Contacts of the strand formed by residues 390 - 396 (chain A) in PDB entry 4TZ1
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 SER 390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A PRO* 3.9 6.8 + - - +
364A GLY* 3.3 14.8 - - - -
365A VAL 2.7 28.5 + - - -
386A GLY 5.4 1.0 + - - -
388A VAL 3.2 3.9 + - - -
389A ASN* 1.3 77.0 + - - +
391A GLU* 1.3 61.6 + - - +
392A THR 3.4 12.6 - - - -
393A LEU* 3.9 21.6 - - - +
426A LYS 3.2 8.0 + - - -
427A ALA* 3.2 3.3 - - - +
428A THR 2.9 24.4 + - - -
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Residues in contact with GLU 391 (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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364A GLY 4.0 5.2 + - - +
366A THR* 5.5 1.7 + - - +
389A ASN* 4.1 3.4 + - - +
390A SER* 1.3 72.8 - - - +
392A THR* 1.3 72.1 + - + +
428A THR* 3.4 17.1 - - + +
429A THR* 3.1 23.8 + - - -
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Residues in contact with THR 392 (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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366A THR* 2.6 41.7 + - - +
390A SER* 3.4 11.3 - - - -
391A GLU* 1.3 91.8 - - + +
393A LEU* 1.3 62.5 + - - +
394A VAL 4.5 4.3 - - - -
395A GLU* 2.6 36.1 + - - +
429A THR* 3.1 11.2 - - - +
432A VAL* 4.0 25.4 - - + -
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Residues in contact with LEU 393 (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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361A PRO* 3.7 30.1 - - + -
366A THR* 3.9 2.9 - - - -
367A ALA* 2.9 28.6 + - - +
368A LEU 3.2 7.3 + - - -
383A VAL* 4.1 14.6 - - + -
385A ALA* 4.2 26.5 - - + +
390A SER* 3.9 15.3 - - - -
392A THR* 1.3 73.5 - - - +
394A VAL* 1.3 63.5 + - + +
417A VAL* 3.7 20.0 - - + -
419A ILE* 4.4 2.0 - - + -
427A ALA* 3.5 26.0 - - + -
429A THR 3.3 1.6 + - - -
430A SER* 3.2 29.2 + - - +
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Residues in contact with VAL 394 (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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368A LEU* 3.3 29.4 - - + +
383A VAL* 4.0 29.8 - - + -
392A THR* 3.8 1.6 - - - -
393A LEU* 1.3 82.9 - - + +
395A GLU* 1.3 65.7 + - - +
396A VAL* 4.4 10.1 - - + -
412A LEU* 4.1 17.0 - - + -
415A VAL* 5.0 4.9 - - + -
417A VAL* 4.7 3.8 - - + -
430A SER 2.9 10.2 + - - +
431A ILE* 3.3 25.5 - - + -
432A VAL 2.9 25.3 + - - +
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Residues in contact with GLU 395 (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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366A THR* 3.8 5.2 + - + +
368A LEU 2.9 9.8 + - - +
369A LYS* 3.4 31.4 - - + +
370A VAL* 2.8 28.9 + - - +
392A THR* 2.6 42.0 + - + +
394A VAL* 1.3 74.8 - - - +
396A VAL* 1.3 61.5 + - - +
397A GLY 3.7 13.7 + - - +
398A SER* 5.3 1.2 - - - -
399A ASP* 5.2 5.5 + - - +
432A VAL* 3.4 15.7 - - + +
434A ASN* 4.7 5.4 + - - +
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Residues in contact with VAL 396 (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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370A VAL* 4.2 11.9 - - + -
394A VAL* 4.4 10.1 - - + -
395A GLU* 1.3 72.5 - - - +
397A GLY* 1.3 61.3 + - - +
410A THR* 3.8 22.9 - - + -
412A LEU* 4.2 27.8 - - + -
432A VAL 2.9 14.8 + - - +
433A VAL* 4.2 19.5 - - + -
434A ASN 2.8 29.3 + - - -
435A SER* 3.0 17.0 + - - +
438A THR* 3.8 21.3 - - + +
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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