Contacts of the strand formed by residues 283 - 289 (chain C) in PDB entry 4ZZ7
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 LEU 283 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251C ASN* 3.6 13.9 - - + +
252C HIS 4.6 2.7 - - - +
253C ALA* 3.5 26.2 - - + +
268C LEU* 3.7 18.3 - - + +
271C ALA* 3.4 24.2 + - + -
272C ALA* 3.3 24.4 - - - +
281C MET 3.4 1.4 + - - -
282C ALA* 1.3 70.3 - - - +
284C SER* 1.3 56.3 + - - +
285C VAL 3.2 28.5 - - - +
388C LEU* 3.5 8.8 - - + +
412C THR* 6.0 0.9 - - - -
413C CYS* 4.3 4.5 - - + -
439C PRO* 3.2 46.9 - - + +
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Residues in contact with SER 284 (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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249C ALA 5.3 0.2 + - - -
250C LYS* 3.5 35.1 + - - +
251C ASN 3.2 16.6 + - - -
272C ALA* 5.5 0.2 - - - +
282C ALA* 3.3 10.6 + - - -
283C LEU* 1.3 74.1 - - - +
285C VAL* 1.3 63.1 + - - +
383C ILE* 6.2 1.1 - - - -
387C VAL 4.0 15.1 - - - +
388C LEU* 3.5 5.8 - - - +
389C GLN* 2.9 27.2 + - - +
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Residues in contact with VAL 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C LYS* 3.6 32.5 - - + -
251C ASN 3.1 3.2 + - - +
252C HIS* 3.1 32.8 - - + +
253C ALA 2.8 25.6 + - - -
283C LEU* 3.2 6.4 - - - +
284C SER* 1.3 84.8 - - - +
286C ALA* 1.3 61.7 + - - +
287C VAL* 3.9 11.0 - - + -
379C TYR* 4.1 12.3 - - + -
388C LEU* 4.2 1.3 - - - -
389C GLN* 3.3 16.4 - - + +
391C VAL* 4.0 20.0 - - + -
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Residues in contact with ALA 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ALA* 3.6 8.1 - - + +
255C VAL* 4.8 4.9 - - + -
268C LEU* 4.8 14.6 - - + -
285C VAL* 1.3 71.4 - - - +
287C VAL* 1.3 61.6 + - - +
288C ALA 3.7 0.7 - - - -
297C LEU* 3.8 26.0 - - + -
388C LEU* 4.0 14.3 - - + +
389C GLN 2.8 12.8 + - - +
390C VAL* 3.2 10.1 - - + +
391C VAL 3.0 23.2 + - - -
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Residues in contact with VAL 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C HIS* 3.7 34.5 - - + -
253C ALA 2.7 16.7 + - - +
254C ILE* 3.5 5.6 - - + +
255C VAL* 3.2 22.4 + - - +
285C VAL* 3.9 7.0 - - + -
286C ALA* 1.3 72.5 - - - +
288C ALA* 1.3 61.7 + - - +
289C VAL 3.6 1.0 + - - -
391C VAL* 3.5 6.5 - - + +
393C VAL* 3.8 24.9 - - + -
399C ALA* 3.3 33.0 - - + -
402C LEU* 4.3 11.4 - - + -
403C ILE* 5.2 2.9 - - + -
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Residues in contact with ALA 288 (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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255C VAL* 4.1 9.6 - - + -
286C ALA 3.7 1.6 + - - -
287C VAL* 1.3 71.1 - - - +
289C VAL* 1.3 60.1 + - - +
290C GLY 3.6 3.1 + - - +
293C ALA* 4.3 5.2 - - + -
294C GLY* 3.6 36.1 - - - +
297C LEU* 4.6 8.3 - - + -
390C VAL* 4.5 9.0 - - + -
391C VAL 2.8 14.7 + - - +
392C ARG* 3.4 4.6 - - + -
393C VAL* 2.9 27.5 + - - +
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Residues in contact with VAL 289 (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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489A GLY 5.4 4.5 - - - -
254C ILE* 4.2 7.9 - - + -
255C VAL 3.1 21.4 + - - +
256C MET* 3.5 31.4 - - + -
257C PRO* 3.7 20.8 - - + +
287C VAL 3.6 1.0 + - - -
288C ALA* 1.3 69.6 - - - +
290C GLY* 1.3 60.8 + - - +
292C ALA* 5.0 0.2 - - - +
293C ALA* 3.9 13.0 + - - +
393C VAL* 3.4 12.8 - - + -
394C ALA 3.4 20.9 - - - +
395C THR* 3.5 22.9 - - - +
396C MET* 3.5 5.6 - - + +
399C ALA* 5.5 0.2 - - + -
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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