + +
290C GLU* 1.3 75.2 - - - +
292C TYR* 1.3 80.2 + - + +
293C ASN* 4.3 4.5 - - - +
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Residues in contact with TYR 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C VAL* 3.7 22.0 - - + -
233C VAL* 4.0 26.0 - - + -
234C TYR* 4.1 14.2 + - - -
243C VAL* 3.3 34.0 - - - +
246C HIS* 4.5 6.3 + - - -
288C MET* 2.9 30.5 + - + +
291C MET* 1.3 102.7 - - + +
293C ASN* 1.3 71.3 + - - +
294C ARG* 3.2 17.8 + - - +
322C ASP* 5.1 1.2 - - - +
325C ILE* 3.8 28.3 - - + -
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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