Contacts of the helix formed by residues 269 - 283 (chain C) in PDB entry 1ML3
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 SER 269 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268C THR* 1.3 82.9 + - - +
270C ILE* 1.3 65.4 + - - +
271C GLN* 3.3 16.9 + - - +
272C GLU* 3.0 36.7 + - - +
273C ILE* 3.1 15.0 + - - +
323C GLU 3.9 5.6 - - - -
324C ARG* 5.6 0.2 - - - -
327C PHE* 3.7 11.7 - - - -
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Residues in contact with ILE 270 (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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269C SER* 1.3 73.1 - - - +
271C GLN* 1.3 76.1 + - - +
273C ILE* 3.5 11.6 + - + -
274C ASP* 2.8 27.7 + - - +
310C TYR* 5.4 0.4 - - - +
315C THR* 3.7 21.8 - - + +
316C LEU* 3.7 24.5 - - + +
319C ASN* 3.2 44.9 - - + +
320C LEU 5.6 3.1 - - - +
323C GLU 4.8 0.2 + - - -
327C PHE* 3.4 30.9 - - + -
328C LYS 4.0 4.3 - - - +
329C ILE* 4.9 3.6 - - + -
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Residues in contact with GLN 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C SER* 3.3 21.5 - - - +
270C ILE* 1.3 89.0 + - + +
272C GLU* 1.3 59.5 + - - +
274C ASP* 3.5 2.6 - - - +
275C ALA* 3.0 29.8 + - - +
316C LEU* 4.1 15.0 - - + -
322C LYS 6.0 1.4 - - - +
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Residues in contact with GLU 272 (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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183C PHE* 3.4 23.3 - - + -
266C ARG* 3.4 26.2 + - - -
268C THR* 3.8 14.9 - - - +
269C SER* 3.0 24.5 + - - +
271C GLN* 1.3 77.5 - - - +
273C ILE* 1.3 61.2 + - - +
275C ALA* 3.7 6.4 + - - +
276C ALA* 3.4 15.1 + - - +
279C ARG* 5.6 0.3 + - - -
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Residues in contact with ILE 273 (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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178C LEU* 3.6 23.3 - - + -
183C PHE* 4.0 26.5 - - + -
262C PHE* 3.8 26.5 - - + -
268C THR* 4.2 4.9 - - - +
269C SER 3.1 14.5 + - - +
270C ILE* 3.7 12.1 - - + +
272C GLU* 1.3 75.9 - - - +
274C ASP* 1.3 66.8 + - - +
275C ALA 3.2 0.2 - - - -
276C ALA* 3.2 2.1 + - - +
277C LEU* 3.0 32.6 + - + +
310C TYR* 5.8 0.4 - - - +
327C PHE* 3.8 27.4 - - + -
329C ILE* 4.1 15.9 - - + -
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Residues in contact with ASP 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C ILE* 2.8 19.0 + - - +
271C GLN* 3.5 5.7 - - - +
273C ILE* 1.3 78.4 - - - +
275C ALA* 1.3 63.0 + - - +
277C LEU* 3.5 2.6 + - - +
278C LYS* 3.1 48.1 + - - +
310C TYR* 2.6 39.7 + - - +
312C SER* 2.7 21.9 + - - -
316C LEU* 3.6 22.4 - - + +
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Residues in contact with ALA 275 (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 GLN 3.0 16.6 + - - +
272C GLU* 3.9 7.2 - - - +
274C ASP* 1.3 80.9 + - - +
276C ALA* 1.3 57.2 + - - +
278C LYS* 3.4 8.8 + - - +
279C ARG* 3.0 38.1 + - - +
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Residues in contact with ALA 276 (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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177C VAL* 4.4 3.8 - - + -
181C GLU* 4.0 10.1 - - + +
183C PHE* 3.6 30.1 - - + -
272C GLU 3.4 9.3 + - - +
273C ILE 3.2 4.3 + - - +
275C ALA* 1.3 76.4 - - - +
277C LEU* 1.3 57.3 + - + +
279C ARG* 3.5 30.1 - - - +
280C ALA* 2.7 37.1 + - - +
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Residues in contact with LEU 277 (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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174C ILE* 4.0 27.1 - - + +
177C VAL* 3.8 32.3 - - + -
178C LEU* 5.3 2.9 - - + +
273C ILE* 3.0 32.9 + - + +
274C ASP 3.9 1.3 - - - +
276C ALA* 1.3 75.8 - - - +
278C LYS* 1.3 62.1 + - - +
280C ALA* 3.5 0.8 + - - -
281C SER* 3.0 23.6 + - - -
289C LEU* 3.6 9.9 - - + +
291C TYR* 5.4 1.4 - - - +
310C TYR* 3.4 54.3 - - + -
329C ILE* 4.2 14.1 - - + -
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Residues in contact with LYS 278 (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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274C ASP* 3.1 38.4 + - - +
275C ALA* 3.6 9.9 - - - +
276C ALA 3.2 0.4 - - - -
277C LEU* 1.3 77.6 - - - +
279C ARG* 1.3 60.6 + - - +
281C SER* 2.3 28.6 + - - -
282C LYS* 3.2 16.7 + - - +
291C TYR* 3.8 45.1 + - + +
293C ASP* 5.2 6.5 + - - +
310C TYR* 4.7 2.7 - - + -
312C SER* 3.4 21.9 + - - -
316C LEU* 5.0 2.0 - - - +
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Residues in contact with ARG 279 (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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181C GLU* 2.7 34.4 + - - -
183C PHE* 5.4 1.4 - - - -
272C GLU 5.6 0.4 + - - -
275C ALA* 3.0 26.7 + - - +
276C ALA* 3.5 27.1 - - - +
278C LYS* 1.3 76.7 - - - +
280C ALA* 1.3 62.5 + - - +
281C SER 3.2 0.2 + - - -
282C LYS* 3.2 9.0 + - - +
283C THR* 3.1 38.4 + - + +
284C TYR* 6.1 1.5 - - + -
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Residues in contact with ALA 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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177C VAL* 3.6 28.3 - - + -
181C GLU* 4.7 0.6 + - - +
276C ALA 2.7 21.0 + - - +
277C LEU 3.9 3.6 - - - +
279C ARG* 1.3 73.9 - - - +
281C SER* 1.3 60.2 + - - +
283C THR* 3.3 11.3 + - - -
284C TYR* 3.6 25.1 + - + +
285C MET* 2.8 34.1 + - + +
289C LEU* 4.3 0.7 - - + -
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Residues in contact with SER 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C LEU 3.0 14.8 + - - -
278C LYS 2.3 24.2 + - - -
280C ALA* 1.3 76.6 - - - +
282C LYS* 1.3 61.5 + - - +
285C MET* 4.5 1.1 - - - -
286C LYS* 3.0 32.4 - - - +
289C LEU* 3.2 31.9 - - - +
290C GLY* 4.1 5.6 - - - -
291C TYR* 3.2 28.9 - - - -
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Residues in contact with LYS 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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278C LYS* 3.2 16.5 + - - +
279C ARG* 3.2 8.9 + - - +
281C SER* 1.3 86.1 + - - +
283C THR* 1.3 65.0 + - + +
286C LYS* 4.2 17.3 + - - +
291C TYR* 4.0 27.1 + - + -
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Residues in contact with THR 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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279C ARG* 3.1 29.6 + - + +
280C ALA* 3.3 0.9 + - - -
281C SER 3.2 1.6 - - - -
282C LYS* 1.3 84.8 - - + +
284C TYR* 1.3 87.7 + - - -
285C MET 3.1 8.4 + - - -
286C LYS* 3.3 17.8 + - - +
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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