Contacts of the helix formed by residues 278 - 291 (chain C) in PDB entry 1M6X
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 278 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C ARG* 5.7 3.3 + - - +
276C LYS* 3.1 4.6 - - + +
277C ASP* 1.3 78.8 - - - +
279C LEU* 1.3 67.1 + - - +
280C VAL* 3.0 5.9 + - - +
281C ARG* 3.1 14.9 + - - +
282C SER* 3.6 8.5 + - - -
5G T 4.7 5.0 + - + +
6G T 3.1 64.5 + - + +
7G C 4.2 11.5 + - - -
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Residues in contact with LEU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LEU* 3.9 35.2 - - + +
178C TYR* 3.9 26.5 - - + -
181C LEU* 4.0 20.6 - - + -
192C PHE* 4.1 2.2 - - + -
275C LEU* 3.6 40.8 - - + -
276C LYS* 2.8 24.8 + - + +
278C ASN* 1.3 77.5 - - - +
280C VAL* 1.3 52.5 + - - +
282C SER* 3.2 7.3 + - - -
283C TYR* 2.8 32.8 + - + +
5G T 5.4 2.7 - - - +
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Residues in contact with VAL 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C PHE* 3.5 40.2 - - + -
277C ASP 3.6 16.2 - - - +
278C ASN* 3.0 2.4 - - - +
279C LEU* 1.3 79.9 - - - +
281C ARG* 1.3 58.4 + - + +
283C TYR* 4.0 5.6 - - + -
284C ASN* 2.7 61.3 + - - +
304C SER* 4.2 7.9 - - - +
24I T 5.0 7.2 - - + -
25I A 4.2 10.5 - - + +
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Residues in contact with ARG 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C ASN* 3.1 10.4 + - - +
280C VAL* 1.3 83.9 - - + +
282C SER* 1.3 55.2 + - - +
284C ASN* 4.4 9.2 - - - +
285C LYS* 2.7 62.1 + - - +
5G T 3.8 10.3 - - + -
6G T 3.3 29.4 - - + +
7G C 3.9 5.4 - - - +
26I G 3.1 45.1 + - - +
27I G 2.8 48.6 + - - -
28I A 3.8 5.8 + - - +
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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
----------------------------------------------------------
174C THR* 5.1 0.3 - - - +
178C TYR* 2.3 37.7 + - - -
278C ASN 3.6 4.8 + - - -
279C LEU* 3.2 10.7 + - - -
281C ARG* 1.3 79.9 - - - +
283C TYR* 1.3 61.4 + - - +
285C LYS* 3.9 3.6 - - - +
286C ALA* 3.2 18.5 + - - +
4G G 3.1 24.2 + - - +
5G T 3.1 34.2 + - - +
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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
----------------------------------------------------------
165C PHE* 3.6 16.7 - + - -
178C TYR* 3.5 50.4 - + + -
181C LEU* 3.8 23.3 - - + -
182C PHE* 3.1 40.2 - - + +
185C THR* 5.3 0.6 + - + -
279C LEU* 2.8 18.6 + - + +
280C VAL* 3.5 7.4 - - - +
282C SER* 1.3 75.0 - - - +
284C ASN* 1.3 79.7 + - - +
286C ALA* 3.1 3.5 + - - +
287C LEU* 2.8 42.1 + - + +
304C SER* 3.6 29.2 + - - -
306C ILE* 5.0 0.5 - - - +
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Residues in contact with ASN 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C VAL* 2.7 33.3 + - - +
281C ARG* 3.6 12.9 - - - +
283C TYR* 1.3 76.2 - - - +
285C LYS* 1.3 65.0 + - - +
287C LEU* 3.1 4.8 + - - +
288C LYS* 2.8 25.6 + - - +
303C LYS* 3.0 33.8 - - + +
304C SER* 3.2 16.8 + - - -
25I A 3.1 41.4 + - - +
26I G 5.1 4.6 + - - +
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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
----------------------------------------------------------
281C ARG* 2.7 39.8 + - - +
282C SER* 3.9 4.9 - - - +
284C ASN* 1.3 73.3 - - - +
286C ALA* 1.3 61.7 + - - +
288C LYS* 3.2 10.3 - - + +
289C LYS* 3.1 23.1 + - + +
3G A 4.5 15.7 + - + -
4G G 3.0 40.5 + - + +
5G T 3.3 25.5 + - + +
28I A 5.5 1.7 + - - +
29I A 4.3 5.1 - - - +
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Residues in contact with ALA 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C PHE* 4.2 5.2 - - + -
178C TYR* 3.9 22.9 - - + -
282C SER 3.2 15.7 + - - +
283C TYR 3.1 4.8 + - - +
285C LYS* 1.3 73.9 - - - +
287C LEU* 1.3 67.6 + - - +
288C LYS 2.9 1.6 - - - -
289C LYS* 2.9 6.2 + - - +
290C ASN* 2.8 40.5 + - - +
4G G 4.3 8.7 - - - +
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ILE* 4.2 12.1 - - + -
164C SER* 4.9 0.7 - - - +
165C PHE* 3.9 22.1 - - + -
283C TYR* 2.8 44.8 + - + +
284C ASN* 3.5 4.7 - - - +
286C ALA* 1.3 73.1 - - - +
288C LYS* 1.3 60.9 + - - +
290C ASN* 4.6 2.7 - - - +
291C ALA* 3.1 21.0 + - - -
292C PRO* 4.2 11.0 - - + -
296C PHE* 3.6 40.2 - - + +
303C LYS* 3.5 32.3 - - + +
306C ILE* 4.5 3.4 - - + -
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Residues in contact with LYS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ASN 2.8 13.3 + - - +
285C LYS* 3.2 15.7 - - + +
287C LEU* 1.3 77.6 - - - +
289C LYS* 1.3 64.1 + - + +
291C ALA* 3.3 18.5 - - - +
296C PHE* 3.7 24.0 - - - +
297C ALA* 3.5 20.6 + - - +
299C LYS* 3.9 14.1 - - - +
303C LYS* 3.9 17.2 - - - +
26I G 3.6 23.3 + - - +
27I G 5.9 0.8 + - - -
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Residues in contact with LYS 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C LYS* 3.1 9.7 + - + +
286C ALA* 2.9 9.5 + - - +
288C LYS* 1.3 80.9 - - + +
290C ASN* 1.3 65.3 + - - +
291C ALA* 2.9 10.4 + - - +
2G A 5.4 1.3 - - - -
3G A 3.5 40.1 + - - +
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Residues in contact with ASN 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C SER* 3.6 17.8 + - - +
165C PHE* 3.9 15.8 - - - -
168C THR* 3.0 46.5 + - + +
286C ALA* 2.8 36.6 + - - +
287C LEU* 4.6 0.7 - - - +
289C LYS* 1.3 74.0 - - - +
291C ALA* 1.3 67.8 + - - +
292C PRO* 2.7 16.9 - - + +
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LEU 3.1 13.9 + - - -
288C LYS 3.3 16.2 - - - +
289C LYS 2.9 5.5 - - - +
290C ASN* 1.3 75.4 - - - +
292C PRO* 1.3 58.4 - - - +
293C TYR* 2.7 28.5 + - - +
296C PHE* 4.1 12.8 - - + -
297C ALA* 4.8 7.4 - - + +
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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
------------------------------------------------------------
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