Contacts of the strand formed by residues 373 - 378 (chain A) in PDB entry 4Z7Q
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 ASP 373 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A THR* 5.0 0.3 - - - +
362A PRO* 3.9 0.9 - - - +
363A LEU* 2.9 35.3 + - + +
364A GLY 2.7 9.3 + - - +
366A LEU* 2.7 32.6 + - + +
367A ASP* 3.2 12.2 - - - +
369A ASP* 4.4 1.2 - - - +
371A TYR 3.1 12.0 - - - +
372A ASN* 1.3 74.2 - - - +
374A ILE* 1.3 69.0 + - - +
392A PHE 3.3 13.9 - - - +
393A LEU* 3.2 23.5 - - + +
394A GLY 2.7 25.4 + - - +
399A LEU* 5.0 1.1 - - - -
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Residues in contact with ILE 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A THR* 4.0 15.5 - - + -
298A VAL* 4.4 6.7 - - + -
307A LEU* 3.6 47.8 - - + -
347A LEU* 5.1 2.5 - - + -
360A ILE* 4.3 5.8 - - + -
361A ALA 3.5 8.5 - - - +
362A PRO* 4.3 8.1 - - + -
363A LEU* 3.3 12.4 - - - +
373A ASP* 1.3 81.3 - - - +
375A ALA* 1.3 61.7 + - - +
376A VAL* 4.1 20.9 - - + -
391A VAL* 3.5 0.7 - - - -
392A PHE* 2.9 47.2 + - + +
399A LEU* 3.6 17.9 - - + -
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Residues in contact with ALA 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ILE* 3.5 4.5 - - - +
361A ALA* 2.9 32.8 + - + +
363A LEU* 3.8 24.2 - - + -
374A ILE* 1.3 76.6 - - - +
376A VAL* 1.3 62.6 + - - +
389A VAL* 4.0 20.9 - - + -
390A LEU 3.3 6.3 - - - +
391A VAL* 4.7 3.1 - - + -
421A LEU* 3.8 8.0 - - + +
435A LEU* 4.5 11.2 - - + -
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Residues in contact with VAL 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A VAL* 3.8 19.7 - - + -
347A LEU* 5.1 1.1 - - + -
356A PHE* 3.6 33.4 - - + -
357A GLY* 3.7 21.3 - - - +
359A ALA 3.5 4.3 - - - +
360A ILE* 4.5 7.9 - - + -
374A ILE* 4.1 16.6 - - + -
375A ALA* 1.3 78.4 - - - +
377A ALA* 1.3 64.8 + - - +
389A VAL* 3.3 5.5 - - - +
390A LEU* 2.7 42.1 + - - +
392A PHE* 4.0 19.7 - - + -
421A LEU* 4.5 0.2 - - - -
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Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ARG 3.2 4.7 - - - +
356A PHE* 5.1 0.2 - - - -
357A GLY 3.0 23.9 + - - -
358A SER 3.5 3.6 + - - -
359A ALA* 3.0 16.3 + - + +
376A VAL* 1.3 76.2 - - - +
378A ALA* 1.3 59.7 + - - +
379A PRO* 3.5 4.2 - - + +
388A GLN 3.6 5.2 - - - +
389A VAL* 4.5 1.6 - - + +
418A GLY* 3.0 42.4 - - - +
421A LEU* 3.9 11.4 - - + -
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Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A GLN* 6.1 0.7 - - + -
354A GLY* 3.1 13.7 - - - +
355A ARG 3.8 1.3 - - - -
356A PHE* 3.9 24.7 - - + +
376A VAL 4.2 0.4 + - - -
377A ALA* 1.3 73.2 - - - +
379A PRO* 1.3 55.5 - - - +
380A TYR 2.8 5.5 + - - -
381A GLY* 2.6 36.3 + - - -
388A GLN* 2.8 27.5 + - + +
390A LEU* 4.7 7.1 - - + +
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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