Contacts of the helix formed by residues 277 - 289 (chain C) in PDB entry 3MP4
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 ALA 277 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C ASP* 5.8 0.2 - - - +
259C SER 3.5 7.4 - - - -
262C GLY* 3.7 12.6 - - - +
275C ASN 3.5 4.0 + - - -
276C LEU* 1.3 81.5 - - - +
278C THR* 1.3 65.2 + - - +
279C GLU* 3.9 6.5 - - - +
280C ASP* 3.2 31.5 + - - +
281C LEU* 3.2 15.9 + - - +
315C SER 4.2 3.6 - - - +
316C SER* 3.7 19.7 - - - +
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Residues in contact with THR 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 4.1 15.7 - - + -
37C GLU* 2.5 29.0 + - - +
68C LEU* 5.0 6.3 - - + -
258C SER* 3.0 25.9 + - - +
259C SER 3.0 18.3 + - - -
260C VAL* 4.0 6.3 - - - -
276C LEU 3.3 1.0 + - - -
277C ALA* 1.3 71.6 - - - +
279C GLU* 1.3 62.2 + - - +
281C LEU* 3.2 3.0 + - - +
282C VAL* 3.0 36.5 + - + +
294C VAL* 6.0 0.2 - - + -
299C LEU* 3.7 19.7 - - + -
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Residues in contact with GLU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C VAL 2.4 31.3 - - - +
261C ALA* 4.0 6.6 - - - +
277C ALA* 3.9 1.2 - - - +
278C THR* 1.3 75.4 + - - +
280C ASP* 1.3 58.0 + - - +
282C VAL* 3.3 4.0 - - - +
283C TYR* 2.9 30.0 + - - +
296C LEU* 3.9 8.9 - - + +
299C LEU* 3.7 29.9 - - + +
300C LEU* 3.4 37.5 - - + +
303C GLY* 4.4 4.2 - - - -
314C THR* 4.8 0.2 + - - -
316C SER* 3.4 32.6 - - - +
318C VAL* 3.9 5.8 - - + +
319C ALA* 4.8 1.7 - - - +
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Residues in contact with ASP 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LEU* 4.1 6.4 - - + +
276C LEU* 5.0 8.1 - - + +
277C ALA* 3.2 27.6 + - + +
279C GLU* 1.3 75.0 - - - +
281C LEU* 1.3 60.6 - - - +
283C TYR* 3.6 0.3 - - - +
284C MET* 3.2 8.5 + - - +
315C SER 3.9 3.1 - - - +
316C SER* 3.1 3.3 + - - -
317C LYS* 3.0 29.2 + - - +
318C VAL* 2.8 39.5 + - - +
238D TYR 4.3 6.7 - - - +
239D GLY* 4.9 4.2 - - - -
240D GLN* 3.1 25.1 + - - +
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Residues in contact with LEU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 3.7 18.2 - - + -
242C LEU* 3.9 22.6 - - + +
245C THR* 4.1 18.4 - - + -
249C LEU* 5.5 0.2 - - + -
256C VAL* 3.6 33.9 - - + -
258C SER* 3.9 18.2 - - - +
276C LEU* 4.1 9.2 - - + -
277C ALA 3.2 12.3 + - - +
278C THR* 3.5 8.1 - - - +
279C GLU 3.1 0.8 - - - -
280C ASP* 1.3 75.4 - - - +
282C VAL* 1.3 62.6 + - - +
284C MET* 3.1 9.3 + - + +
285C LEU* 2.9 49.7 + - + +
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Residues in contact with VAL 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 3.6 23.3 - - + -
278C THR* 3.0 19.2 + - + +
279C GLU* 3.3 10.5 - - - +
281C LEU* 1.3 73.0 - - - +
283C TYR* 1.3 63.0 + - - +
285C LEU* 4.1 9.4 - - - -
286C GLU* 2.7 49.4 + - + +
292C THR* 4.9 6.5 - - + +
294C VAL* 4.7 12.3 - - + -
296C LEU* 3.3 35.4 - - + +
299C LEU* 4.1 11.7 - - + -
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Residues in contact with TYR 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C GLU 2.9 18.3 + - - +
280C ASP 3.6 5.8 - - - +
282C VAL* 1.3 80.5 - - + +
284C MET* 1.3 66.2 + - - +
286C GLU* 3.3 4.1 + - - +
287C GLY* 3.0 20.5 + - - -
296C LEU* 4.5 13.9 - - + -
318C VAL* 3.8 25.1 - - + -
208D VAL* 2.8 47.0 + - - +
210D THR* 4.0 8.5 - - + +
238D TYR* 4.1 26.5 - + + -
240D GLN* 3.7 28.0 - - + -
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Residues in contact with MET 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LEU* 3.7 36.1 - - + +
245C THR* 4.8 0.9 - - + -
246C LEU* 4.4 17.7 - - + +
249C LEU* 3.9 28.3 - - + -
280C ASP 3.2 4.6 + - - +
281C LEU* 3.1 16.9 + - + +
283C TYR* 1.3 81.7 - - - +
285C LEU* 1.3 61.5 + - + +
287C GLY* 3.2 1.9 + - - -
288C LEU* 2.9 30.0 + - + +
210D THR* 3.7 6.2 - - - +
211D PRO* 3.7 28.3 - - + -
240D GLN* 3.0 28.5 - - - +
243D ALA* 4.3 7.0 - - - -
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Residues in contact with LEU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 4.2 19.3 - - + -
35C ILE* 4.1 8.1 - - + -
249C LEU* 3.9 22.9 - - + -
256C VAL* 5.1 0.4 - - + -
281C LEU* 2.9 44.0 + - + +
282C VAL* 3.7 4.0 - - - +
284C MET* 1.3 79.5 - - + +
286C GLU* 1.3 58.1 + - - +
288C LEU* 3.0 6.7 + - + +
289C GLY 2.9 21.5 + - - -
290C ILE* 2.9 42.6 + - + +
292C THR* 3.6 31.4 - - + -
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Residues in contact with GLU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C VAL* 2.7 34.7 + - + +
283C TYR* 3.8 3.9 - - - +
285C LEU* 1.3 69.4 - - + +
287C GLY* 1.3 60.8 + - - +
289C GLY* 2.7 21.6 + - - +
290C ILE 4.4 7.2 - - - +
292C THR* 4.5 10.2 + - - +
294C VAL 3.6 20.6 - - - +
296C LEU* 4.5 22.6 + - - +
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Residues in contact with GLY 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C TYR* 3.0 14.6 + - - -
284C MET 3.6 2.5 - - - -
286C GLU* 1.3 77.4 - - - +
288C LEU* 1.3 59.2 + - - +
289C GLY 3.5 0.3 + - - -
210D THR* 3.4 27.8 + - - -
212D GLY* 5.5 0.9 - - - -
213D ILE* 4.7 11.9 + - - +
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Residues in contact with LEU 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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29C LEU* 4.4 18.6 - - + +
246C LEU* 4.4 12.6 - - + -
249C LEU* 5.2 0.4 - - + -
284C MET* 2.9 37.4 + - + +
285C LEU* 3.2 11.7 - - + +
286C GLU 3.0 0.4 - - - -
287C GLY* 1.3 80.4 - - - +
289C GLY* 1.3 58.9 + - - +
290C ILE* 3.9 26.5 - - + +
211D PRO* 3.7 17.5 - - + -
212D GLY* 3.3 36.1 - - - +
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Residues in contact with GLY 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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31C LYS* 4.5 3.5 - - - +
286C GLU* 2.7 16.9 + - - -
287C GLY 3.2 1.0 + - - -
288C LEU* 1.3 79.9 - - - +
290C ILE* 1.3 62.2 + - - +
291C HIS 3.9 1.4 + - - -
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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