Contacts of the strand formed by residues 387 - 393 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272K ALA* 4.6 6.4 + - - +
273K PHE* 4.1 3.9 - - - -
284K SER* 4.0 20.8 - - - +
332K VAL* 4.5 3.1 - - + -
336K ILE* 4.2 19.3 - - + -
367K THR* 3.5 20.2 - - - +
369K ILE* 3.8 25.1 - - + -
383K ILE* 3.8 42.8 - - + -
385K GLY 2.8 10.7 + - - +
386K PRO* 1.3 83.1 - - + +
388K LEU* 1.3 66.9 + - - +
389K GLN* 4.3 4.3 - - + +
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Residues in contact with LEU 388 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268K LEU* 4.3 17.3 - - + +
272K ALA* 4.0 14.8 - - + -
273K PHE* 3.8 16.4 - - + -
283K LEU 3.6 22.0 - - - +
284K SER 3.9 3.6 - - - -
285K VAL 4.2 0.4 - - - -
286K ALA* 3.9 28.5 - - + +
297K LEU* 6.4 0.7 - - + -
301K MET* 3.8 33.4 - - + -
367K THR 3.0 7.7 + - - +
368K LEU* 3.5 12.0 - - + +
369K ILE* 2.9 28.1 + - - +
387K VAL* 1.3 75.5 - - - +
389K GLN* 1.3 70.2 + - - +
390K VAL* 5.5 1.1 - - + -
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Residues in contact with GLN 389 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250K LYS* 3.2 32.0 + - - -
284K SER* 3.2 15.6 + - - +
285K VAL* 3.4 8.2 - - + +
286K ALA* 2.8 32.2 + - - +
369K ILE* 3.4 14.8 - - + +
372K VAL* 4.0 27.8 - - + +
378K SER* 3.3 38.5 + - - -
379K TYR* 3.6 9.5 - - - +
383K ILE* 3.9 10.4 - - - +
387K VAL* 4.3 6.5 - - + +
388K LEU* 1.3 78.7 - - - +
390K VAL* 1.3 59.9 + - - +
391K VAL 4.0 0.6 + - - -
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Residues in contact with VAL 390 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286K ALA* 3.4 11.7 - - + +
288K ALA* 4.5 8.5 - - + -
294K GLY 4.9 1.6 - - - +
297K LEU* 4.2 22.4 - - + -
298K VAL* 3.8 20.0 - - + -
368K LEU* 3.6 28.0 - - + -
369K ILE 2.8 11.5 + - - +
370K ASP* 3.6 18.2 - - - +
371K HIS* 3.4 6.2 + - - -
372K VAL* 3.1 24.2 + - - +
388K LEU* 5.4 2.5 - - + -
389K GLN* 1.3 75.8 - - - +
391K VAL* 1.3 72.8 + - - +
392K ARG* 4.5 5.6 - - + +
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Residues in contact with VAL 391 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285K VAL* 3.9 20.0 - - + -
286K ALA 3.1 5.3 + - - +
287K VAL* 3.5 9.0 - - + -
288K ALA 2.9 26.0 + - - -
372K VAL* 3.2 39.3 - - + +
373K THR* 5.0 3.4 - - - +
374K PRO* 5.4 4.5 - - + -
379K TYR* 4.0 13.2 - - + -
390K VAL* 1.3 76.2 - - - +
392K ARG* 1.3 72.7 + - - +
393K VAL* 4.2 6.2 + - + -
402K LEU* 3.5 26.9 - - + -
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Residues in contact with ARG 392 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288K ALA* 3.8 6.5 - - + +
290K GLY 5.6 0.2 - - - +
291K ASP* 3.0 49.0 + - - +
294K GLY* 3.3 31.9 + - - -
295K ASP* 3.7 16.9 + - - +
298K VAL* 4.0 2.6 - - - +
370K ASP* 2.9 39.8 + - - +
371K HIS* 3.3 33.4 + - - +
372K VAL 4.6 2.4 + - - -
390K VAL* 4.5 5.4 - - + +
391K VAL* 1.3 82.8 - - - +
393K VAL* 1.3 68.1 + - - +
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Residues in contact with VAL 393 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287K VAL* 3.7 29.6 - - + -
288K ALA 3.3 3.9 + - - +
289K VAL* 4.0 10.3 - - - -
290K GLY* 2.8 32.2 + - - -
391K VAL* 4.3 10.5 - - + -
392K ARG* 1.3 80.4 - - - +
394K ALA* 1.3 56.1 + - - +
395K THR 3.5 18.4 - - - +
398K ASP* 3.9 22.9 - - + +
399K ALA* 3.9 7.6 - - + +
402K LEU* 4.6 5.8 - - + -
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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