Contacts of the strand formed by residues 404 - 410 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294I LEU* 3.7 14.1 - - - +
306I SER* 5.1 0.5 - - - -
353I ILE* 4.0 19.1 - - + -
356I TYR* 3.7 18.6 + - + -
357I ILE* 3.9 25.4 - - + -
381I ILE* 5.5 0.4 - - + -
384I THR* 3.3 11.4 - - + -
386I PHE* 3.6 32.1 - - + -
400I ILE* 4.3 6.2 - - + +
402I GLY 2.9 10.3 + - - +
403I PRO* 1.3 79.0 - - + +
405I MET* 1.3 59.2 + - - +
406I GLN* 2.9 33.1 + - - +
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Residues in contact with MET 405 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290I ALA* 4.7 17.5 - - - +
291I HIS* 5.2 2.9 - - - +
294I LEU* 4.0 15.8 - - + +
295I PHE* 4.2 22.4 - - + -
308I THR* 4.1 18.2 - - - +
318I PHE* 5.7 0.2 - - - -
322I SER* 3.6 33.0 - - - +
384I THR 2.7 15.0 + - - +
385I VAL* 3.4 33.8 - - + -
386I PHE* 2.8 36.4 + - - +
404I VAL* 1.3 69.3 - - - +
406I GLN* 1.3 64.6 + - - +
407I ILE* 3.7 17.0 - - + -
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Residues in contact with GLN 406 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306I SER* 3.0 32.1 + - - +
307I ARG* 4.0 1.7 - - + -
308I THR* 2.9 30.9 + - - -
356I TYR* 2.9 26.5 + - - -
386I PHE* 3.7 3.3 - - - -
389I VAL* 4.0 13.7 - - + -
395I ILE* 3.3 38.7 - - + +
396I ALA* 5.6 0.4 - - - -
404I VAL* 2.9 38.8 + - - +
405I MET* 1.3 76.9 - - - +
407I ILE* 1.3 61.7 + - - +
408I LEU* 4.0 5.8 - - + +
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Residues in contact with ILE 407 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308I THR* 3.3 5.8 - - - +
310I VAL* 3.7 28.3 - - + -
315I TYR* 3.8 19.1 + - + +
318I PHE* 4.5 6.5 - - + -
319I VAL* 4.0 23.8 - - + -
322I SER* 4.3 11.4 - - - -
368I LEU* 5.3 0.9 - - + -
385I VAL* 4.0 9.4 - - + -
386I PHE 3.0 15.4 + - - +
387I GLY* 4.6 3.4 - - - -
388I ASP 3.4 9.2 + - - -
389I VAL* 3.2 21.4 + - - +
405I MET* 3.7 34.8 - - + -
406I GLN* 1.3 75.5 - - - +
408I LEU* 1.3 63.4 + - - +
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Residues in contact with LEU 408 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307I ARG* 3.9 21.8 - - + -
308I THR 2.7 33.8 + - - +
309I PHE* 3.3 25.1 - - + -
310I VAL* 2.7 34.5 + - - +
315I TYR* 4.1 3.4 - - - -
389I VAL* 3.6 35.7 - - + +
390I GLN 4.2 5.2 - - - -
391I ASP* 3.4 25.8 - - - +
396I ALA* 4.7 6.7 - - + -
406I GLN* 4.0 7.4 - - + +
407I ILE* 1.3 77.7 - - - +
409I LYS* 1.3 56.9 + - - +
419I ARG* 4.0 4.5 - - - +
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Residues in contact with LYS 409 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310I VAL 3.4 6.1 - - - +
312I GLU* 4.0 30.3 - - + +
315I TYR* 3.7 45.9 - - + -
316I ASP* 5.3 2.8 + - - -
388I ASP* 4.7 10.0 + - - +
389I VAL 4.7 3.2 + - - +
408I LEU* 1.3 73.8 - - - +
410I PHE* 1.3 58.0 + - - +
415I GLU* 4.7 0.2 - - - +
419I ARG* 2.7 29.2 + - - +
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Residues in contact with PHE 410 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276I ILE* 4.0 6.3 - - + -
277I ILE 3.6 14.4 - - - -
278I MET* 3.8 19.3 - - - -
309I PHE* 3.5 30.5 - - + -
310I VAL 3.1 22.7 + - - -
311I GLN* 3.3 46.3 - - + -
312I GLU* 2.9 29.5 + - - +
409I LYS* 1.3 75.6 - - - +
411I LYS* 1.3 59.4 + - - +
412I THR 3.4 23.6 - - - -
415I GLU* 3.9 10.3 - - - +
416I VAL* 3.6 22.9 - - + -
419I ARG* 3.7 13.0 - - - +
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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