Contacts of the strand formed by residues 387 - 393 (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 VAL 387 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272C ALA* 4.7 5.9 + - - +
273C PHE* 4.1 2.8 - - - -
284C SER* 4.0 19.3 - - - +
332C VAL* 4.2 5.2 - - + -
336C ILE* 4.0 16.8 - - + -
364C VAL* 5.6 0.2 - - + -
367C THR* 3.4 24.0 - - + +
369C ILE* 3.5 26.9 - - + -
383C ILE* 4.0 40.7 - - + +
385C GLY 2.9 9.9 + - - +
386C PRO* 1.3 84.2 - - + +
388C LEU* 1.3 66.3 + - - +
389C GLN* 4.4 1.6 - - + -
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Residues in contact with LEU 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C LEU* 4.6 14.6 - - + +
272C ALA* 4.1 15.0 - - + -
273C PHE* 3.9 16.6 - - + -
283C LEU* 3.5 23.6 - - + +
284C SER 3.5 11.2 - - - +
285C VAL 3.9 1.8 - - - +
286C ALA* 4.0 18.4 - - + +
297C LEU* 6.2 2.2 - - + -
301C MET* 4.2 28.9 - - + -
367C THR 3.0 7.5 + - - +
368C LEU* 3.6 11.6 - - + +
369C ILE* 2.9 27.2 + - - +
387C VAL* 1.3 73.5 - - - +
389C GLN* 1.3 78.8 + - - +
390C VAL* 5.2 2.0 - - + -
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Residues in contact with GLN 389 (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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250C LYS* 3.3 32.6 + - - -
284C SER 2.9 11.4 + - - +
285C VAL* 3.3 10.7 - - + +
286C ALA* 2.8 26.3 + - - +
339C ALA* 5.0 0.8 - - - +
369C ILE* 3.3 25.0 - - + +
372C VAL* 4.0 23.3 - - + +
378C SER* 3.4 38.1 + - - -
379C TYR* 3.7 7.0 - - - +
383C ILE* 3.9 8.9 - - + +
387C VAL* 4.4 4.9 - - + -
388C LEU* 1.3 79.3 - - - +
390C VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C ALA* 3.2 16.2 - - + +
288C ALA* 4.5 7.2 - - + -
294C GLY 5.4 1.1 - - - +
297C LEU* 3.9 25.6 - - + -
298C VAL* 4.2 16.2 - - + -
368C LEU* 3.6 29.2 - - + -
369C ILE 2.9 7.2 + - - +
370C ASP* 4.0 15.0 - - - +
371C HIS 3.5 6.8 + - - -
372C VAL* 3.0 25.9 + - - +
388C LEU* 5.1 3.6 - - + -
389C GLN* 1.3 78.3 - - - +
391C VAL* 1.3 69.4 + - - +
392C ARG* 4.9 3.8 - - + +
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Residues in contact with VAL 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C VAL* 4.0 17.0 - - + -
286C ALA 3.0 7.3 + - - +
287C VAL* 3.5 5.7 - - - -
288C ALA 2.8 25.3 + - - -
372C VAL* 3.4 38.4 - - + +
373C THR* 5.0 1.3 - - - +
374C PRO* 5.5 6.5 - - + -
379C TYR* 4.2 13.2 - - + -
390C VAL* 1.3 74.5 - - - +
392C ARG* 1.3 70.3 + - - +
393C VAL* 3.9 13.5 - - + -
402C LEU* 3.6 26.5 - - + -
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Residues in contact with ARG 392 (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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288C ALA* 3.4 6.3 - - + +
290C GLY 4.9 0.7 - - - +
291C ASP* 3.1 51.0 + - + +
294C GLY* 3.5 30.0 + - - -
295C ASP* 3.4 22.8 + - - +
298C VAL* 3.9 4.4 - - - +
370C ASP* 2.8 42.0 + - - -
371C HIS* 3.6 30.2 + - - +
372C VAL 4.9 1.4 + - - +
390C VAL* 4.9 3.4 - - + +
391C VAL* 1.3 82.1 - - - +
393C VAL* 1.3 66.3 + - - +
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Residues in contact with VAL 393 (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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287C VAL* 3.8 27.6 - - + -
288C ALA 2.9 14.0 + - - +
289C VAL* 3.9 7.9 - - - -
290C GLY* 2.8 27.4 + - - +
391C VAL* 3.9 11.7 - - + -
392C ARG* 1.3 80.3 - - - +
394C ALA* 1.3 59.5 + - - +
395C THR 3.5 21.5 - - - +
398C ASP* 4.1 13.0 - - + -
399C ALA* 3.9 12.6 - - + +
402C LEU* 4.4 8.7 - - + -
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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