Contacts of the strand formed by residues 403 - 409 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221G GLU* 3.9 22.0 - - + +
222G ILE* 3.7 27.5 - - + +
225G ASN* 3.9 26.2 - - - +
385G LYS* 4.2 21.5 - - + -
386G PHE 3.1 17.3 - - - +
387G PRO* 3.8 6.7 - - + -
388G PHE* 3.4 7.3 - - - -
402G GLY* 1.3 77.7 - - - +
404G VAL* 1.3 69.7 + - - +
405G LYS* 4.0 14.6 - - + -
419G HIS 4.0 0.5 - - - +
420G ILE* 3.6 1.6 - - - -
421G LEU* 2.7 37.3 + - + +
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Residues in contact with VAL 404 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384G GLY 3.8 0.2 - - - +
385G LYS* 3.3 5.7 - - - +
386G PHE 2.8 31.0 + - - +
388G PHE* 3.6 18.6 - - + -
403G MET* 1.3 75.9 - - - +
405G LYS* 1.3 64.1 + - - +
406G ILE* 4.3 5.2 - - + -
419G HIS 3.6 8.1 - - - +
420G ILE* 3.9 13.5 - - + -
428G MET* 4.2 4.0 - - - -
458G ALA* 3.6 37.0 - - + +
459G PHE* 3.8 28.0 - - + +
462G ALA* 3.6 18.0 - - + +
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Residues in contact with LYS 405 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G ASP* 2.6 37.2 + - - +
221G GLU* 2.7 29.9 + - - +
222G ILE* 4.6 3.1 - - + -
371G GLU* 2.8 34.4 + - - +
383G VAL* 4.3 14.1 - - + -
384G GLY 3.3 8.7 - - - +
385G LYS* 4.4 4.9 - - + -
403G MET* 4.0 20.0 - - + -
404G VAL* 1.3 76.9 - - - +
406G ILE* 1.3 65.3 + - - +
407G LEU* 4.0 11.9 - - + -
417G GLY 4.0 0.3 - - - +
418G ALA* 3.7 3.5 - - - -
419G HIS* 2.7 48.0 + - + +
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Residues in contact with ILE 406 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382G LYS 3.7 0.3 - - - +
383G VAL* 3.4 6.4 - - - +
384G GLY 2.7 36.6 + - - +
404G VAL* 4.3 3.1 - - + -
405G LYS* 1.3 81.3 - - - +
407G LEU* 1.3 69.0 + - - +
415G VAL* 4.2 9.9 - - + -
417G GLY 3.8 0.4 - - - -
418G ALA* 4.0 11.7 - - + -
442G CYS* 3.9 20.4 - - - -
459G PHE* 3.6 23.8 - - + -
462G ALA* 3.5 35.0 - - + +
463G ASN* 3.5 39.3 - - - +
466G ALA* 4.1 6.4 - - + +
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Residues in contact with LEU 407 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369G LYS 3.4 24.2 - - - +
370G SER 3.8 2.0 - - - -
371G GLU* 3.6 42.4 - - + +
374G LEU* 3.9 20.2 - - + -
381G TYR* 4.0 6.3 - - + -
382G LYS 3.4 2.7 - - - +
383G VAL* 3.9 21.3 - - + -
405G LYS* 4.0 11.2 - - - -
406G ILE* 1.3 83.5 - - - +
408G GLY* 1.3 52.9 + - - +
415G VAL* 3.6 2.8 - - - +
416G LEU* 2.7 33.5 + - - -
417G GLY 3.0 18.0 + - - +
419G HIS* 4.1 14.6 - - + +
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Residues in contact with GLY 408 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381G TYR* 3.2 5.4 - - - +
382G LYS* 2.8 40.9 + - - +
406G ILE 4.1 1.0 - - - -
407G LEU* 1.3 74.8 - - - +
409G GLN* 1.3 64.3 + - - -
413G ASP 4.8 0.2 - - - -
414G ARG 3.3 9.4 - - - -
416G LEU* 3.9 4.0 - - - -
442G CYS* 4.0 21.1 - - - -
466G ALA* 5.1 0.6 - - - +
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Residues in contact with GLN 409 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379G ILE* 4.3 7.4 - - + -
380G GLU* 3.4 14.4 + - - +
382G LYS* 3.9 2.1 - - - -
408G GLY* 1.3 72.5 - - - -
410G LYS* 1.3 63.1 + - - +
411G SER* 2.4 52.3 + - - +
412G THR* 2.5 35.2 + - + +
413G ASP* 2.7 30.8 + - - -
414G ARG* 2.8 16.2 + - + +
416G LEU* 3.6 19.3 - - + +
2028G SO4 2.5 37.8 + - - +
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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