Contacts of the strand formed by residues 334 - 339 (chain A) in PDB entry 5IZL
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 LYS 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A LYS 3.9 0.2 + - - -
333A ALA* 1.3 75.7 - - - +
335A PHE* 1.3 60.9 + - - +
336A HIS* 5.6 0.7 + - - -
345A MET* 4.3 19.3 - - + +
346A GLY 3.4 7.2 - - - +
347A ARG* 3.6 27.8 - - - +
417A GLU* 5.5 2.5 - - - +
432A ARG* 3.4 21.0 + - - +
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Residues in contact with PHE 335 (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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325A PHE* 4.9 1.6 - + - -
328A PRO 4.9 1.3 - - - -
329A LEU* 4.2 24.2 - - + -
330A GLN 4.6 5.8 - - - -
333A ALA* 4.0 18.6 - - + -
334A LYS* 1.3 75.0 - - - +
336A HIS* 1.3 67.4 + - - +
337A ILE* 3.2 15.2 - - + +
345A MET* 3.3 10.0 - - - +
346A GLY 3.0 28.8 + - - -
348A LEU* 4.4 15.9 - - + -
350A PHE* 4.7 3.8 - + - -
431A SER 3.3 28.3 - - - +
432A ARG* 3.4 38.8 - - + -
445A ALA* 3.8 20.0 - - + -
446A PHE* 4.0 19.1 - + + -
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Residues in contact with HIS 336 (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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101A ARG* 4.6 8.5 - - - -
334A LYS 6.0 0.2 - - - -
335A PHE* 1.3 74.3 - - - +
337A ILE* 1.3 59.7 + - - +
338A THR* 4.1 1.6 + - - -
343A THR* 5.5 8.3 - - - -
344A VAL 3.8 5.4 - - - +
345A MET* 3.6 27.6 - - + -
429A ILE 3.4 1.4 - - - +
430A GLY* 3.3 5.5 - - - -
431A SER* 3.0 30.6 + - - +
432A ARG* 4.3 1.9 - - - -
433A LEU* 3.4 41.0 + - + +
434A ASP* 3.2 51.0 + - + -
436B ASP* 4.5 12.1 + - - +
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Residues in contact with ILE 337 (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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335A PHE* 3.2 32.1 - - + +
336A HIS* 1.3 73.5 - - - +
338A THR* 1.3 65.6 + - - +
339A VAL* 3.7 5.4 + - + +
342A GLU 3.9 0.2 - - - +
343A THR* 3.1 2.7 - - - -
344A VAL* 2.7 42.2 + - - +
346A GLY* 3.4 29.8 - - - +
348A LEU* 4.4 3.4 - - + -
414A VAL* 4.2 17.9 - - + -
416A PHE* 3.9 24.2 - - + -
428A VAL* 3.8 23.8 - - + -
429A ILE 3.3 4.7 - - - +
446A PHE* 4.7 11.0 - - + -
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Residues in contact with THR 338 (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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101A ARG 5.8 0.7 - - - +
104A ILE* 4.0 32.9 - - + +
108A GLN* 4.4 1.8 - - - +
336A HIS* 4.1 1.4 + - - +
337A ILE* 1.3 70.5 - - - +
339A VAL* 1.3 58.7 + - - +
340A GLY 3.3 24.0 - - - +
341A HIS* 5.0 0.9 - - - -
342A GLU 3.7 6.1 - - - +
343A THR* 2.9 28.0 - - + +
427A LEU* 3.3 9.1 - - + +
428A VAL* 3.4 1.0 - - - -
429A ILE* 2.8 43.1 + - + +
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Residues in contact with VAL 339 (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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312A VAL* 6.4 0.2 - - + -
337A ILE* 3.7 11.3 + - + +
338A THR* 1.3 70.2 - - - +
340A GLY* 1.3 58.8 + - - +
341A HIS 3.1 7.8 + - - -
342A GLU* 3.0 19.9 + - - +
344A VAL* 5.9 0.4 - - + -
416A PHE* 5.0 10.3 - - + -
420A VAL* 3.9 25.3 - - + +
421A THR 5.1 0.9 - - - +
422A CYS* 4.2 17.8 - - + +
426A CYS* 4.4 11.0 - - - -
427A LEU 4.0 3.1 - - - -
428A VAL* 4.8 9.6 - - + -
450A LEU* 5.5 2.2 - - + -
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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