Contacts of the strand formed by residues 403 - 409 (chain A) 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 MET 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A GLU* 3.9 23.8 - - + +
222A ILE* 3.6 27.7 - - + +
225A ASN* 3.9 25.4 - - - +
385A LYS* 4.1 24.7 - - - -
386A PHE 3.1 17.3 - - - +
387A PRO* 3.8 7.2 - - + -
388A PHE* 3.5 6.6 - - - -
402A GLY* 1.3 77.6 - - - +
404A VAL* 1.3 66.8 + - - +
405A LYS* 4.2 11.0 - - + -
419A HIS 3.9 0.5 - - - +
420A ILE* 3.6 1.2 - - - -
421A LEU* 2.7 40.8 + - + +
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Residues in contact with VAL 404 (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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385A LYS* 3.2 6.6 - - - +
386A PHE 2.9 29.3 + - - +
388A PHE* 3.9 13.0 - - + -
403A MET* 1.3 80.7 - - - +
405A LYS* 1.3 62.4 + - - +
406A ILE* 4.0 17.3 - - + -
419A HIS 3.4 8.1 - - - +
420A ILE* 4.2 7.9 - - + +
428A MET* 4.1 8.7 - - - -
458A ALA* 3.7 33.0 - - + +
459A PHE* 3.9 19.3 - - + +
462A ALA* 3.7 22.9 - - + +
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Residues in contact with LYS 405 (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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219A ASP* 2.7 35.0 + - - -
221A GLU* 2.6 35.9 + - - +
222A ILE* 4.9 2.9 - - - -
371A GLU* 2.6 28.0 + - - -
383A VAL* 3.8 20.0 - - + -
384A GLY 3.3 3.6 - - - +
385A LYS* 3.8 15.0 - - + +
403A MET* 4.2 14.3 - - + -
404A VAL* 1.3 74.5 - - - +
406A ILE* 1.3 65.3 + - - +
407A LEU* 4.3 7.9 - - + -
417A GLY 3.9 0.5 - - - +
418A ALA* 3.6 2.4 - - - -
419A HIS* 2.7 50.9 + - + +
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Residues in contact with ILE 406 (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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382A LYS 3.7 0.2 - - - +
383A VAL* 3.4 5.4 - - - +
384A GLY 2.7 36.3 + - - +
404A VAL* 4.0 7.2 - - + -
405A LYS* 1.3 81.5 - - - +
407A LEU* 1.3 68.3 + - - +
408A GLY 4.1 0.3 + - - -
415A VAL* 4.4 7.0 - - + -
417A GLY 3.6 3.4 - - - +
418A ALA* 3.8 14.1 - - + -
442A CYS* 3.9 19.7 - - - -
459A PHE* 3.6 31.2 - - + -
462A ALA* 3.7 28.7 - - + +
463A ASN* 3.3 30.7 - - - +
466A ALA* 4.3 3.2 - - + +
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Residues in contact with LEU 407 (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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369A LYS 3.5 23.6 - - - +
370A SER 3.7 2.2 - - - -
371A GLU* 3.6 43.7 - - + +
374A LEU* 3.9 20.2 - - + -
381A TYR* 4.0 5.2 - - + -
382A LYS 3.4 2.7 - - - +
383A VAL* 3.8 26.9 - - + -
405A LYS* 4.3 6.3 - - - -
406A ILE* 1.3 82.0 - - - +
408A GLY* 1.3 52.6 + - - +
415A VAL* 3.7 2.9 - - - +
416A LEU* 2.7 32.7 + - - -
417A GLY 3.0 16.7 + - - +
419A HIS* 3.9 13.9 - - + +
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Residues in contact with GLY 408 (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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381A TYR* 3.2 6.4 - - - +
382A LYS* 2.8 45.8 + - - +
406A ILE 4.1 1.2 - - - -
407A LEU* 1.3 74.4 - - - +
409A GLN* 1.3 64.1 + - - -
414A ARG 3.2 9.6 - - - -
416A LEU* 4.3 1.8 - - - -
442A CYS* 4.0 20.0 - - - -
466A ALA* 5.1 1.0 - - - +
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Residues in contact with GLN 409 (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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379A ILE* 4.2 7.4 - - + +
380A GLU* 2.8 41.0 + - - +
382A LYS* 3.9 2.4 - - - -
408A GLY* 1.3 70.5 - - - -
410A LYS* 1.3 69.4 + - - +
411A SER* 2.4 39.6 + - - +
412A THR* 3.1 26.7 + - + +
413A ASP* 2.8 23.4 + - - -
414A ARG* 2.8 16.5 + - + +
416A LEU* 3.9 22.4 - - + +
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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