Contacts of the strand formed by residues 400 - 404 (chain E) in PDB entry 6O81
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 400 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326E LYS* 3.9 28.5 + - + +
327E ILE* 5.1 8.5 - - + -
328E SER* 4.4 8.7 + - - -
331E ASP* 4.1 24.6 + - - +
332E VAL 3.3 8.4 + - - +
333E ILE* 3.3 15.4 - - + -
334E LEU 2.8 23.4 + - - -
398E VAL* 3.3 4.9 - - - +
399E SER* 1.3 89.2 + - - +
401E VAL* 1.3 63.2 + - - +
432E VAL* 4.0 1.8 - - - -
433E PRO 4.0 3.8 - - - +
435E LEU* 4.7 11.0 - - + -
241G LEU* 3.8 31.5 - - + +
242G ASN* 6.0 1.8 - - - +
245G ASP* 5.4 4.6 + - - -
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Residues in contact with VAL 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334E LEU* 3.5 29.6 - - + +
395E LEU* 3.8 19.3 - - + -
398E VAL* 4.3 0.2 - - + -
400E LYS* 1.3 75.3 - - - +
402E LEU* 1.3 55.6 + - - +
403E LEU* 3.8 28.3 - - + -
423E LEU* 4.4 5.6 - - + -
427E ALA* 4.0 8.7 - - + -
432E VAL* 3.7 20.6 - - + -
433E PRO 3.3 6.4 + - - +
434E VAL* 3.3 19.0 - - + -
435E LEU* 2.5 37.8 + - - +
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Residues in contact with LEU 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323E ALA* 5.8 2.0 - - + -
327E ILE* 5.2 6.1 - - + -
333E ILE* 3.7 15.5 - - + +
334E LEU 2.6 22.5 + - - +
335E VAL* 3.4 19.2 - - + +
336E TYR 4.1 0.9 + - - -
342E VAL* 3.8 26.2 - - + +
345E ILE* 3.9 28.0 - - + -
346E LEU* 4.2 15.9 - - + -
400E LYS 4.0 1.4 + - - -
401E VAL* 1.3 71.6 - - - +
403E LEU* 1.3 65.7 + - - +
435E LEU* 3.4 33.0 - - + +
437E CYS* 3.7 20.6 - - - -
501E ILE* 5.1 2.0 - - + -
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Residues in contact with LEU 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336E TYR* 4.2 15.0 - - + +
342E VAL* 3.7 10.6 - - - +
401E VAL* 3.8 8.5 - - + +
402E LEU* 1.3 83.2 - - - +
404E GLY* 1.3 62.5 + - - +
405E ALA 3.9 0.2 - - - -
420E THR* 3.8 35.7 - - + +
423E LEU* 3.8 27.6 - - + -
424E ALA* 4.9 3.6 - - + -
434E VAL* 4.1 24.2 - - + -
435E LEU 2.5 14.4 + - - +
436E VAL* 3.4 23.1 - - + -
437E CYS* 3.1 25.8 + - - -
497E VAL* 5.8 0.7 - - + -
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Residues in contact with GLY 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336E TYR 4.9 9.0 + - - +
339E SER* 3.9 16.3 - - - -
341E LEU* 6.2 1.3 - - - -
342E VAL* 3.7 17.8 - - - +
403E LEU* 1.3 75.1 - - - +
405E ALA* 1.3 63.3 + - - -
406E HIS* 3.9 8.6 + - - -
416E SER* 3.3 16.3 + - - -
417E ARG* 5.3 0.9 + - - +
420E THR* 5.9 0.3 - - - +
436E VAL* 6.0 0.2 - - - -
437E CYS 4.4 2.7 - - - -
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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