Contacts of the strand formed by residues 404 - 410 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A LEU* 3.2 13.3 - - - +
306A SER* 5.1 0.5 - - - -
353A ILE* 4.0 18.4 - - + -
356A TYR* 3.6 15.0 - - + -
357A ILE* 3.9 25.4 - - + -
381A ILE* 5.7 0.2 - - + -
384A THR* 3.4 9.6 - - + +
386A PHE* 3.5 31.2 - - + -
400A ILE* 4.2 12.4 - - + +
402A GLY 2.8 11.0 + - - +
403A PRO* 1.3 77.5 - - + +
405A MET* 1.3 57.4 + - - +
406A GLN* 3.0 34.1 + - - +
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Residues in contact with MET 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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290A ALA* 4.7 16.8 - - + +
291A HIS* 5.0 4.9 - - + +
294A LEU* 3.5 20.3 - - + +
295A PHE* 4.0 20.0 - - + -
308A THR* 4.2 14.4 - - - +
318A PHE* 5.2 2.5 - - + -
322A SER* 3.4 27.6 - - - +
384A THR 2.7 15.9 + - - +
385A VAL* 3.8 15.9 - - + -
386A PHE* 2.8 35.2 + - - +
404A VAL* 1.3 73.1 - - - +
406A GLN* 1.3 62.0 + - - +
407A ILE* 3.3 35.9 - - + -
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Residues in contact with GLN 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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294A LEU* 4.4 1.0 - - - +
306A SER* 2.9 32.9 + - - +
307A ARG* 3.9 1.5 - - + -
308A THR* 2.8 31.5 + - - +
356A TYR* 2.9 27.8 + - - -
386A PHE* 3.8 4.9 - - - -
389A VAL* 4.0 10.8 - - + -
395A ILE* 3.3 36.2 + - + +
396A ALA* 5.6 0.2 - - - -
404A VAL* 3.0 37.4 + - - +
405A MET* 1.3 76.0 - - - +
407A ILE* 1.3 61.2 + - - +
408A LEU* 3.7 9.3 - - + +
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Residues in contact with ILE 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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308A THR* 3.3 7.6 - - - +
310A VAL* 3.7 28.0 - - + -
315A TYR* 3.8 20.7 + - + +
318A PHE* 4.6 3.4 - - + -
319A VAL* 4.0 24.5 - - + -
322A SER* 4.2 11.0 - - - +
368A LEU* 5.0 0.7 - - + -
385A VAL* 3.8 13.0 - - + -
386A PHE 3.0 14.5 + - - +
387A GLY* 4.6 0.7 - - - -
388A ASP 3.4 9.2 + - - -
389A VAL* 3.1 22.0 + - - +
405A MET* 3.3 36.1 - - + -
406A GLN* 1.3 76.3 - - - +
408A LEU* 1.3 62.5 + - - +
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Residues in contact with LEU 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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307A ARG* 4.1 16.8 - - + -
308A THR 2.8 18.5 + - - +
309A PHE* 3.4 27.4 - - + -
310A VAL* 2.8 33.6 + - - +
315A TYR* 4.1 3.3 - - - -
389A VAL* 3.7 33.4 - - + +
390A GLN 4.4 1.6 - - - -
391A ASP* 3.3 30.5 - - - +
396A ALA* 4.8 5.4 - - + -
406A GLN* 3.7 20.6 - - + +
407A ILE* 1.3 78.3 - - - +
409A LYS* 1.3 56.5 + - - +
419A ARG* 3.8 8.3 - - - +
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Residues in contact with LYS 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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310A VAL 3.4 7.9 - - - +
312A GLU* 3.9 27.8 - - + +
315A TYR* 3.6 46.8 - - + -
316A ASP* 5.4 2.6 + - - -
388A ASP* 3.9 18.5 + - - +
389A VAL 4.8 2.8 + - - -
408A LEU* 1.3 74.0 - - - +
410A PHE* 1.3 64.0 + - - +
419A ARG* 2.8 22.0 + - - +
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Residues in contact with PHE 410 (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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276A ILE* 3.8 16.4 - - + -
277A ILE 3.7 9.4 - - - -
278A MET* 3.9 9.6 - - - -
309A PHE* 3.4 30.5 - - + -
310A VAL 3.1 30.1 + - - -
311A GLN* 3.2 46.3 - - + -
312A GLU* 2.8 28.5 + - - +
409A LYS* 1.3 77.1 - - - +
411A LYS* 1.3 61.2 + - - +
412A THR 3.4 23.8 - - - -
415A GLU* 3.5 18.2 - - - +
416A VAL* 3.6 22.7 - - + -
419A ARG* 3.6 6.1 - - - +
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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