Contacts of the helix formed by residues 279 - 285 (chain C) in PDB entry 2VM8
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 ILE 279 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254C LYS* 4.2 8.1 - - + -
256C MET* 4.1 16.6 - - + -
277C GLU* 3.7 25.6 - - + +
278C PRO* 1.3 80.5 - - - +
280C THR* 1.3 64.9 + - - +
281C ALA* 3.6 22.2 - - + -
282C SER* 2.8 32.6 + - - +
283C LEU* 3.0 16.1 + - - +
303C THR* 6.1 3.4 - - + +
330C GLY 2.9 24.0 - - - +
331C SER 2.9 26.0 - - - +
332C ALA* 3.6 15.0 - - + +
355C THR* 5.5 2.5 - - + -
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Residues in contact with THR 280 (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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279C ILE* 1.3 67.0 - - - +
281C ALA* 1.3 70.4 + - - +
283C LEU* 3.2 9.4 + - - +
284C GLY* 3.0 17.8 + - - -
330C GLY 3.1 9.1 + - - -
331C SER* 4.1 2.1 - - - -
357C GLY* 2.9 25.5 + - - +
360C GLU* 3.8 3.8 - - + -
361C ARG* 3.1 40.4 - - - +
364C VAL* 4.0 12.6 - - + -
365C ILE* 6.4 0.7 - - - -
434C PHE* 3.1 40.6 - - + -
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Residues in contact with ALA 281 (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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256C MET* 4.1 2.0 - - + -
279C ILE* 3.2 22.2 + - + +
280C THR* 1.3 82.4 - - - +
282C SER* 1.3 62.4 + - - +
283C LEU 3.2 0.2 + - - -
284C GLY 3.2 6.1 + - - -
285C THR* 3.3 8.3 + - - +
303C THR* 5.7 1.6 - - + -
307C LEU* 3.3 38.6 - - + +
331C SER 5.0 0.2 + - - -
355C THR* 4.2 7.9 - - + -
356C ASN 4.9 1.2 + - - -
433C ILE* 3.8 16.6 - - + -
434C PHE* 3.7 11.2 - - - -
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Residues in contact with SER 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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255C VAL 2.7 28.0 + - - -
256C MET* 3.6 26.7 - - - +
278C PRO* 3.6 5.0 - - - +
279C ILE* 2.8 32.0 + - - +
281C ALA* 1.3 76.3 - - - +
283C LEU* 1.3 57.2 + - - +
284C GLY 3.5 0.7 + - - -
285C THR 3.8 4.7 - - - +
307C LEU* 4.3 4.0 - - - -
313C THR* 4.4 3.3 - - - +
314C PRO* 3.6 19.6 - - - +
317C LEU* 3.5 16.1 - - - +
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Residues in contact with LEU 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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278C PRO* 4.0 24.2 - - + +
279C ILE* 3.0 28.1 + - - +
280C THR* 3.2 4.7 + - - +
282C SER* 1.3 74.6 - - - +
284C GLY* 1.3 56.8 + - - +
314C PRO* 3.4 7.0 - - - +
317C LEU* 3.8 14.8 - - + +
318C ASN* 3.1 58.2 + - - +
321C LEU* 4.0 13.0 - - + -
329C THR* 4.7 4.0 - - - -
361C ARG* 6.1 0.7 - - + -
364C VAL* 4.4 8.5 - - + -
365C ILE* 4.2 24.2 - - + -
368C LYS* 3.3 15.8 - - - +
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Residues in contact with GLY 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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280C THR 3.0 12.5 + - - -
281C ALA 3.2 0.2 + - - -
282C SER 3.3 0.4 - - - -
283C LEU* 1.3 80.5 - - - +
285C THR* 1.3 61.5 + - - +
314C PRO* 4.6 4.8 - - - +
364C VAL* 4.0 14.8 - - - -
368C LYS* 4.2 11.7 + - - -
434C PHE* 4.3 5.4 - - - -
437C MET* 3.2 27.4 - - - +
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Residues in contact with THR 285 (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 ALA 3.3 13.0 + - - +
282C SER 3.8 2.4 - - - +
284C GLY* 1.3 77.0 - - - +
286C ASP* 1.3 72.4 + - - +
289C HIS* 3.4 23.6 + - - -
301C PHE* 4.0 9.0 - - + -
307C LEU* 3.6 20.1 - - + +
313C THR* 5.7 0.9 - - - +
314C PRO* 3.4 21.1 - - - +
433C ILE* 3.8 26.2 + - + +
434C PHE* 4.4 12.1 - - + -
437C MET* 5.3 2.2 - - - -
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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