Contacts of the strand formed by residues 403 - 409 (chain B) 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 MET 403 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B GLU* 3.8 32.8 - - + +
222B ILE* 4.0 17.7 - - + +
225B ASN* 4.4 15.7 - - - +
385B LYS* 4.3 19.5 - - + -
386B PHE 3.2 16.8 - - - +
387B PRO* 3.7 10.1 - - + -
388B PHE* 3.9 5.6 - - - -
402B GLY* 1.3 77.8 - - - +
404B VAL* 1.3 68.3 + - - +
405B LYS* 3.8 25.1 - - + +
419B HIS 4.0 0.5 - - - +
420B ILE* 3.7 0.9 - - - -
421B LEU* 2.7 34.9 + - + +
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Residues in contact with VAL 404 (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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384B GLY 3.7 0.3 - - - +
385B LYS* 3.3 4.5 - - - -
386B PHE 2.7 34.4 + - - +
388B PHE* 3.7 17.9 - - + -
403B MET* 1.3 76.8 - - - +
405B LYS* 1.3 64.3 + - - +
406B ILE* 4.3 5.8 - - + -
419B HIS 3.5 7.0 - - - +
420B ILE* 4.1 12.8 - - + -
428B MET* 4.2 3.6 - - - -
458B ALA* 3.6 38.4 - - + +
459B PHE* 3.8 26.7 - - + +
462B ALA* 3.4 19.5 - - + +
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Residues in contact with LYS 405 (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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219B ASP* 2.7 36.9 + - - +
221B GLU* 2.8 30.5 + - - +
222B ILE* 4.4 4.3 - - + -
371B GLU* 2.8 28.0 + - - +
383B VAL* 4.0 17.0 - - + -
384B GLY 3.4 3.1 - - - +
385B LYS* 4.3 2.5 - - + +
403B MET* 3.8 19.5 - - + -
404B VAL* 1.3 75.5 - - - +
406B ILE* 1.3 66.2 + - - +
407B LEU* 3.9 16.4 - - + -
418B ALA* 3.7 2.3 - - - -
419B HIS* 2.6 52.5 + - + +
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Residues in contact with ILE 406 (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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382B LYS 3.6 0.3 - - - +
383B VAL* 3.3 9.4 - - - +
384B GLY 2.7 37.6 + - - +
404B VAL* 4.4 2.5 - - + -
405B LYS* 1.3 81.4 - - - +
407B LEU* 1.3 70.4 + - - +
415B VAL* 4.6 6.5 - - + -
417B GLY 3.7 2.5 - - - +
418B ALA* 3.9 13.5 - - + -
442B CYS* 3.8 20.6 - - - -
459B PHE* 3.7 22.7 - - + -
462B ALA* 3.6 30.3 - - + +
463B ASN* 3.6 36.6 - - - +
466B ALA* 3.9 6.2 - - + +
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Residues in contact with LEU 407 (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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219B ASP* 4.8 0.9 - - - +
369B LYS 3.1 26.7 - - - +
370B SER 3.8 1.6 - - - -
371B GLU* 3.6 42.6 - - + +
374B LEU* 3.8 18.6 - - + -
381B TYR* 4.0 13.2 - - + -
382B LYS 3.4 2.2 - - - -
383B VAL* 4.0 6.7 - - + -
405B LYS* 3.9 15.7 - - - -
406B ILE* 1.3 83.0 - - - +
408B GLY* 1.3 52.0 + - - +
415B VAL* 3.6 3.3 - - - -
416B LEU* 2.7 31.9 + - - -
417B GLY 3.0 16.3 + - - +
419B HIS* 3.7 16.6 - - + +
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Residues in contact with GLY 408 (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* 3.0 7.7 - - - +
382B LYS* 2.7 46.1 + - - +
406B ILE* 4.1 1.6 - - - +
407B LEU* 1.3 74.8 - - - +
409B GLN* 1.3 64.1 + - - -
413B ASP 5.0 0.2 - - - -
414B ARG 3.1 9.6 - - - -
416B LEU* 4.1 1.8 - - - -
442B CYS* 4.0 17.2 - - - -
466B ALA* 5.0 0.4 - - - +
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Residues in contact with GLN 409 (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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379B ILE* 3.8 15.2 - - - +
380B GLU 3.8 5.4 - - - +
382B LYS* 3.9 1.7 - - - -
408B GLY* 1.3 71.1 - - - -
410B LYS* 1.3 61.3 + - - +
411B SER* 3.7 11.9 - - - +
412B THR* 3.3 24.9 + - - +
413B ASP* 2.8 33.1 + - - -
414B ARG* 2.8 16.2 + - - +
416B LEU* 3.6 30.5 - - + +
2005B SO4 2.6 38.1 + - - +
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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