Contacts of the strand formed by residues 381 - 387 (chain H) in PDB entry 1ZMC
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371H GLU* 2.6 40.2 + - + +
374H LEU* 3.7 35.9 - - + -
375H LYS* 3.6 29.1 - - + +
379H ILE* 3.2 16.8 - - + +
380H GLU* 1.3 74.8 + - - +
382H LYS* 1.3 74.6 + - - +
383H VAL* 3.6 23.5 - - + +
407H LEU* 4.0 8.1 - - + -
408H GLY 3.1 16.4 - - - +
410H LYS* 3.4 16.6 + - - +
416H LEU* 4.4 5.6 - - + -
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Residues in contact with LYS 382 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381H TYR* 1.3 78.0 - - - +
383H VAL* 1.3 65.2 + - - +
406H ILE 3.6 0.6 - - - +
407H LEU* 3.3 5.7 - - - -
408H GLY* 2.6 37.2 + - - +
409H GLN 4.1 13.9 - - - -
410H LYS* 3.9 38.6 + - + +
413H ASP* 2.6 35.5 + - - +
466H ALA* 3.1 29.5 + - - +
467H SER 3.4 14.5 + - - +
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Residues in contact with VAL 383 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371H GLU* 4.6 7.9 - - - +
381H TYR* 3.6 26.7 - - + +
382H LYS* 1.3 80.5 - - - +
384H GLY* 1.3 61.8 + - - +
385H LYS* 4.1 31.0 - - + -
405H LYS* 4.1 17.3 - - + -
406H ILE 3.3 7.6 - - - +
407H LEU* 4.0 3.1 - - + -
465H ALA 4.5 2.8 - - - +
466H ALA* 4.1 8.4 - - - -
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Residues in contact with GLY 384 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383H VAL* 1.3 75.4 - - - +
385H LYS* 1.3 62.8 + - - +
404H VAL 3.9 0.3 - - - +
405H LYS* 3.3 2.8 - - - +
406H ILE* 2.7 39.0 + - - +
462H ALA* 3.4 22.5 - - - +
465H ALA* 3.9 5.4 - - - -
466H ALA* 3.6 12.6 - - - +
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Residues in contact with LYS 385 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221H GLU* 2.5 44.1 + - - +
371H GLU* 5.6 0.7 - - - -
383H VAL* 4.1 17.7 - - + -
384H GLY* 1.3 78.9 - - - +
386H PHE* 1.3 63.8 + - - +
387H PRO* 4.4 4.1 - - - +
403H MET* 4.2 16.4 - - - -
404H VAL 3.3 6.1 - - - +
405H LYS* 4.1 13.2 - - + +
462H ALA* 4.5 1.8 - - - -
465H ALA* 4.3 10.5 - - - +
471H SER* 5.6 0.3 + - - -
474H PHE* 4.8 7.6 - - - -
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Residues in contact with PHE 386 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385H LYS* 1.3 76.4 - - - +
387H PRO* 1.3 92.6 - - + +
390H ALA* 3.5 33.9 - - + -
391H ASN* 3.8 8.3 - - + -
403H MET* 3.2 4.1 - - - -
404H VAL* 2.8 37.5 + - - +
457H GLU 5.1 0.4 - - - -
458H ALA* 3.6 40.0 - - + +
461H GLU* 3.4 27.1 - - + -
462H ALA* 3.8 9.2 - - + +
471H SER* 3.3 29.6 - - - -
473H ASN* 3.8 10.8 - - + -
474H PHE* 3.6 13.7 - + + -
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Residues in contact with PRO 387 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385H LYS* 4.4 1.1 - - + +
386H PHE* 1.3 103.7 - - + +
388H PHE* 1.3 62.5 + - - +
389H ALA* 2.9 14.4 + - + +
390H ALA* 3.1 17.1 + - + +
402H GLY 3.5 10.1 - - - +
403H MET* 3.8 5.1 - - + -
474H PHE* 3.6 52.0 - - + -
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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