Contacts of the helix formed by residues 269 - 278 (chain C) in PDB entry 2W93
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 LYS 269 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C GLY 5.0 2.8 + - - -
261C GLY* 5.6 2.4 - - - -
262C VAL 4.8 2.7 + - - +
267C LEU 3.9 0.6 + - - -
268C SER* 1.3 72.5 - - - +
270C PRO* 1.3 65.9 - - + +
271C GLU* 3.2 5.8 - - - +
272C VAL* 2.8 50.5 + - + +
273C LYS 3.1 7.4 + - - -
350C PRO* 4.9 3.6 + - - +
351C ALA 2.9 28.3 + - - -
352C ARG* 4.0 2.0 - - - +
353C THR* 3.4 38.7 + - + +
397C GLN* 6.5 0.9 - - + -
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Residues in contact with PRO 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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268C SER 3.3 6.9 - - - +
269C LYS* 1.3 84.4 - - + +
271C GLU* 1.3 65.1 + - + +
273C LYS* 3.3 11.0 + - + +
274C GLU* 3.2 23.6 + - - +
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Residues in contact with GLU 271 (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 LYS* 3.1 6.8 + - + +
270C PRO* 1.3 81.2 - - + +
272C VAL* 1.3 57.8 + - + +
274C GLU* 3.7 5.1 + - - +
275C ALA* 3.1 29.1 + - - +
350C PRO* 3.5 30.6 - - + +
351C ALA* 4.0 8.5 + - - +
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Residues in contact with VAL 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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243C PHE* 3.7 22.9 - - + -
260C GLY 3.4 18.8 - - - +
261C GLY* 4.3 5.4 - - - -
262C VAL 3.5 30.7 - - - +
263C TYR* 4.1 7.4 - - + -
268C SER* 4.3 1.6 - - - -
269C LYS* 2.8 48.4 + - + +
271C GLU* 1.3 70.9 - - - +
273C LYS* 1.3 63.3 + - - +
275C ALA* 3.3 1.4 + - - +
276C VAL* 3.1 24.1 + - - +
350C PRO* 4.0 8.7 - - + -
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Residues in contact with LYS 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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263C TYR* 4.1 9.6 - - + -
265C GLY 3.6 18.4 - - - +
266C THR* 3.8 36.9 - - - +
268C SER* 3.9 8.2 - - - +
269C LYS 3.1 6.7 + - - +
270C PRO* 3.3 12.3 + - + +
272C VAL* 1.3 77.6 - - - +
274C GLU* 1.3 57.8 + - + +
276C VAL* 3.9 0.7 - - - +
277C GLU* 2.8 71.0 + - - +
300C SER* 4.4 8.3 + - - -
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Residues in contact with GLU 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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270C PRO 3.2 13.1 + - - +
271C GLU* 4.3 4.9 - - - +
273C LYS* 1.3 79.2 - - + +
275C ALA* 1.3 61.2 + - - +
277C GLU* 4.5 4.8 - - - +
278C SER* 2.8 49.5 + - - -
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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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213C ASN* 4.5 3.6 + - - +
215C VAL* 3.9 14.7 - - - +
243C PHE* 3.9 13.7 - - + -
271C GLU 3.1 20.1 + - - +
272C VAL 3.8 2.9 - - - +
273C LYS 3.3 0.6 - - - -
274C GLU* 1.3 78.0 - - - +
276C VAL* 1.3 62.0 + - - +
278C SER* 3.3 13.6 + - - -
279C ALA 4.0 2.1 + - - -
348C ALA 5.6 3.6 - - - +
350C PRO* 3.8 22.0 - - + -
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Residues in contact with VAL 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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215C VAL* 4.7 10.3 - - + -
217C LEU* 5.3 7.0 - - + -
243C PHE* 3.6 38.1 - - + -
263C TYR* 3.7 47.8 - - + -
272C VAL 3.1 16.8 + - - +
275C ALA* 1.3 77.0 - - - +
277C GLU* 1.3 59.6 + - - +
279C ALA* 3.1 27.5 + - - +
282C ILE* 4.2 10.5 - - + +
301C TYR* 4.2 11.2 - - + -
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Residues in contact with GLU 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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263C TYR* 2.8 32.4 + - + +
265C GLY* 4.6 1.2 - - - -
273C LYS* 2.8 60.0 + - - +
274C GLU* 3.9 6.1 - - - +
276C VAL* 1.3 75.8 - - - +
278C SER* 1.3 57.3 + - - +
279C ALA 3.3 4.6 + - - +
298C SER 4.3 2.4 - - - +
299C TYR 4.1 0.3 - - - -
300C SER* 3.1 29.1 + - - +
301C TYR* 3.6 30.4 - - + +
302C LYS* 4.0 8.0 + - - +
303C THR 5.3 0.2 + - - -
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Residues in contact with SER 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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213C ASN* 3.0 25.5 + - - +
274C GLU* 2.8 44.4 + - - -
275C ALA* 3.3 9.7 + - - -
277C GLU* 1.3 75.1 - - - +
279C ALA* 1.3 66.8 + - - +
280C ASP* 3.6 2.3 + - - +
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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