Contacts of the strand formed by residues 413 - 419 (chain B) in PDB entry 3FO5
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 413 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409B GLU* 3.2 4.2 - - - -
410B ILE 2.9 34.6 + - - +
411B SER* 3.0 16.7 - - - +
412B GLN* 1.3 80.8 - - - +
414B ARG* 1.3 63.8 + - - +
428B MET* 3.4 29.6 - - + -
429B GLU 3.4 11.0 - - - +
430B MET* 4.2 15.9 - - + -
570B TYR* 3.4 12.0 - - + +
573B PHE* 3.8 16.4 - - + -
574B LYS* 6.3 1.6 - - - +
577B GLU* 6.1 0.7 - - - +
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Residues in contact with ARG 414 (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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406B LEU* 3.8 15.4 - - + +
408B SER 3.6 3.1 - - - -
409B GLU* 3.4 39.8 + - - +
412B GLN 4.9 2.5 - - - +
413B VAL* 1.3 73.8 - - - +
415B LEU* 1.3 61.3 + - - +
416B TYR* 3.3 37.7 + - + -
427B HIS 3.8 0.9 - - - +
428B MET* 3.2 9.1 - - - +
429B GLU* 2.9 50.1 + - + +
543B LYS* 5.6 1.8 - - - +
570B TYR* 4.2 0.4 - - - -
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Residues in contact with LEU 415 (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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406B LEU* 3.7 2.8 - - - +
407B SER* 2.8 31.3 + - - -
408B SER* 3.0 24.4 + - - +
414B ARG* 1.3 72.9 - - - +
416B TYR* 1.3 66.1 + - - +
426B PHE* 4.1 12.6 - - + -
427B HIS 3.5 6.7 - - - +
428B MET* 3.5 24.2 - - + -
561B ASN 4.1 21.8 - - - +
562B VAL* 4.1 19.1 - - + +
569B PHE* 4.0 21.3 - - + -
570B TYR* 3.4 26.6 + - + +
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Residues in contact with TYR 416 (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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404B TRP* 3.8 12.3 - - + -
405B VAL* 3.2 11.9 - - - -
406B LEU* 3.6 36.1 - - + +
414B ARG* 3.3 47.3 + - + -
415B LEU* 1.3 76.4 - - - +
417B THR* 1.3 64.8 + - - +
426B PHE* 3.2 8.0 - - - +
427B HIS* 2.8 68.3 + + + +
429B GLU* 3.4 29.5 + - + -
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Residues in contact with THR 417 (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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403B ASN 3.7 1.4 - - - +
404B TRP* 3.4 5.9 - - - -
405B VAL* 2.8 41.6 + - - +
407B SER* 3.2 23.9 + - - +
415B LEU* 5.1 1.1 - - + -
416B TYR* 1.3 78.8 - - - +
418B LEU* 1.3 60.8 + - - +
419B GLU* 4.1 15.6 + - - +
424B LEU* 4.2 10.9 - - + +
425B SER 3.2 12.3 - - - +
426B PHE* 4.4 1.1 - - + -
562B VAL* 3.6 36.8 - - + +
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Residues in contact with LEU 418 (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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398B LEU* 4.1 10.5 - - + -
401B LYS* 3.6 28.0 - - + -
403B ASN* 3.1 56.8 - - - +
404B TRP* 3.5 31.2 - - + +
417B THR* 1.3 74.0 - - - +
419B GLU* 1.3 61.9 + - - +
420B ASP* 3.3 18.5 + - - +
423B PHE 3.3 0.7 - - - +
424B LEU 3.7 1.0 - - - -
425B SER* 2.8 50.3 + - - +
549B GLN* 5.7 0.2 - - - +
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Residues in contact with GLU 419 (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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356B LYS* 5.6 3.5 - - - -
359B ARG* 3.8 17.5 + - - -
360B LEU* 3.7 26.0 - - - +
363B LYS* 3.7 22.2 + - - +
364B TYR* 2.9 17.6 + - - +
403B ASN* 4.8 8.4 + - - +
417B THR* 4.3 12.6 + - - +
418B LEU* 1.3 72.7 - - - +
420B ASP* 1.3 64.6 + - - +
423B PHE 3.9 0.7 - - - -
424B LEU* 4.0 14.1 - - + +
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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
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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