Contacts of the helix formed by residues 280 - 292 (chain C) in PDB entry 3MSS
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 VAL 280 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273C LEU* 3.8 32.3 - - + +
281C GLU* 1.3 63.4 + - - +
282C GLU* 3.3 7.2 - - - +
283C PHE* 3.0 5.4 + - - +
284C LEU* 2.8 39.3 + - + +
311C PHE* 3.6 30.5 - - + -
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Residues in contact with GLU 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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280C VAL* 1.3 78.5 - - - +
282C GLU* 1.3 56.5 + - + +
284C LEU* 3.4 11.9 + - - +
285C LYS* 2.9 43.0 + - + +
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Residues in contact with GLU 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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280C VAL 3.3 5.1 - - - +
281C GLU* 1.3 76.9 - - - +
283C PHE* 1.3 59.8 + - + +
285C LYS* 3.3 9.9 + - - +
286C GLU* 3.0 27.1 + - - +
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Residues in contact with PHE 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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271C LYS* 3.6 44.9 - - + -
272C THR 4.0 12.3 - - - -
273C LEU* 3.9 31.9 - - + -
280C VAL* 3.0 9.6 + - - +
282C GLU* 1.3 76.3 - - + +
284C LEU* 1.3 68.5 + - - +
286C GLU* 3.2 10.4 + - - +
287C ALA* 3.1 17.5 + - - +
306C THR* 4.1 9.6 - - + -
311C PHE* 3.5 48.2 - + + -
313C ILE* 3.6 33.9 - - + +
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Residues in contact with LEU 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 VAL* 2.8 36.0 + - + +
281C GLU* 4.0 13.9 - - - +
283C PHE* 1.3 73.0 - - + +
285C LYS* 1.3 65.1 + - - +
287C ALA* 3.3 6.8 + - + +
288C ALA* 3.1 22.5 + - - +
306C THR* 3.6 37.5 - - + +
311C PHE* 3.7 22.2 - - + -
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Residues in contact with LYS 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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1C STI 6.4 2.2 - - - -
281C GLU* 2.9 30.5 + - + +
282C GLU* 3.6 8.3 - - - +
284C LEU* 1.3 75.5 - - - +
286C GLU* 1.3 63.8 + - - +
288C ALA* 3.3 7.6 + - + +
289C VAL* 3.0 35.3 + - + +
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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
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1C STI 3.1 55.1 + - + -
271C LYS* 3.0 30.2 + - - -
282C GLU 3.0 14.1 + - - +
283C PHE* 3.4 13.5 - - - +
284C LEU 3.2 0.2 - - - -
285C LYS* 1.3 77.7 - - - +
287C ALA* 1.3 62.7 + - - +
289C VAL* 3.3 7.3 + - - +
290C MET* 3.0 31.2 + - - +
313C ILE* 4.2 7.6 - - + +
381C ASP 4.1 4.4 - - - +
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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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283C PHE 3.1 9.9 + - - +
284C LEU* 3.6 12.1 - - + +
286C GLU* 1.3 77.6 - - - +
288C ALA* 1.3 63.7 + - - +
290C MET* 3.1 8.0 + - - +
291C LYS* 3.1 34.8 + - - +
301C LEU* 4.5 1.1 - - - +
304C VAL* 4.1 21.1 - - + -
306C THR* 4.9 10.3 - - + +
313C ILE* 3.7 18.9 - - + +
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Residues in contact with ALA 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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284C LEU 3.1 17.1 + - - +
285C LYS* 3.8 7.9 - - + +
286C GLU 3.2 0.2 - - - -
287C ALA* 1.3 78.3 - - - +
289C VAL* 1.3 63.3 - - + +
291C LYS* 3.3 22.9 + - + +
292C GLU* 3.5 17.9 + - - +
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Residues in contact with VAL 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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1C STI 3.9 47.6 - - + +
285C LYS* 3.0 29.8 + - + +
286C GLU* 3.6 9.9 - - - +
288C ALA* 1.3 75.2 - - + +
290C MET* 1.3 59.0 + - - +
292C GLU* 3.0 27.5 + - - +
293C ILE* 3.4 13.2 - - + +
359C PHE* 4.7 18.6 - - + -
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Residues in contact with MET 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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1C STI 3.4 71.3 - - + +
235C TRP* 5.5 0.9 - - - -
286C GLU* 3.0 24.1 + - - +
287C ALA* 3.1 5.8 + - - +
289C VAL* 1.3 75.8 - - - +
291C LYS* 1.3 62.0 + - - +
292C GLU 3.3 0.7 + - - -
293C ILE* 3.3 27.0 + - + +
299C VAL* 4.5 8.7 - - + +
301C LEU* 3.8 34.6 - - + +
313C ILE* 3.9 13.5 - - + -
315C THR* 3.9 19.5 - - + -
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Residues in contact with LYS 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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233C ASP* 2.6 27.8 + - - +
235C TRP* 3.5 52.9 + - + +
236C GLU* 5.2 0.4 + - - -
287C ALA* 3.1 23.4 + - - +
288C ALA* 3.6 14.7 - - - +
289C VAL 3.2 0.4 - - - -
290C MET* 1.3 77.1 - - - +
292C GLU* 1.3 69.0 + - - +
293C ILE 3.4 1.6 + - - +
301C LEU* 3.6 13.7 - - + -
304C VAL* 4.0 21.8 - - - +
306C THR* 4.9 5.1 + - - -
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Residues in contact with GLU 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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288C ALA 3.5 16.0 - - - +
289C VAL* 3.0 12.3 + - - +
291C LYS* 1.3 86.9 - - - +
293C ILE* 1.3 58.4 + - - +
353C TYR* 3.8 1.6 + - - -
357C LYS* 3.6 25.0 + - - -
359C PHE* 4.1 18.2 - - + -
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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