Contacts of the strand formed by residues 409 - 416 (chain A) in PDB entry 2ZB5
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 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A PRO* 3.4 2.3 - - - +
369A THR* 2.6 48.3 + - - -
371A ARG* 3.5 22.1 - - - -
408A PRO* 1.3 74.5 - - - +
410A TYR* 1.3 64.9 + - - +
411A GLY 3.9 0.2 - - - -
429A SER* 4.0 1.7 - - - -
430A GLY 3.5 12.3 - - - -
431A PHE* 3.7 25.4 - - - +
435A ILE* 3.3 17.5 - - - +
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Residues in contact with TYR 410 (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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367A VAL 4.2 2.2 - - - -
408A PRO 5.9 0.2 - - - -
409A SER* 1.3 76.9 - - - +
411A GLY* 1.3 60.7 + - - +
412A VAL* 5.8 1.3 - - + -
429A SER* 3.2 4.0 - - - -
430A GLY 2.9 40.5 + - - +
432A GLY* 3.6 22.9 - - - -
433A PRO* 2.7 32.7 + - - +
434A LEU 4.4 1.6 + - - -
435A ILE* 3.6 14.7 - - + +
441A MET* 3.5 33.7 - - + -
454A LEU* 3.7 32.8 - - + -
456A ILE* 4.3 5.4 - - + +
466A VAL* 5.0 0.5 - - - +
468A ASN* 2.9 22.2 + - - -
476A PHE* 3.9 5.8 - - + -
478A VAL* 3.8 24.9 - - + -
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Residues in contact with GLY 411 (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 ALA* 3.0 6.6 - - - +
367A VAL 2.8 35.5 + - - -
369A THR* 3.4 22.1 + - - -
409A SER 3.8 0.2 + - - -
410A TYR* 1.3 74.7 - - - +
412A VAL* 1.3 63.6 + - - +
413A LEU* 4.1 4.7 - - - -
427A ILE* 4.9 2.5 - - - -
428A ALA 3.4 8.1 - - - -
429A SER* 4.0 4.0 - - - -
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Residues in contact with VAL 412 (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 LYS* 4.4 25.8 - - + +
365A TRP 3.0 19.1 - - - +
366A ALA* 4.6 5.4 - - + -
410A TYR* 5.2 2.0 - - + -
411A GLY* 1.3 79.0 - - - +
413A LEU* 1.3 68.4 + - - +
414A SER* 3.8 3.5 + - - +
426A LYS 3.5 6.8 - - - +
427A ILE* 3.5 1.4 - - - +
428A ALA* 2.9 31.7 + - + +
443A LEU* 4.6 4.5 - - + -
454A LEU* 5.9 0.4 - - + -
470A LEU* 3.6 23.1 - - + -
472A TRP* 6.2 1.1 - - + -
476A PHE* 3.6 32.5 - - + -
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Residues in contact with LEU 413 (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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288A MET* 3.8 28.0 - - + -
299A LEU* 4.6 3.1 - - + -
319A PHE* 4.4 13.0 - - + -
339A LEU* 5.2 1.1 - - + -
349A LEU* 4.0 31.6 - - + -
351A LEU* 4.7 1.1 - - + -
363A ALA 3.7 0.3 - - - +
364A LYS* 3.3 2.8 - - - -
365A TRP* 2.8 47.5 + - + +
367A VAL* 3.7 29.6 - - + -
411A GLY 4.6 0.7 - - - -
412A VAL* 1.3 80.5 - - - +
414A SER* 1.3 59.5 + - - +
425A ILE* 4.1 15.7 - - + -
426A LYS 3.5 4.7 - - - -
427A ILE* 4.6 14.1 - - + -
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Residues in contact with SER 414 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A GLN* 3.7 25.1 + - - -
363A ALA 3.0 10.5 - - - -
364A LYS* 3.9 12.2 + - - -
412A VAL* 4.4 4.3 + - - -
413A LEU* 1.3 76.0 - - - +
415A VAL* 1.3 67.1 + - - +
424A LYS 4.1 1.0 - - - +
425A ILE* 3.6 1.1 - - - +
426A LYS* 3.1 47.8 + - - +
427A ILE 5.9 0.2 - - - -
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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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299A LEU* 4.2 21.3 - - + -
321A LEU* 3.6 28.7 - - + -
337A VAL* 5.2 2.7 - - + -
362A GLN* 3.2 10.1 - - - +
363A ALA* 2.9 36.8 + - + +
365A TRP* 4.4 5.8 - - + -
414A SER* 1.3 80.9 - - - +
416A ASP* 1.3 74.8 + - - +
417A LEU* 3.5 3.2 + - + +
423A LEU* 3.9 8.1 - - + -
424A LYS 4.8 6.3 - - - +
425A ILE* 3.7 30.1 - - + -
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Residues in contact with ASP 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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361A ASN* 3.8 8.8 + - - +
362A GLN* 4.6 7.5 + - - +
415A VAL* 1.3 75.3 - - - +
417A LEU* 1.3 58.6 + - - +
418A SER* 2.6 40.4 + - - +
420A THR* 5.4 0.4 - - - -
421A VAL* 3.1 38.8 - - + +
423A LEU* 3.0 27.8 - - + +
424A LYS 5.1 4.3 + - - +
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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