Contacts of the strand formed by residues 414 - 420 (chain A) in PDB entry 2ZJ4
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 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365A CYS* 4.4 0.7 - - - -
366A ARG* 5.4 0.7 - - - +
367A ARG* 3.0 51.0 + - - +
369A ILE* 4.1 5.8 - - + -
410A VAL* 3.3 4.9 - - - +
411A PHE* 2.5 43.5 + - - +
412A ARG 4.4 0.7 - - - +
413A ASP* 1.3 82.8 - - - +
415A VAL* 1.3 62.0 + - - +
416A CYS* 4.1 16.6 - - - -
440A ALA* 3.4 5.9 - - + +
441A LEU* 3.2 22.9 + - - +
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Residues in contact with VAL 415 (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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362A ILE* 4.3 15.7 - - + +
365A CYS* 2.8 44.9 - - + -
367A ARG 3.1 6.7 + - - -
368A LEU* 3.4 15.7 - - + +
369A ILE* 3.0 24.3 + - - +
413A ASP 4.0 0.2 + - - -
414A ASP* 1.3 70.6 - - - +
416A CYS* 1.3 63.1 + - - +
417A PHE* 3.7 16.7 + - + -
441A LEU* 3.4 22.7 - - + +
443A VAL* 3.7 27.4 - - + -
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Residues in contact with CYS 416 (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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369A ILE* 3.3 24.5 - - - +
371A ILE* 4.4 2.2 - - + -
410A VAL* 4.9 2.2 - - - -
414A ASP* 4.1 11.7 - - - -
415A VAL* 1.3 77.2 - - - +
417A PHE* 1.3 61.4 + - - +
418A PHE* 3.4 25.3 - - + -
435A CYS* 3.7 24.5 - - + -
440A ALA* 3.9 18.8 - - - -
441A LEU 2.8 10.8 + - - +
442A THR* 3.4 3.4 - - + -
443A VAL* 2.9 25.6 + - - +
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Residues in contact with PHE 417 (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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355A LEU* 5.6 1.1 - - + -
362A ILE* 5.3 0.2 - - + -
368A LEU* 4.4 8.5 - - + -
369A ILE 2.8 8.7 + - - +
370A LEU* 3.6 29.3 - - + -
371A ILE* 2.8 34.0 + - - +
415A VAL* 3.7 28.7 - - + -
416A CYS* 1.3 77.9 - - - +
418A PHE* 1.3 59.5 + - - +
419A LEU* 4.0 6.2 + - + +
443A VAL* 3.2 28.0 - - + -
445A ILE* 3.8 28.7 - - + -
484A LEU* 4.2 13.7 - - + -
487A PHE* 3.4 50.9 - + - -
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Residues in contact with PHE 418 (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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371A ILE* 3.5 35.0 - - + -
416A CYS* 3.4 39.7 - - + -
417A PHE* 1.3 71.8 - - - +
419A LEU* 1.3 62.5 + - - +
420A SER 3.9 0.3 + - - -
428A THR* 3.5 28.7 - - + +
431A GLY 3.5 5.4 - - - -
432A LEU* 3.2 52.0 - - + -
435A CYS* 3.8 9.0 - - + -
442A THR* 3.9 5.8 - - + -
443A VAL 2.8 14.2 + - - +
444A GLY* 3.6 2.4 - - - -
445A ILE 2.8 27.6 + - - +
453A ILE* 4.1 19.7 - - + +
457A THR* 4.2 3.8 - - + -
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Residues in contact with LEU 419 (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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1A AGP 4.2 1.9 + - - -
370A LEU* 4.8 11.2 - - + -
371A ILE 3.3 7.5 + - - +
372A ALA* 3.5 20.6 - - + +
373A CYS 4.8 0.2 + - - -
376A SER* 3.2 40.1 - - - +
377A TYR* 5.2 0.4 - - - +
379A ALA* 4.5 2.7 - - + -
380A GLY* 3.7 22.9 - - - +
397A VAL* 6.2 0.2 - - + -
417A PHE* 4.3 14.1 - - + +
418A PHE* 1.3 73.4 - - - +
420A SER* 1.3 63.4 + - - +
428A THR* 4.0 5.7 + - - +
445A ILE* 3.4 35.7 - - + +
480A GLN* 4.3 6.7 - - + +
484A LEU* 4.0 26.9 - - + -
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Residues in contact with SER 420 (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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1A AGP 2.6 24.5 + - - -
376A SER* 3.6 2.2 - - - -
418A PHE 3.9 0.8 + - - -
419A LEU* 1.3 76.2 - - - +
421A GLN* 1.3 62.9 + - - +
422A SER* 3.5 2.1 + - - -
423A GLY* 2.9 24.9 + - - -
424A GLU 4.1 0.2 + - - -
425A THR* 3.6 3.5 + - - -
428A THR* 4.6 1.8 - - - -
445A ILE 2.9 11.2 + - - -
446A THR* 3.1 28.7 - - - -
453A ILE* 3.7 25.1 - - - +
480A GLN* 3.8 4.4 + - - -
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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