Contacts of the strand formed by residues 414 - 417 (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 VAL 414 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405E ALA* 4.2 6.1 - - + -
407E ALA 3.7 2.2 - - - -
408E LEU* 3.8 20.9 - - + -
412E GLY 4.1 7.4 - - - +
413E SER* 1.3 77.0 - - - +
415E MET* 1.3 59.3 + - - +
416E SER* 3.6 21.0 + - - +
420E THR* 4.9 7.9 - - + +
436E VAL* 4.0 24.0 - - + -
490E ASP 3.1 13.0 - - - +
491E VAL* 3.4 4.9 - - - -
492E THR* 3.3 25.8 + - - +
497E VAL* 3.8 32.1 - - + -
509E CYS* 4.8 1.8 - - - -
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Residues in contact with MET 415 (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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270E SER* 5.6 1.3 - - - -
271E ALA* 4.8 11.7 - - + +
406E HIS* 3.2 4.0 + - + +
407E ALA* 2.7 64.2 + - + +
409E LEU* 4.6 9.1 - - + +
413E SER 3.9 1.4 - - - -
414E VAL* 1.3 69.3 - - - +
416E SER* 1.3 66.8 + - - +
446E ARG* 4.1 21.3 - - - +
448E GLN* 3.9 24.7 - - - +
454E SER* 5.1 3.6 - - - +
489E TYR* 3.7 44.2 - - + -
490E ASP 3.3 10.8 - - - +
491E VAL* 4.4 6.7 - - + +
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Residues in contact with SER 416 (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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404E GLY 3.3 11.5 + - - -
405E ALA* 3.2 12.8 - - - -
406E HIS* 3.1 26.4 + - - -
414E VAL* 3.6 10.0 + - - +
415E MET* 1.3 77.0 + - - +
417E ARG* 1.3 68.2 + - - +
420E THR* 3.9 23.3 - - - +
489E TYR* 3.2 31.8 - - - -
490E ASP 3.4 7.6 + - - -
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Residues in contact with ARG 417 (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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220E SER* 3.0 36.0 + - - -
221E GLY* 4.9 1.2 - - - -
267E ARG* 4.6 8.1 - - - +
336E TYR* 3.6 25.1 - - + +
337E GLY* 5.1 4.5 - - - -
338E CYS 5.4 3.9 + - - +
366E TRP* 4.3 25.6 - - + +
368E GLU* 3.0 39.4 + - - +
404E GLY 6.0 0.7 - - - +
406E HIS* 3.3 29.4 + - + +
416E SER* 1.3 79.0 - - - +
418E VAL* 1.3 62.5 + - + +
419E GLY 3.3 0.9 - - - -
420E THR* 2.8 19.2 + - - +
488E VAL* 3.5 32.9 - - - +
489E TYR* 5.4 3.2 + - - -
490E ASP* 3.0 12.5 - - - +
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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