Contacts of the strand formed by residues 387 - 393 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272J ALA* 4.6 5.2 + - - +
273J PHE* 4.0 2.6 - - - -
284J SER* 3.7 22.0 - - - +
332J VAL* 4.3 4.0 - - + -
336J ILE* 3.9 21.8 - - + -
364J VAL* 5.6 0.2 - - + -
367J THR* 3.4 16.8 - - + +
369J ILE* 3.6 31.2 - - + -
383J ILE* 3.9 33.1 - - + +
385J GLY 2.7 20.7 + - - +
386J PRO* 1.3 80.6 - - + +
388J LEU* 1.3 60.0 + - - +
389J GLN* 4.2 6.1 - - + +
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Residues in contact with LEU 388 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268J LEU* 4.5 13.5 - - + -
272J ALA* 4.0 16.2 - - + -
273J PHE* 3.8 18.0 - - + -
283J LEU* 3.9 10.3 - - + +
284J SER 3.5 18.6 - - - +
285J VAL 3.9 0.7 - - - -
286J ALA* 3.7 22.9 - - + +
297J LEU* 6.3 1.3 - - + -
301J MET* 4.0 30.7 - - + -
367J THR 3.0 8.2 + - - +
368J LEU* 3.5 9.1 - - + +
369J ILE 3.0 24.1 + - - -
387J VAL* 1.3 70.7 - - - +
389J GLN* 1.3 75.4 + - - +
390J VAL* 4.8 6.3 - - + -
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Residues in contact with GLN 389 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250J LYS* 3.1 34.0 + - - +
284J SER 2.9 12.1 + - - +
285J VAL* 3.3 13.0 - - + +
286J ALA 2.9 24.9 + - - -
339J ALA* 5.2 0.2 - - - +
369J ILE* 3.5 16.1 - - + +
372J VAL* 4.0 25.0 - - + +
378J SER* 3.1 38.3 + - - +
379J TYR* 3.6 10.5 - - - +
383J ILE* 3.9 7.7 - - + +
387J VAL* 4.2 15.0 - - + +
388J LEU* 1.3 74.7 - - - +
390J VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 390 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286J ALA* 3.4 17.0 - - + +
288J ALA* 4.7 6.1 - - + -
294J GLY 5.0 1.6 - - - +
297J LEU* 4.2 22.7 - - + -
298J VAL* 4.2 16.4 - - + -
301J MET* 6.3 0.7 - - + -
368J LEU* 3.5 28.5 - - + -
369J ILE 2.8 12.7 + - - +
370J ASP* 4.1 14.4 - - - +
371J HIS 3.3 8.5 + - - -
372J VAL* 3.3 22.2 + - - +
388J LEU* 4.7 5.2 - - + +
389J GLN* 1.3 76.1 - - - +
391J VAL* 1.3 70.4 + - - +
392J ARG* 4.8 4.9 - - + +
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Residues in contact with VAL 391 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285J VAL* 4.1 17.9 - - + -
286J ALA 3.0 8.1 + - - +
287J VAL* 3.4 7.6 - - + -
288J ALA 2.9 25.1 + - - -
371J HIS 5.5 0.2 - - - +
372J VAL* 3.2 44.2 - - + +
373J THR* 5.3 4.5 - - - -
374J PRO* 5.6 3.8 - - + -
379J TYR* 4.5 11.0 - - + -
390J VAL* 1.3 73.7 - - - +
392J ARG* 1.3 76.6 + - - +
393J VAL* 4.4 5.6 - - + -
402J LEU* 3.8 24.5 - - + -
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Residues in contact with ARG 392 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288J ALA 3.5 8.3 - - - +
290J GLY 5.1 0.4 - - - +
291J ASP* 3.3 32.2 + - + +
294J GLY* 3.2 37.3 + - - -
295J ASP* 2.6 30.0 + - - +
298J VAL* 3.5 5.4 - - - +
370J ASP* 2.7 42.6 + - - +
371J HIS* 3.6 27.7 + - - +
372J VAL 4.9 1.4 + - - -
390J VAL* 4.8 4.6 - - + +
391J VAL* 1.3 83.0 - - - +
393J VAL* 1.3 69.3 + - - +
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Residues in contact with VAL 393 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287J VAL* 3.7 30.5 - - + -
288J ALA 3.4 5.8 + - - +
289J VAL* 4.2 6.3 - - - -
290J GLY* 2.9 27.2 + - - +
391J VAL* 4.4 9.2 - - + -
392J ARG* 1.3 80.7 - - - +
394J ALA* 1.3 59.3 + - - +
395J THR 3.5 19.1 - - - +
398J ASP* 3.8 20.2 - - + +
399J ALA* 3.9 10.1 - - + +
402J LEU* 4.7 6.3 - - + -
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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