Contacts of the strand formed by residues 350 - 354 (chain A) in PDB entry 1OZ2
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 350 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A GLY 4.1 6.3 + - - +
349A MET* 1.3 78.3 - - - +
351A LEU* 1.3 65.1 + - - +
365A ALA 3.3 6.7 - - - +
366A SER* 2.7 29.2 + - - +
380A ASP* 2.8 17.7 + - - +
400A VAL* 3.7 6.9 + - + +
424A TRP* 3.8 18.2 - - + -
427A TYR* 3.7 29.5 + - + -
428A LEU* 4.2 9.4 - - + -
431A THR* 3.9 14.5 - - - +
433A ALA* 3.8 22.4 - - + -
434A SER 2.9 11.6 + - - +
435A ALA* 3.5 4.0 - - - -
436A VAL* 2.9 23.6 + - - +
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PHE* 4.6 7.0 - - + -
350A LYS* 1.3 79.1 - - - +
352A GLU* 1.3 68.7 + - - +
353A ALA* 4.7 0.9 - - + -
365A ALA* 2.9 50.2 + - + +
366A SER 3.9 15.9 - - - +
367A VAL* 4.0 14.8 - - + -
375A PHE* 4.9 0.2 - - + -
377A VAL* 4.7 11.7 - - + -
397A ILE* 3.7 38.8 - - + -
398A HIS 3.5 9.9 - - - +
400A VAL* 4.1 8.9 - - - +
424A TRP* 3.5 10.0 - - - -
436A VAL* 4.3 2.7 - - + -
441A PHE* 4.1 17.0 - - + -
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Residues in contact with GLU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 1.3 77.2 - - - +
353A ALA* 1.3 63.2 + - - +
362A VAL* 4.0 13.2 - - + -
363A CYS 3.3 4.9 - - - +
397A ILE* 3.5 1.4 - - - -
398A HIS* 2.9 40.7 + - + +
399A PRO 3.7 5.4 - - - +
400A VAL* 4.1 1.3 - - - -
401A GLY* 2.9 22.8 + - - -
402A TRP* 3.3 8.1 + - - +
403A CYS* 2.8 33.4 + - - +
404A GLN 5.1 0.3 + - - -
410A LEU* 3.8 19.5 - - + +
424A TRP* 2.9 35.9 + - + +
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Residues in contact with ALA 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 4.7 1.1 - - + -
352A GLU* 1.3 76.3 - - - +
354A VAL* 1.3 62.7 + - - +
355A ASP 3.6 0.3 + - - -
362A VAL* 3.4 5.0 - - - +
363A CYS 2.8 34.7 + - - +
365A ALA* 4.1 4.9 - - + -
377A VAL* 3.7 23.8 - - + -
379A PHE* 3.4 16.3 - - + -
388A TYR* 3.6 15.9 - - - +
396A TYR 3.3 6.5 - - - +
397A ILE* 4.2 6.5 - - + -
398A HIS* 5.4 0.4 - - - -
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Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ALA* 1.3 71.6 - - - +
355A ASP* 1.3 73.4 + - - +
356A ARG* 3.2 8.9 + - - +
359A PRO* 3.7 29.2 - - + +
361A LEU 3.2 6.7 - - - +
362A VAL* 4.2 17.9 - - + +
379A PHE* 3.4 1.4 - - - -
388A TYR* 2.7 27.9 + - - -
395A PRO 4.9 1.3 - - - +
396A TYR* 2.8 51.1 + - + +
398A HIS* 4.7 8.1 - - - +
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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
------------------------------------------------------------
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