Contacts of the strand formed by residues 381 - 387 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371C GLU* 2.6 50.3 + - + +
374C LEU* 3.8 32.8 - - + -
375C LYS* 3.2 30.2 - - + -
379C ILE* 3.1 27.6 - - + +
380C GLU* 1.3 78.7 - - - +
382C LYS* 1.3 74.9 + - - +
383C VAL* 3.7 12.9 - - + +
407C LEU* 4.0 11.0 - - + -
408C GLY 3.2 15.0 - - - +
410C LYS* 4.0 4.4 - - - +
416C LEU* 4.5 0.4 - - + -
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Residues in contact with LYS 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381C TYR* 1.3 79.0 - - - +
383C VAL* 1.3 64.7 + - - +
406C ILE 3.6 0.3 - - - +
407C LEU* 3.4 6.6 - - - -
408C GLY* 2.7 37.1 + - - +
409C GLN 3.8 16.8 - - - -
410C LYS* 4.0 27.6 + - + +
413C ASP* 2.7 36.3 + - - +
466C ALA* 3.3 27.1 + - - +
467C SER 3.5 13.4 + - - +
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Residues in contact with VAL 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C GLU* 4.1 9.4 - - - +
381C TYR* 3.7 26.2 - - + +
382C LYS* 1.3 79.5 - - - +
384C GLY* 1.3 62.7 + - - +
385C LYS* 3.7 34.3 + - + -
405C LYS* 4.3 13.5 - - + -
406C ILE 3.4 7.2 - - - +
407C LEU* 3.9 5.8 - - + -
465C ALA 4.7 2.1 - - - +
466C ALA* 4.2 8.4 - - - -
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Residues in contact with GLY 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383C VAL* 1.3 75.6 - - - +
385C LYS* 1.3 63.0 + - - +
404C VAL 3.7 0.9 - - - +
405C LYS* 3.5 3.1 - - - -
406C ILE 2.8 34.5 + - - -
462C ALA* 3.6 11.2 - - - +
465C ALA* 4.0 5.6 - - - -
466C ALA* 3.6 25.2 - - - +
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Residues in contact with LYS 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C GLU* 2.6 41.5 + - - +
371C GLU* 5.7 0.4 - - - -
383C VAL* 3.7 24.2 - - + -
384C GLY* 1.3 79.6 - - - +
386C PHE* 1.3 64.5 + - - +
387C PRO* 4.5 2.9 - - + +
403C MET* 4.3 18.6 - - - -
404C VAL 3.3 5.8 - - - +
405C LYS* 4.3 7.2 - - + +
462C ALA* 4.4 2.0 - - - -
465C ALA* 4.3 12.3 - - - +
471C SER* 5.3 1.4 - - - -
474C PHE* 4.8 7.1 - - - -
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Residues in contact with PHE 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C LYS* 1.3 76.9 - - - +
387C PRO* 1.3 79.0 - - - +
388C PHE 3.9 0.2 + - - -
390C ALA* 3.5 32.5 - - + -
391C ASN* 3.9 6.5 - - - -
403C MET* 3.3 3.9 - - - +
404C VAL* 2.9 32.2 + - - +
457C GLU 5.1 0.4 - - - -
458C ALA* 3.6 41.6 - - + +
461C GLU* 3.4 22.2 - - + -
462C ALA* 3.9 9.6 - - + +
471C SER* 3.0 31.2 - - - -
473C ASN* 3.9 11.4 - - + -
474C PHE* 3.7 22.0 - - + -
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Residues in contact with PRO 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C LYS* 4.5 1.1 - - + +
386C PHE* 1.3 102.4 - - + +
388C PHE* 1.3 65.4 + - - +
389C ALA* 4.0 12.1 - - + +
390C ALA* 3.0 19.6 + - + +
402C GLY 3.4 11.9 - - - +
403C MET* 3.8 4.7 - - + -
458C ALA* 5.5 0.2 - - - -
474C PHE* 3.9 48.2 - - + -
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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