Contacts of the strand formed by residues 404 - 410 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C LEU* 3.4 14.2 - - - +
306C SER* 5.0 0.3 - - - -
353C ILE* 3.9 13.0 - - + -
356C TYR 6.1 0.2 - - - +
357C ILE* 3.9 25.1 - - + -
384C THR* 3.4 8.5 - - + -
386C PHE* 3.6 29.2 - - + -
395C ILE* 5.9 2.0 - - + -
400C ILE* 3.6 32.3 - - + +
402C GLY 2.8 10.1 + - - +
403C PRO* 1.3 80.0 - - + +
405C MET* 1.3 57.8 + - - +
406C GLN* 3.1 33.8 + - - +
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Residues in contact with MET 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C ALA* 3.5 40.2 - - + +
291C HIS* 4.1 7.6 - - + +
294C LEU* 3.4 24.4 - - + +
295C PHE* 4.1 12.8 - - + -
308C THR* 3.8 21.5 - - + +
318C PHE* 5.2 0.2 - - + -
322C SER* 4.4 15.3 - - - +
384C THR 2.7 15.8 + - - +
385C VAL* 4.2 13.2 - - + -
386C PHE* 2.8 32.7 + - - +
404C VAL* 1.3 71.9 - - - +
406C GLN* 1.3 64.2 + - - +
407C ILE* 4.0 27.4 - - + -
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Residues in contact with GLN 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C LYS* 3.6 12.7 - - - +
306C SER* 2.9 35.8 + - - +
307C ARG* 4.0 1.3 - - + -
308C THR* 2.8 31.4 + - - +
386C PHE* 3.8 10.0 - - - -
389C VAL* 4.1 11.0 - - + -
395C ILE* 3.3 42.7 - - + +
396C ALA* 4.9 0.9 - - - -
400C ILE* 5.4 3.2 - - - +
404C VAL* 3.1 46.7 + - - +
405C MET* 1.3 78.1 - - - +
407C ILE* 1.3 62.0 + - - +
408C LEU* 3.7 9.0 - - + +
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Residues in contact with ILE 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C THR* 3.3 7.0 - - - +
310C VAL* 3.7 27.4 - - + -
315C TYR* 3.7 17.7 + - + -
318C PHE* 4.5 3.1 - - + -
319C VAL* 3.8 21.5 - - + -
322C SER* 4.1 24.9 - - - +
368C LEU* 5.2 0.4 - - + -
385C VAL* 3.7 22.9 - - + -
386C PHE 3.0 15.2 + - - +
387C GLY* 4.6 4.5 - - - -
388C ASP* 3.2 10.0 + - - -
389C VAL* 3.0 21.1 + - - +
405C MET* 4.0 15.3 - - + -
406C GLN* 1.3 77.2 - - - +
408C LEU* 1.3 63.3 + - - +
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Residues in contact with LEU 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C ARG* 4.0 20.0 - - + -
308C THR 2.7 23.2 + - - +
309C PHE* 3.4 19.1 - - + -
310C VAL* 2.8 30.1 + - - +
315C TYR* 4.1 3.4 - - - -
389C VAL* 3.4 37.2 - - + +
390C GLN 4.3 0.2 - - - -
391C ASP* 3.3 31.0 - - - +
396C ALA* 4.7 4.9 - - + -
406C GLN* 3.7 22.4 - - + +
407C ILE* 1.3 76.1 - - - +
409C LYS* 1.3 59.9 + - - +
419C ARG* 3.7 10.1 - - - +
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Residues in contact with LYS 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C PHE* 5.3 0.2 - - - -
310C VAL 3.4 5.6 - - - +
312C GLU* 4.0 31.9 - - + +
315C TYR* 3.6 47.8 - - + +
316C ASP* 4.9 4.4 + - - -
388C ASP* 4.5 20.7 + - - +
389C VAL 4.7 2.6 + - - -
408C LEU* 1.3 73.2 - - - +
410C PHE* 1.3 58.6 + - - +
411C LYS* 6.3 0.2 - - + -
419C ARG* 2.6 29.7 + - - +
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Residues in contact with PHE 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C ILE* 3.9 6.5 - - + -
277C ILE 3.7 5.4 - - - -
278C MET* 3.7 22.7 - - - -
309C PHE* 3.7 12.6 - - + -
310C VAL 3.2 25.9 + - - -
311C GLN* 3.1 47.7 - - + -
312C GLU* 2.9 26.2 + - - +
409C LYS* 1.3 78.3 - - - +
411C LYS* 1.3 64.5 + - - +
412C THR 3.4 29.2 - - - -
415C GLU* 3.7 10.5 - - + +
416C VAL* 3.5 29.2 - - + -
419C ARG* 3.5 12.3 - - - +
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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