Contacts of the helix formed by residues 221 - 230 (chain C) in PDB entry 2W4V
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 GLN 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217C ASP* 2.6 23.9 - - + +
218C GLN 2.9 5.2 + - - +
220C ILE* 1.3 95.6 - - + +
222C ALA* 1.3 58.4 + - - +
223C ASN 3.2 2.5 - - - -
224C PRO* 3.1 24.0 - - - +
225C VAL* 4.2 6.1 + - - +
330C LEU* 6.3 0.6 - - - +
334C ALA* 3.5 27.2 - - - +
337C ILE* 2.9 48.2 - - + +
338C LEU* 4.2 3.4 - - + +
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Residues in contact with ALA 222 (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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218C GLN 2.9 7.8 + - - +
219C ILE* 2.8 21.0 + - - +
221C GLN* 1.3 71.5 - - - +
223C ASN* 1.3 62.7 + - - +
225C VAL* 3.0 26.9 - - + +
226C LEU* 3.1 18.4 + - + +
262C ILE* 5.7 7.2 - - + -
338C LEU* 4.3 10.5 - - + -
442C VAL* 4.9 14.8 - - + +
446C LEU* 5.7 6.1 - - + -
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Residues in contact with ASN 223 (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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187C LYS* 3.1 44.8 - - + +
190C ILE* 4.7 8.7 - - - +
219C ILE 4.1 3.9 + - - -
220C ILE* 3.1 17.8 + - - +
222C ALA* 1.3 71.9 - - - +
224C PRO* 1.3 69.9 - - + +
225C VAL 3.1 0.2 + - - -
226C LEU* 3.2 3.5 + - - -
227C GLU* 2.7 49.0 + - + +
245C LYS* 4.4 13.6 + - - +
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Residues in contact with PRO 224 (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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187C LYS* 4.9 2.9 - - - +
220C ILE* 3.3 7.4 - - + +
221C GLN* 3.1 37.0 - - - +
223C ASN* 1.3 100.4 - - + +
225C VAL* 1.3 59.5 + - - +
227C GLU* 4.2 4.9 - - + +
228C ALA* 3.3 21.5 + - - +
327C GLU* 4.5 9.7 - - - +
330C LEU* 5.0 7.6 - - + +
331C CYS* 4.8 5.9 - - - +
334C ALA* 4.2 11.2 - - + -
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Residues in contact with VAL 225 (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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221C GLN 4.2 2.7 - - - +
222C ALA* 3.0 23.8 - - - +
224C PRO* 1.3 76.0 - - - +
226C LEU* 1.3 79.0 + - + +
228C ALA* 3.2 6.7 + - - -
229C TYR* 2.6 42.4 - - + -
331C CYS* 4.2 13.2 - - + +
334C ALA* 3.9 27.8 - - + -
335C PHE* 4.5 7.0 - - + +
338C LEU* 4.0 18.2 - - + -
340C PHE* 5.5 1.3 - - + -
345C LYS* 5.4 0.9 - - - +
438C LEU* 4.8 5.6 - - + -
442C VAL* 4.6 9.2 - - + -
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Residues in contact with LEU 226 (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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222C ALA* 3.1 18.5 + - + +
223C ASN* 3.9 4.3 - - - +
225C VAL* 1.3 83.2 - - + +
227C GLU* 1.3 60.4 + - - +
229C TYR* 3.5 1.1 + - - -
230C GLY* 2.8 28.9 + - - -
243C PHE* 4.1 10.5 - - + -
245C LYS* 4.6 20.0 - - + +
262C ILE* 4.9 15.3 - - + -
264C THR* 4.6 8.7 - - + -
435C PHE* 3.5 29.4 - - + -
438C LEU* 3.8 31.9 - - + -
439C VAL* 3.9 14.6 - - + -
442C VAL* 5.2 4.9 - - + -
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Residues in contact with GLU 227 (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 THR* 5.1 12.5 - - - +
223C ASN* 2.7 39.5 + - + +
224C PRO* 4.2 4.9 - - + +
226C LEU* 1.3 70.7 - - - +
228C ALA* 1.3 61.5 + - - +
231C ASN* 2.3 71.6 + - + +
239C ASN* 5.1 4.7 - - - +
241C SER* 4.5 1.1 + - - -
243C PHE* 3.7 7.3 - - - -
245C LYS* 3.1 26.4 + - - +
283C HIS* 2.9 8.0 - - + +
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Residues in contact with ALA 228 (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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224C PRO 3.3 16.6 + - - +
225C VAL* 3.2 7.5 + - - +
227C GLU* 1.3 79.4 - - - +
229C TYR* 1.3 58.8 + - + +
282C TYR* 3.6 1.0 - - - -
283C HIS* 3.3 20.1 + - - -
284C ILE* 2.3 53.4 + - + +
287C GLN* 5.7 0.7 - - + -
327C GLU* 4.1 18.6 - - - +
331C CYS* 4.9 7.9 - - + -
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Residues in contact with TYR 229 (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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225C VAL* 2.6 38.3 + - + +
226C LEU 4.1 2.2 - - - +
228C ALA* 1.3 82.1 - - + +
230C GLY* 1.3 54.4 + - - +
231C ASN 3.8 0.9 - - - -
282C TYR* 4.1 5.1 - + - +
284C ILE* 2.6 32.7 - - + +
331C CYS* 6.4 1.6 - - + -
345C LYS* 5.6 0.9 + - - -
348C MET* 4.0 22.9 - - + +
349C PHE* 4.6 19.4 + - - -
352C THR* 4.0 10.3 - - + +
431C TYR* 1.5 50.6 + + + +
434C MET* 3.4 31.6 - - + +
435C PHE* 4.3 17.7 - - + -
438C LEU* 3.7 20.2 - - + -
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Residues in contact with GLY 230 (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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226C LEU 2.8 17.7 + - - -
229C TYR* 1.3 76.8 - - - +
231C ASN* 1.4 72.2 + - - +
242C ARG* 2.9 25.7 + - - -
243C PHE* 3.1 19.3 - - - -
267C LEU* 4.4 9.6 - - - -
431C TYR* 4.0 0.4 - - - -
435C PHE* 4.5 3.1 - - - -
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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