Contacts of the strand formed by residues 404 - 410 (chain G) in PDB entry 1ZUM
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 VAL 404 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294G LEU* 3.2 17.7 - - - +
306G SER* 4.9 0.5 - - - -
353G ILE* 4.0 10.8 - - + -
356G TYR 6.3 0.2 - - - -
357G ILE* 3.9 25.6 - - + -
384G THR* 3.3 10.3 - - + -
386G PHE* 3.6 31.4 - - + -
395G ILE* 5.8 1.6 - - + -
400G ILE* 3.3 32.1 - - + +
402G GLY 2.8 11.1 + - - +
403G PRO* 1.3 79.3 - - + +
405G MET* 1.3 58.6 + - - +
406G GLN* 3.2 29.6 + - - +
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Residues in contact with MET 405 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G ALA* 4.9 15.0 - - - +
291G HIS* 5.2 4.5 - - - +
294G LEU* 3.5 21.5 - - + +
295G PHE* 4.1 15.7 - - + -
308G THR* 4.3 15.3 - - - +
318G PHE* 5.5 0.2 - - + -
322G SER* 3.4 26.0 - - - +
384G THR 2.7 15.3 + - - +
385G VAL* 3.4 23.3 - - + -
386G PHE* 2.8 35.3 + - - +
404G VAL* 1.3 73.7 - - - +
406G GLN* 1.3 62.9 + - - +
407G ILE* 3.3 36.8 - - + -
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Residues in contact with GLN 406 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G LYS* 3.7 12.3 - - - +
294G LEU* 4.8 0.2 - - - +
306G SER* 2.8 36.8 + - - +
307G ARG* 4.0 1.7 - - + -
308G THR* 2.9 31.4 + - - -
386G PHE* 3.7 5.0 - - - -
389G VAL* 4.0 14.4 - - + -
395G ILE* 3.5 48.4 - - + +
400G ILE* 5.1 3.6 - - - +
404G VAL* 3.2 40.3 + - - +
405G MET* 1.3 75.6 - - - +
407G ILE* 1.3 63.3 + - - +
408G LEU* 3.8 5.3 - - + +
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Residues in contact with ILE 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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308G THR* 3.4 13.5 - - - +
310G VAL* 3.8 20.9 - - + -
315G TYR* 3.8 17.8 + - + +
318G PHE* 4.6 3.4 - - + -
319G VAL* 3.9 25.1 - - + +
322G SER* 4.2 12.3 - - - +
368G LEU* 5.3 0.4 - - + -
385G VAL* 3.8 9.2 - - + -
386G PHE 2.9 17.4 + - - +
387G GLY* 4.5 4.0 - - - -
388G ASP 3.4 9.2 + - - -
389G VAL* 3.1 22.6 + - - +
405G MET* 3.3 37.0 - - + -
406G GLN* 1.3 77.0 - - - +
408G LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 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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307G ARG* 4.1 19.1 - - + -
308G THR 2.8 21.3 + - - +
309G PHE* 3.4 24.5 - - + -
310G VAL* 2.8 29.8 + - - +
315G TYR* 4.0 3.4 - - - -
389G VAL* 3.5 37.0 - - + +
390G GLN 4.3 2.0 - - - +
391G ASP* 3.4 30.5 - - - +
396G ALA* 4.8 4.7 - - + -
406G GLN* 3.8 17.5 - - + +
407G ILE* 1.3 77.7 - - - +
409G LYS* 1.3 60.6 + - - +
419G ARG* 3.8 7.9 - - - +
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Residues in contact with LYS 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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309G PHE* 5.4 0.2 - - - -
310G VAL 3.4 4.5 - - - -
312G GLU* 3.8 35.4 - - + +
315G TYR* 3.6 46.2 - - + +
316G ASP* 5.1 2.6 + - - -
388G ASP* 4.3 11.9 + - - +
389G VAL 4.7 2.8 + - - -
408G LEU* 1.3 74.6 - - - +
410G PHE* 1.3 63.9 + - - +
419G ARG* 2.9 22.6 + - - +
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Residues in contact with PHE 410 (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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276G ILE* 4.0 7.9 - - + -
277G ILE 3.6 7.0 - - - -
278G MET* 3.7 23.6 - - - -
309G PHE* 3.7 19.7 - - + -
310G VAL 3.1 31.0 + - - -
311G GLN* 3.2 44.2 - - + -
312G GLU* 2.8 28.3 + - - +
409G LYS* 1.3 76.8 - - - +
411G LYS* 1.3 58.7 + - - +
412G THR 3.3 31.4 - - - -
415G GLU* 3.8 8.3 - - - +
416G VAL* 3.6 20.0 - - + -
419G ARG* 3.7 15.7 - - - +
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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