Contacts of the helix formed by residues 272 - 281 (chain C) in PDB entry 3RMD
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 ASP 272 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214C THR* 4.5 0.2 - - - -
215C GLY 3.2 2.3 - - - +
217C ASN* 2.7 47.5 + - - -
218C VAL* 3.7 20.2 - - + -
219C GLU* 3.4 19.1 + - + +
220C SER* 4.5 3.3 + - - -
270C VAL* 3.8 4.8 + - + +
271C LEU* 1.3 70.5 - - - +
273C TYR* 1.3 68.0 + - - +
274C ILE* 3.0 19.8 + - - +
275C ASP* 2.8 32.7 + - - +
276C LEU 3.0 8.5 + - - -
359C PHE* 5.2 2.8 - - - -
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Residues in contact with TYR 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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214C THR* 3.5 14.6 + - + +
215C GLY 2.8 22.1 + - - +
216C TRP* 4.0 18.2 - + + -
271C LEU 3.0 6.3 + - - -
272C ASP* 1.3 70.1 - - - +
274C ILE* 1.3 54.2 + - - +
276C LEU* 3.9 6.5 - - + -
277C TYR* 2.6 37.7 + - + +
331C VAL* 3.8 19.7 - - + -
334C ILE* 4.2 17.9 - - + -
335C ASP* 2.8 53.8 + - + -
338C ARG* 4.1 1.4 - - - +
340C PHE* 3.3 39.7 + + + +
341C ILE* 3.8 19.7 - - + -
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Residues in contact with ILE 274 (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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215C GLY 4.1 0.8 + - - -
216C TRP* 2.9 44.7 - - + +
217C ASN* 3.6 29.4 - - - +
272C ASP* 2.9 31.6 + - - +
273C TYR* 1.3 77.0 - - - +
275C ASP* 1.3 69.9 + - - +
277C TYR* 3.8 2.4 - - - +
278C LYS* 3.0 46.9 + - - +
288C TYR* 3.4 22.7 - - + +
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Residues in contact with ASP 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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219C GLU* 4.7 9.9 - - - +
260C ARG* 5.8 1.6 + - - -
272C ASP* 2.8 30.6 + - - +
274C ILE* 1.3 79.7 - - - +
276C LEU* 1.3 68.0 + - - +
278C LYS* 3.7 12.6 + - - +
279C LYS* 2.9 26.5 + - - +
359C PHE* 3.6 22.2 - - + -
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Residues in contact with LEU 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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271C LEU* 4.0 20.9 - - + +
272C ASP 3.0 10.4 + - - +
273C TYR* 3.6 14.4 - - + +
275C ASP* 1.3 80.6 - - - +
277C TYR* 1.3 63.2 + - - +
279C LYS 3.1 0.2 + - - -
280C PHE* 3.0 55.1 + - + +
340C PHE* 3.8 22.9 - - + +
341C ILE* 3.6 31.6 - - + -
344C SER* 3.6 17.9 - - - +
358C VAL* 4.9 2.7 - - + -
359C PHE* 3.6 21.9 - - + -
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Residues in contact with TYR 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C TRP* 4.1 13.7 - + + -
273C TYR* 2.6 26.2 + + + +
274C ILE 3.8 3.6 - - - +
276C LEU* 1.3 74.2 - - - +
278C LYS* 1.3 58.8 + - - +
281C SER* 2.8 59.9 + - - -
283C THR* 4.0 8.7 - - + +
285C GLN* 3.7 7.3 + - + -
288C TYR* 4.0 21.3 - + - -
293C ILE* 3.8 35.0 - - + +
296C PHE* 3.7 18.0 - - - -
297C GLU* 2.8 33.6 + - + -
334C ILE* 4.3 13.9 - - + -
338C ARG* 4.6 3.1 - - - -
340C PHE* 4.1 17.7 - + - -
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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 ILE* 3.0 34.9 + - - +
275C ASP* 3.7 12.6 + - - +
276C LEU 3.2 0.2 - - - -
277C TYR* 1.3 80.6 - - - +
279C LYS* 1.3 59.5 + - - +
281C SER* 4.4 5.4 + - - -
282C PHE 5.1 2.3 + - - -
288C TYR* 3.8 48.9 - - + +
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Residues in contact with LYS 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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275C ASP 2.9 18.1 + - - +
276C LEU 3.1 2.9 + - - +
278C LYS* 1.3 79.8 - - - +
280C PHE* 1.3 104.8 + - + +
281C SER 3.8 0.2 - - - -
282C PHE* 4.4 15.9 + - - -
347C MET* 5.5 0.9 - - - -
358C VAL 3.8 17.3 + - - -
359C PHE* 3.9 34.2 + - + +
361C PRO* 4.9 5.1 - - - +
565C SER* 6.3 0.2 - - - -
2I G 2.9 38.8 + - - +
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Residues in contact with PHE 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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276C LEU* 3.0 44.2 + - + +
279C LYS* 1.3 115.8 - - + +
281C SER* 1.3 62.5 + - - +
282C PHE* 3.1 24.9 - + - -
338C ARG* 4.8 1.0 + - - -
340C PHE* 3.4 37.7 - + + -
343C LEU* 3.9 17.7 - - + -
344C SER* 4.2 7.9 - - - -
347C MET* 3.9 11.2 - - + -
358C VAL* 4.7 8.1 - - + -
359C PHE* 4.9 0.4 - + - -
561C LEU* 3.5 33.0 - - + -
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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
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277C TYR* 2.8 57.4 + - - -
278C LYS* 4.4 4.9 + - - -
279C LYS 3.8 0.2 - - - -
280C PHE* 1.3 70.9 - - - +
282C PHE* 1.3 75.0 + - - +
283C THR* 3.1 27.3 + - - +
288C TYR* 5.0 0.2 + - - -
338C ARG* 3.5 25.8 + - - +
340C PHE* 3.9 3.0 - - - -
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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