Contacts of the strand formed by residues 381 - 387 (chain B) in PDB entry 1ZMD
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 TYR 381 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371B GLU* 2.6 41.1 + - + +
374B LEU* 3.7 40.2 - - + -
375B LYS* 3.3 33.7 - - + +
379B ILE* 3.2 17.3 - - + -
380B GLU* 1.3 76.6 + - - +
382B LYS* 1.3 74.3 + - - +
383B VAL* 3.6 17.7 - - + +
407B LEU* 4.2 3.4 - - + -
408B GLY 3.1 16.4 - - - +
410B LYS* 3.5 16.6 + - - +
416B LEU* 4.5 4.7 - - + -
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Residues in contact with LYS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B TYR* 1.3 78.3 - - - +
383B VAL* 1.3 64.8 + - - +
406B ILE 3.6 0.3 - - - +
407B LEU* 3.4 6.1 - - - -
408B GLY* 2.7 37.2 + - - +
409B GLN 3.9 14.6 - - - -
410B LYS* 3.9 38.5 + - + +
413B ASP* 2.7 35.4 + - - +
466B ALA* 3.2 28.3 + - - +
467B SER 3.4 13.3 + - - +
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Residues in contact with VAL 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLU* 4.3 9.6 - - - +
381B TYR* 3.6 26.9 - - + +
382B LYS* 1.3 79.3 - - - +
384B GLY* 1.3 62.0 + - - +
385B LYS* 3.7 36.0 + - + -
405B LYS* 4.1 13.0 - - + -
406B ILE 3.3 7.2 - - - +
407B LEU* 4.0 5.8 - - + -
465B ALA 4.6 2.6 - - - +
466B ALA* 4.1 8.3 - - - -
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Residues in contact with GLY 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B VAL* 1.3 74.8 - - - +
385B LYS* 1.3 62.5 + - - +
404B VAL 3.7 0.7 - - - +
405B LYS* 3.3 3.6 - - - -
406B ILE* 2.8 38.6 + - - +
462B ALA* 3.6 12.1 - - - +
465B ALA* 3.9 4.7 - - - -
466B ALA* 3.5 25.9 - - - +
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Residues in contact with LYS 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B GLU* 2.6 42.4 + - - +
371B GLU* 5.2 1.9 + - - -
383B VAL* 3.7 23.1 - - + -
384B GLY* 1.3 78.9 - - - +
386B PHE* 1.3 65.8 + - - +
387B PRO* 4.5 2.9 - - + +
403B MET* 4.3 17.0 - - - -
404B VAL 3.3 6.7 - - - +
405B LYS* 4.1 8.7 - - + +
462B ALA* 4.5 1.3 - - - -
465B ALA* 4.3 12.7 - - - +
471B SER* 5.4 1.0 + - - -
474B PHE* 5.0 6.4 - - - -
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Residues in contact with PHE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B LYS* 1.3 77.3 - - - +
387B PRO* 1.4 92.7 - - + +
388B PHE 3.8 0.2 + - - -
390B ALA* 3.6 31.9 - - + -
391B ASN* 4.0 7.2 - - + -
403B MET* 3.3 3.7 - - - +
404B VAL* 2.9 32.1 + - - +
457B GLU 5.0 0.4 - - - -
458B ALA* 3.6 41.0 - - + +
461B GLU* 3.5 40.4 - - + -
462B ALA* 3.9 9.4 - - + +
471B SER* 3.6 20.4 - - - -
473B ASN* 4.0 5.6 - - + -
474B PHE* 3.7 14.6 - - + -
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Residues in contact with PRO 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B LYS 4.5 0.9 - - - +
386B PHE* 1.4 103.1 - - + +
388B PHE* 1.3 64.0 + - - +
389B ALA* 2.9 14.4 - - + +
390B ALA* 3.1 20.1 + - + +
402B GLY 3.5 11.0 - - - +
403B MET* 3.9 4.5 - - + -
474B PHE* 3.8 50.5 - - + -
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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