Contacts of the strand formed by residues 381 - 387 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371E GLU* 2.7 32.9 + - + +
374E LEU* 3.8 33.0 - - + -
375E LYS* 3.0 37.5 - - + +
379E ILE* 3.0 24.9 - - + +
380E GLU* 1.3 78.4 + - - +
382E LYS* 1.3 66.7 + - - +
383E VAL* 3.7 15.4 - - + +
407E LEU* 3.9 20.6 - - + -
408E GLY 3.2 14.4 - - - +
410E LYS* 3.3 16.8 + - - +
416E LEU* 4.6 5.4 - - + -
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Residues in contact with LYS 382 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381E TYR* 1.3 77.1 - - - +
383E VAL* 1.3 64.4 + - - +
406E ILE 3.7 0.6 - - - +
407E LEU* 3.4 6.2 - - - -
408E GLY* 2.7 35.8 + - - +
409E GLN 3.9 12.9 + - - -
410E LYS* 4.0 36.3 + - + +
413E ASP* 2.6 38.2 + - - +
466E ALA* 3.0 29.8 + - - +
467E SER 3.7 11.3 + - - +
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Residues in contact with VAL 383 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371E GLU* 4.3 8.5 - - - +
381E TYR* 3.7 16.4 - - + +
382E LYS* 1.3 79.1 - - - +
384E GLY* 1.3 62.7 + - - +
385E LYS* 3.8 37.0 - - + -
405E LYS* 4.2 10.3 - - + -
406E ILE 3.5 7.4 - - - +
407E LEU* 3.7 17.3 - - + -
465E ALA 4.6 2.4 - - - +
466E ALA* 4.3 7.0 - - - -
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Residues in contact with GLY 384 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383E VAL* 1.3 75.3 - - - +
385E LYS* 1.3 61.8 + - - +
404E VAL 3.8 0.5 - - - +
405E LYS* 3.4 2.4 - - - -
406E ILE* 2.9 34.3 + - - +
462E ALA* 3.6 22.9 - - - +
465E ALA* 4.0 5.6 - - - -
466E ALA* 3.6 14.5 - - - +
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Residues in contact with LYS 385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E GLU* 2.6 42.5 + - - +
371E GLU* 5.3 0.9 - - - -
383E VAL* 3.8 23.1 - - + -
384E GLY* 1.3 78.1 - - - +
386E PHE* 1.3 65.8 + - - +
387E PRO* 4.3 3.8 - - + +
403E MET* 4.1 20.0 - - - -
404E VAL 3.2 6.5 - - - +
405E LYS* 4.2 7.9 - - + +
462E ALA* 4.4 2.2 - - - -
465E ALA* 4.3 11.1 - - - +
471E SER* 5.2 1.0 + - - -
474E PHE* 4.8 7.4 - - - -
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Residues in contact with PHE 386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385E LYS* 1.3 76.2 - - - +
387E PRO* 1.3 91.5 - - - +
388E PHE 3.8 0.2 + - - -
390E ALA* 3.4 35.4 - - + -
391E ASN* 3.8 9.2 - - + -
403E MET* 3.3 2.6 - - - -
404E VAL* 2.9 33.1 + - - +
457E GLU 5.5 0.2 - - - -
458E ALA* 3.6 35.7 - - + +
461E GLU* 3.3 37.5 - - + -
462E ALA* 3.8 9.2 - - + +
471E SER* 3.5 21.5 - - - -
473E ASN* 3.7 11.7 - - + -
474E PHE* 3.8 15.7 - - + -
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Residues in contact with PRO 387 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385E LYS* 4.4 1.3 - - + +
386E PHE* 1.3 106.9 - - + +
388E PHE* 1.3 64.5 + - - +
389E ALA* 4.0 12.8 - - + +
390E ALA* 3.1 17.7 + - + +
402E GLY 3.5 11.0 - - - +
403E MET* 3.9 5.6 - - + -
474E PHE* 3.8 51.8 - - + -
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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