Contacts of the strand formed by residues 400 - 408 (chain A) in PDB entry 2ZT5
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 GLY 400 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LYS* 5.9 2.9 - - - -
395A SER 3.3 1.4 - - - +
396A LYS* 4.5 8.5 - - - -
397A THR* 2.7 40.1 + - - -
398A SER 3.3 2.0 + - - -
399A TYR* 1.3 78.9 - - - +
401A TRP* 1.3 66.8 + - - -
402A ILE* 3.5 0.9 + - - +
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Residues in contact with TRP 401 (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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165A LYS* 5.7 3.3 + - - +
371A ASP 4.9 3.6 - - - -
372A LYS* 3.7 15.9 - - - -
373A LEU 4.3 1.6 - - - -
374A ARG* 3.2 75.9 - - + +
394A GLU* 3.6 18.4 - - - +
395A SER 3.5 6.7 - - - -
396A LYS* 3.5 64.3 - - + +
399A TYR 4.7 0.9 - - - +
400A GLY* 1.3 72.5 - - - -
402A ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 402 (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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287A ILE* 3.2 51.4 - - + -
288A ARG* 6.3 1.1 - - - +
394A GLU* 3.0 6.3 - - - +
395A SER* 2.9 40.1 + - - +
397A THR* 3.9 18.2 - - + +
399A TYR* 4.1 16.6 - - + +
400A GLY 3.8 7.0 - - - +
401A TRP* 1.3 80.8 - - - +
403A GLU* 1.3 63.4 + - - +
404A ILE* 3.5 10.6 + - + +
529A ARG* 4.9 5.8 - - - +
533A THR* 5.0 0.4 - - - +
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Residues in contact with GLU 403 (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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376A ARG* 5.7 0.5 + - - -
378A HIS* 5.0 1.4 + - - -
392A ASP* 2.9 45.4 - - + +
393A ALA 3.5 5.8 - - - +
394A GLU* 4.0 9.3 + - + +
402A ILE* 1.3 73.6 - - - +
404A ILE* 1.3 59.2 + - - +
405A VAL 4.6 0.7 - - - +
406A GLY* 4.1 3.5 - - - -
529A ARG* 2.8 44.5 + - - +
1101A B4P 2.6 72.6 + - - +
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Residues in contact with ILE 404 (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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363A LEU* 4.0 28.5 - - + -
368A ILE* 4.7 9.6 - - + -
373A LEU* 4.7 4.5 - - + -
393A ALA* 2.8 19.9 + - + +
395A SER* 3.7 27.8 - - - +
402A ILE* 4.0 8.5 - - + +
403A GLU* 1.3 77.0 - - - +
405A VAL* 1.3 72.3 + - + +
526A GLY 3.3 23.2 + - - -
529A ARG* 3.9 16.8 - - + +
530A ILE* 3.8 15.3 - - + +
533A THR* 3.6 22.7 - - - +
1101A B4P 3.3 12.6 + - - -
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Residues in contact with VAL 405 (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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359A ILE* 3.6 33.9 - - + -
363A LEU* 3.9 28.7 - - + -
391A TRP 4.1 0.3 - - - +
392A ASP* 3.2 4.3 - - - +
393A ALA* 2.7 40.8 + - + -
403A GLU* 4.6 1.1 - - - -
404A ILE* 1.3 91.4 - - + +
406A GLY* 1.3 64.6 + - - +
407A CYS* 4.0 0.3 + - - +
524A SER 3.2 11.9 - - - +
525A PHE* 3.8 29.4 - - + -
530A ILE* 4.0 1.6 - - + -
1101A B4P 3.4 3.0 + - - -
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Residues in contact with GLY 406 (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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390A CYS* 4.9 1.1 - - - -
392A ASP* 3.4 14.6 - - - -
403A GLU* 4.1 8.3 - - - -
405A VAL* 1.3 75.6 - - - +
407A CYS* 1.3 58.5 + - - -
408A ALA* 4.0 1.1 - - - -
522A GLU 3.1 3.2 - - - +
523A PRO* 3.3 1.6 - - - +
524A SER* 2.5 47.5 + - - -
1101A B4P 3.7 9.0 + - - -
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Residues in contact with CYS 407 (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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352A LEU* 4.5 13.1 - - - +
355A PHE* 4.2 9.9 - - - -
356A ILE* 4.9 10.5 - - + -
359A ILE* 4.2 22.0 - - + -
375A PHE* 6.2 1.1 - - + -
390A CYS* 3.5 5.0 - - - -
391A TRP* 2.8 41.9 + - + +
392A ASP* 3.9 1.2 + - - -
405A VAL 5.3 0.4 - - - +
406A GLY* 1.3 74.2 - - - +
408A ALA* 1.3 59.2 + - - +
521A ILE* 4.0 23.8 - - - -
522A GLU 3.5 2.5 - - - -
523A PRO* 4.1 14.8 - - - -
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Residues in contact with ALA 408 (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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352A LEU* 4.7 1.6 - - - -
384A ALA* 6.1 0.2 - - + -
386A TYR* 4.4 15.3 - - + +
387A ALA* 4.0 17.5 - - + -
389A ASP 3.6 8.1 - - - +
390A CYS* 3.7 13.9 - - - -
406A GLY 4.0 0.8 - - - -
407A CYS* 1.3 77.2 - - - +
409A ASP* 1.3 59.4 + - - +
410A ARG* 3.4 8.7 - - + +
521A ILE* 3.2 8.1 - - - +
522A GLU* 2.9 35.8 + - + +
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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