Contacts of the strand formed by residues 251 - 258 (chain C) in PDB entry 4N32
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 TYR 251 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209C PHE* 3.8 29.6 - + + +
210C SER 4.0 9.4 + - - -
245C THR 5.1 1.4 + - - -
246C ALA* 3.6 30.5 + - + -
249C LEU* 3.4 52.5 - - + +
250C ILE* 1.3 73.7 - - - +
252C TRP* 1.3 63.1 + - - +
253C ILE* 4.0 1.4 - - - +
297C ASN* 3.1 4.4 - - - +
298C ILE* 2.8 38.7 + - + +
316C LEU* 3.2 36.4 - - + +
317C PHE* 3.6 14.8 - - - -
318C ILE* 3.6 26.5 - - + -
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Residues in contact with TRP 252 (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 LYS 3.1 27.4 + - - -
215C THR 3.9 1.1 - - - -
216C TRP* 3.2 35.6 - + + +
219C ALA* 4.4 4.3 - - + -
230C LEU* 4.0 6.0 - - + +
251C TYR* 1.3 72.6 - - - +
253C ILE* 1.3 62.8 + - - +
295C CYS* 3.5 34.3 - - + -
296C GLY 3.3 22.7 - - - -
297C ASN* 3.7 16.9 - - + +
309C ALA* 4.0 11.2 - - + -
310C PRO 3.1 25.4 - - - -
311C CYS 3.9 6.5 - - - -
313C LYS 3.3 19.5 + - - -
315C PHE* 3.5 33.1 - + + +
316C LEU 2.7 11.2 + - - +
317C PHE* 3.8 8.6 - - + +
318C ILE* 3.1 24.1 + - - +
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Residues in contact with ILE 253 (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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216C TRP* 2.9 24.6 + - - -
230C LEU* 3.8 8.8 - - - +
231C THR* 3.6 27.8 - - + +
233C VAL* 4.1 6.5 - - + -
251C TYR 3.5 4.2 + - - +
252C TRP* 1.3 78.9 - - - +
254C GLY* 1.3 59.5 + - - +
255C LEU* 3.0 28.6 + - + +
266C TRP* 4.0 8.5 - - + -
296C GLY 3.2 20.0 + - - +
297C ASN* 4.2 2.9 - - - -
298C ILE* 3.9 25.4 - - + -
306C TRP* 3.7 33.0 - - + +
318C ILE* 4.4 6.3 - - + -
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Residues in contact with GLY 254 (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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216C TRP* 3.9 7.0 - - - -
230C LEU* 3.5 24.2 - - - +
231C THR 2.7 21.4 + - - -
253C ILE* 1.3 70.2 - - - +
255C LEU* 1.3 57.8 + - - +
256C THR 3.6 0.7 + - - -
265C SER 3.4 0.5 - - - +
266C TRP* 3.4 12.4 - - - -
267C VAL* 2.9 33.1 + - - +
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Residues in contact with LEU 255 (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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216C TRP* 3.5 6.1 + - - -
253C ILE* 3.0 13.1 + - + -
254C GLY* 1.3 73.2 - - - +
256C THR* 1.3 64.8 + - - +
264C TRP* 4.0 19.1 - - + -
265C SER 3.5 7.2 - - - +
266C TRP* 3.6 20.2 - - + -
272C PHE* 3.5 32.1 - - + -
281C TRP* 4.0 16.4 - - + -
295C CYS* 3.4 2.4 - - - -
296C GLY* 2.8 41.8 + - - -
306C TRP* 3.5 37.2 - - + -
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Residues in contact with THR 256 (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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217A TYR* 2.7 28.8 + - - +
221A GLN* 3.1 14.2 + - - -
216C TRP* 3.6 24.7 - - + -
254C GLY 4.5 2.2 - - - +
255C LEU* 1.3 75.7 - - - +
257C LYS* 1.3 58.9 + - - +
258C ALA* 5.3 1.6 - - + -
264C TRP* 3.6 9.6 - - - -
265C SER* 2.7 52.3 + - - +
267C VAL* 4.9 5.8 - - + +
294C HIS 3.2 8.0 + - - -
295C CYS* 3.5 6.7 - - - -
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Residues in contact with LYS 257 (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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217A TYR* 4.1 1.7 + - - -
221A GLN* 3.1 26.6 + - - +
256C THR* 1.3 76.8 + - - +
258C ALA* 1.3 61.1 + - - +
262C GLY* 3.4 32.3 - - - +
263C ASP 3.4 5.4 - - - -
264C TRP* 3.7 27.1 - - + +
288C ASN* 3.5 24.9 + - - +
293C GLU 3.1 19.1 + - - -
294C HIS* 2.9 51.8 + - + +
308C ASP* 5.1 0.4 + - - -
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Residues in contact with ALA 258 (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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224A VAL* 4.2 9.9 - - + -
256C THR* 3.7 1.8 + - + -
257C LYS* 1.3 76.8 - - - +
259C GLY* 1.3 63.5 + - - +
262C GLY* 4.8 0.2 - - - -
263C ASP* 2.9 28.9 + - - +
265C SER* 3.5 23.1 - - - +
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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