Contacts of the strand formed by residues 450 - 455 (chain B) in PDB entry 5ZR1
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 ILE 450 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B ILE* 5.7 2.2 - - + -
383B LEU* 4.4 17.9 - - + -
411B TYR* 6.3 0.2 - - + -
418B ILE* 4.6 0.7 - - - -
419B LYS* 5.0 2.0 - - + -
420B LEU* 3.3 34.8 - - + +
422B LEU* 3.9 17.5 - - + -
444B LEU* 3.3 52.7 - - + +
445B SER 5.1 1.4 - - - +
447B ILE* 3.1 30.4 + - + +
448B ARG* 3.2 6.6 - - - +
449B GLN* 1.3 84.1 - - + +
451B ALA* 1.3 59.9 + - - +
452B ILE* 4.1 8.7 + - + +
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Residues in contact with ALA 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B LEU* 3.9 30.1 - - + +
334B LEU* 5.4 0.9 - - + -
338B ILE* 5.5 1.1 - - + -
418B ILE* 4.1 27.8 - - + -
420B LEU 3.0 8.4 + - - +
421B ILE* 3.5 13.4 - - + +
422B LEU 3.2 22.9 + - - +
450B ILE* 1.3 73.6 - - - +
452B ILE* 1.3 65.2 + - - +
453B VAL* 3.8 0.6 + - - -
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Residues in contact with ILE 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU* 3.5 10.1 - - - +
313B SER* 3.3 24.5 - - - +
314B LEU 3.4 17.5 + - - -
422B LEU* 3.7 43.5 - - + +
424B VAL* 5.0 2.9 - - + -
441B LEU* 5.0 3.6 - - + +
444B LEU* 4.5 1.6 - - + +
445B SER* 3.3 42.8 - - - +
450B ILE* 4.4 14.1 - - + +
451B ALA* 1.3 75.4 - - - +
453B VAL* 1.3 66.0 + - - +
454B ALA* 4.1 15.0 - - + -
473B TYR* 5.3 6.3 - - + -
475B PHE* 5.3 0.7 - - + -
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Residues in contact with VAL 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU* 3.8 26.5 - - + -
314B LEU* 3.6 5.4 - - + -
316B PHE* 3.9 15.5 - - + -
326B LEU* 3.7 28.8 - - + +
329B PHE* 4.2 17.5 - - + -
330B ALA* 5.2 1.6 - - + -
334B LEU* 4.3 9.0 - - + -
421B ILE* 4.4 9.9 - - + -
422B LEU 3.2 9.6 + - - +
423B VAL* 3.3 14.0 - - + +
424B VAL 3.0 23.1 + - - +
451B ALA 4.5 0.4 - - - +
452B ILE* 1.3 79.2 - - - +
454B ALA* 1.3 59.8 + - - +
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Residues in contact with ALA 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B LEU 3.0 10.8 + - - +
315B LEU* 3.7 18.4 - - + -
316B PHE* 2.9 29.5 + - - -
326B LEU* 4.4 2.0 - - - -
424B VAL* 3.4 20.0 - - + +
427B LEU* 4.2 11.9 - - + -
452B ILE* 4.1 14.1 - - + -
453B VAL* 1.3 75.2 - - - +
455B SER* 1.3 62.6 + - - +
475B PHE* 4.6 5.6 - - + -
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Residues in contact with SER 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B LEU* 4.3 0.2 - - - -
316B PHE* 3.2 17.3 - - - +
322B LYS* 4.0 21.5 + - - +
326B LEU* 3.9 12.6 - - - +
424B VAL 3.1 6.7 + - - -
425B HIS* 3.6 5.0 - - - +
426B ASN* 2.9 25.1 + - - -
427B LEU* 2.5 36.6 + - - +
454B ALA* 1.3 77.6 - - - +
456B THR* 1.3 59.3 + - - +
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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